CROSS REFERENCE TO RELATED APPLICATIONS The present application is a regular application claiming priority from Provisional U.S. Patent Application Serial No. 60/000,703, filed June 29, 1995, and Provisional U.S. Patent Application No. 60/000859, filed July 3, 1995. This application is also a continuation-in-part of U.S. Patent Application Serial No. 08/589,027, filed January 19, 1996. Each of these applications is incorporated herein by reference in its entirety for all purposes.

GOVERNMENT RIGHTS The present invention was made with U.S Government support under ATP Grant No. 70NANB5H1031. The government has certain rights in this invention.

BACKGROUND OF THE INVENTION The relationship between structure and function of macromolecules is of fundamental importance in the understanding of biological systems. These relationships are important to understanding, for example, the functions of enzymes, structure of signalling proteins, ways in which cells communicate with each other, as well as mechanisms of cellular control and metabolic feedback. Genetic information is critical in continuation of life processes. Life is substantially informationally based and its genetic content controls the growth and reproduction of the organism. The amino acid seguences of polypeptides, which are critical features of all living systems, are encoded by the genetic material of the cell. Further, the properties of these polypeptideε, e.g., as enzymes, functional proteins, and structural proteins, are determined by the seguence of amino acids which make them up. As structure and function are

integrally related, many biological functions may be explained by elucidating the underlying structural features which provide those functions, and these structures are determined by the underlying genetic information in the form of polynucleotide seguences. In addition to encoding polypeptides, polynucleotide sequences can also be specifically involved in, for example, the control and regulation of gene expression.

The study of this genetic information has proved to be of great value in providing a better understanding of life processes, as well as diagnosing and treating a large number of disorders. In particular, disorders which are caused by mutations, deletions or repeats in specific portions of the genome, may be readily diagnosed and/or treated using genetic techniques. Similarly, disorders caused by external agents may be diagnosed by detecting the presence of genetic material which is unique to the external agent, e.g., bacterial or viral DNA.

While current genetic methods are generally capable of identifying these genetic seguences, such methods generally rely on a multiplicity of distinct processes to elucidate the nucleic acid seguences, with each process introducing a potential for error into the overall process. These processes also draw from a large number of distinct disciplines, including chemistry, molecular biology, medicine and others. It would therefore be desirable to integrate the various process used in genetic diagnosis, in a single process, at a minimum cost, and with a maximum ease of operation.

Interest has been growing in the fabrication of microfluidic devices. Typically, advances in the semiconductor manufacturing arts have been translated to the fabrication of micro echanical structures, e.g., micropumps, microvalves and the like, and microfluidic deviceε including miniature chambers and flow passageε. A number of researchers have attempted employ theεe microfabrication techniques in the m. liaturization of some of the processes involved in genetic analysis in particular. For

example, published PCT Application No. WO 94/05414, to Northrup and White, incorporated herein by reference in its entirety for all purpoεes, reports an integrated micro-PCR apparatus for collection and amplification of nucleic acidε from a specimen. However, there remains a need for an apparatus which combines the various procesεing and analytical operationε involved in nucleic acid analyεiε. The preεent invention meetε theεe and other needε.

SUMMARY OF THE INVENTION

The present invention generally provides miniature integrated fluidic systems for carrying out a variety of preparative and analytical operations, as well aε methodε of operating theεe εyεtemε and methodε of uεing theεe εyεtems. In a first aspect, the present invention provides a miniature fluidic system which comprises a body having at least first and second chambers dispoεed therein. Each of these first and second chambers haε a fluid inlet and iε in fluid connection. At leaεt one of theεe firεt and εecond chambers is a hybridization chamber for analyzing a component of a fluid sample. The hybridization chamber includeε a polymer array which haε a plurality of different polymer εequenceε coupled to a surface of a εingle εubεtrate, each of the plurality of different polymer sequences being coupled to the surface in a different, known location. The syεtem further includes a sample inlet, fluidly connected to at least one of the firεt and second chamberε, for introducing a fluid εample into the system, and a fluid transport system for moving a fluid sample from the first chamber to the second chamber. In a preferred aεpect, the fluid direction system comprises a pneumatic manifold for applying a differential pressure between the first chamber and the εecond chamber, to move said fluid εample from the firεt chamber to the εecond chamber. In a related aεpect, the p ^** -jεent invention provides a miniature fluidic system, which is substantially the same aε that deεcribed above, except that in place or in addition to a

hybridization chamber, the εyεtem compriεeε a εeparation channel for separating a component of εaid fluid εample. The separation channel is fluidly connected to at least one of the chambers and includes at least first and second electrodes in electrical contact with opposite ends of the separation channel for applying a voltage acrosε said separation channel.

Similarly, in an additional aspect, the present invention provides a substantially similar fluidic system as described, except where at least one of the chambers compriseε an in vitro transcription reaction chamber, the in vitro transcription reaction chamber having an effective amount of an RNA polymerase and four different nucleoside triphosphateε, diεposed therein.

Further, the syεtem may compriεe a body wherein at leaεt one of the chamberε is a cell lysis chamber which includes a cell lysiε system, for lysing cells in said fluid sample.

In a still further related aspect, at least one of the chambers may be a nucleic acid purification chamber, for separating nucleic acids in said fluid sample from other contaminants in εaid fluid εample.

The preεent invention alεo provideε a miniature fluidic system which comporiseε a differential preεεure delivery system for transporting fluids through the εyεtem. In particular, in one aεpect, the preεent invention provideε a miniature fluidic εyεtem, which includeε a body having at least a first reaction chamber fluidly connected to a second reaction chamber by a fluid pasεage. The εyεtem alεo includes a sample inlet, fluidly connected to the first chamber, for introducing a fluid sample into the syεtem. The εyεtem further includeε a differential pressure delivery εystem for maintaining the firεt chamber at a firεt pressure and the second chamber at a second pressure, wherein the firεt preεsure is greater than ambient presεure and the εecond pressure is greater than said first presεure. When the εecond chamber iε brought to ambient pressure, the first preεεure

forces a liquid sample in the first chamber into the εecond chamber.

In an alternate aεpect, the fluidic εystem employε a differential preεεure delivery εource for maintaining the firεt chamber at a firεt preεεure and the εecond chamber at a second preεεure, where the εecond preεεure iε leεs than ambient presεure and the first presεure iε less than the second presεure. When the firεt chamber iε brought to ambient preεεure, the second pressure draws a liquid sample in the first chamber into the second chamber.

The present invention also provides methods of directing, controlling and manipulating fluids in miniature or micro-fluidic systems.

For example, in one aspect, the present invention provides a method for directing a fluid sample in a miniature fluidic system which compriseε providing a microfabricated device having at leaεt firεt and εecond chamberε diεposed therein, wherein each of εaid at leaεt firεt and εecond chamberε iε in fluid connection with a common chamber or channel, haε at leaεt first and second controllable valveε disposed acrosε εaid fluid connection, reεpectively, and includeε at leaεt one vent. The method compriεeε applying a positive preεεure to the common chamber or channel. The at leaεt first controllable valve is selectively opened, whereby the positive presεure forceε the fluid εample from the common chamber or channel into the firεt chamber.

The method may further comprise applying a positive pressure to the first chamber and selectively opening the least first controllable valve, whereby the positive preεεure forceε said fluid sample from the leaεt first chamber into the common chamber or channel.

The present invention also provides methods of mixing at least two discrete fluid componentε in a microfabricated fluidic system. Specifically, the method comprises providing a microfabricated channel having a vent disposed at an intermediate location in said channel. Typically, the vent includes a gas permeable, fluid barrier

disposed across the vent. At least two diεcrete fluid componentε are then introduced into the channel εeparated by a gas bubble. Upon flowing the at least two fluid components past the vent, the bubble will exit the vent, allowing the at least two fluid components to mix.

The present invention alεo provideε methodε of repeatedly meaεuring a known volume of a fluid in a miniature fluidic system. In particular, the method compriseε providing a microfabricated device having at leaεt firεt and εecond chambers disposed therein, wherein the at least first and second chambers are in fluid connection, and wherein at least one of the chambers iε a volumetric chamber having a known volume. The volumetric chamber iε filled with the fluid to create a firεt aliquot of the fluid. This aliquot is then transported to the at least second chamber and the filling and transporting steps are repeated.

BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 shows a schematic representation of a nucleic acid diagnostic system for analysis of nucleic acids from sampleε.

Figureε 2A and 2b εhow schematic representationε of two alternate reaction chamber deεignε from a cut-away view. Figure 3 shows a schematic representation of a miniature integrated diagnostic device having a number of reaction chambers arranged in a serial geometry.

Figures 4A-C show a representation of a microcapillary electrophoresiε device. Figureε 4A and 4B εhow the microcapillary configured for carrying out alternate loading strategies for the microcapillary whereas Figure 4C illustrates the microcapillary in running mode.

Figure 5A illustrateε a top view of a miniature integrated device which employε a centralized geometry. Figure 5B εhowε a εide view of the εame device wherein the central chamber iε a pumping chamber, and employing diaphragm valve structures for sealing reaction chambers.

Figure 6 εhowε εchematic illustrations of pneumatic control manifolds for transporting fluid within a miniature integrated device. Figure 6A showε a manifold configuration suitable for application of negative preεεure, or vacuum, whereas Figure 6B showε a manifold configuration for application of poεitive pressures. Figure 6C illustrateε a pressure profile for moving fluids among several reaction chambers.

Figure 7A shows a schematic illustration of a reaction chamber incorporating a PZT element for uεe in mixing the contentε of the reaction chamber. Figure 7B εhows mixing within a reaction chamber applying the PZT mixing element as shown in Figure 7A. Figure 7C is a bar graph εhowing a comparison of hybridization intensities using mechanical mixing, acouεtic mixing, εtagnant hybridization and optimized acoustic mixing.

Figure 8 iε a εchematic illuεtration of a side and top view of a base-unit for uεe with a miniature integrated device. Figure 9 iε a time temperature profile of thermal cycling in a miniature reaction chamber and a diεplay of the programmed cycling parameterε.

Figure IOA iε a gel εhowing a time course of an RNA fragmentation reaction. Figure 10B is a gel showing a comparison of the product of an in vitro transcription reaction in a microchamber vs. a control (teεt tube) . Figure IOC is a compariεon of the PCR product produced in a PCR thermal cycler and that produced by a microreactor.

Figure 11 εhowε an embodiment of a reaction chamber employing an electronic pH control εystem.

Figure 12A-C show a schematic representation of a miniature integrated device employing a pneumatic fluid direction εyεtem utilizing a gaε permeable fluid barrier bound vents, e.g., a poorly wetting or hydrophobic membrane,and pneumatically controlled valves. Figure 12A showε an embodiment of a single chamber employing this system. Figure 12B is a schematic illustration of a debubbling chamber for

linking discrete fluid plugs that are εepareted by a gaε bubble. Figure 12C schematically illustrateε thiε system in an integrated device having numerous chambers, including degassing chamber, dosing or volumetric chamber, storage and reaction chambers. Figure 12D is an illustration of an injection molded substrate which embodies the syεtem schematically illustrated in Figure 12C.

Figure 13 is a εchematic representation of a device configuration for carrying generic sample preparation reactions.

Figure 14 is a schematic representation of a device configuration for carrying multiple parallel reactions.

Figure 15 showε a demonεtration of integrated reactionε in a microfabricated polycarbonate device. Figure 15A shows the layout of the device including the thermal configuration of the device. Figure 15B showε the reεultε of PCR amplification and εubεequent in vitro transcription within the chambers of the device.

DETAILED DESCRIPTION OF THE INVENTION

I. General

It is a general object of the present invention to provide a miniaturized integrated nucleic acid diagnostic devices and syεtems incorporating these devices. The device of the invention is generally capable of performing one or more sample acquisition and preparation operations, in combination with one or more sample analysis operations. For example, the device can integrate several or all of the operations involved in sample acquiεition and εtorage, εample preparation and εample analyεiε, within a εingle, miniaturized, integrated unit. The device iε uεeful in a variety of applicationε and most notably, nucleic acid based diagnostic applications and de novo seguencing applications. The device of the invention will typically be one component of a larger diagnostic εyεtem which further includes a reader device for scanning and obtaining the data from the device, and a computer based interface for controlling the

device and/or interpretation of the data derived from the device.

To carry out its primary function, one embodiment of the device of the invention will typically incorporate a plurality of distinct reaction chamberε for carrying out the sample acquiεition, preparation and analyεis operationε. In particular, a sample to be analyzed is introduced into the device whereupon it will be delivered to one of these diεtinct reaction chamberε which are deεigned for carrying out a variety of reactionε aε a prelude to analyεis of the εample. These preparative reactions generally include, e.g., sample extraction, PCR amplification, nucleic acid fragmentation and labeling, extension reactions, transcription reactions and the like. Following sample preparation, the sample can be subjected to one or more different analysiε operationε. A variety of analyεiε operations may generally be performed, including size based analysiε uεing, e.g., microcapillary electrophoreεis, and/or εequence baεed analyεis using, e.g., hybridization to an oligonucleotide array. In addition to the various reaction chambers, the device will generally comprise a series of fluid channels which allow for the transportation of the sample or a portion thereof, among the various reaction chambers. Further chambers and components may also be included to provide reagents, bufferε, sample manipulation, e.g., mixing, pumping, fluid direction (i.e., valveε) heating and the like.

II. Inteσratable Operations A. Sample Acquisition

The sample collection portion of the device of the present invention generally provides for the identification of the sample, while preventing contamination of the sample by external elements, or contamination of the environment by the sample. Generally, this is carried out by introducing a sample for analysiε, e.g., preamplified εample, tiεεue, blood, saliva, etc., directly into a sample collection chamber within

the device. Typically, the prevention of crosε-contamination of the sample may be accompliεhed by directly injecting the sample into the sample collection chamber through a sealable opening, e.g., an injection valve, or a septum. Generally, sealable valves are preferred to reduce any potential threat of leakage during or after sample injection. Alternatively, the device may be provided with a hypodermic needle integrated within the device and connected to the sample collection chamber, for direct acquisition of the sample into the sample chamber. This can substantially reduce the opportunity for contamination of the sample.

In addition to the foregoing, the εample collection portion of the device may alεo include reagentε and/or treatmentε for neutralization of infectiouε agentε, stabilization of the specimen or sample, pH adjustments, and the like. Stabilization and pH adjustment treatments may include, e.g., introduction of heparin to prevent clotting of blood samples, addition of buffering agents, addition of protease or nuclease inhibitors, preservativeε and the like. Such reagents may generally be stored within the sample collection chamber of the device or may be stored within a separately accessible chamber, wherein the reagentε may be added to or mixed with the εample upon introduction of the εample into the device. These reagents may be incorporated within the device in either liquid or lyophilized form, depending upon the nature and stability of the particular reagent used.

B. Sample Preparation

In between introducing the sample to be analyzed into the device, and analyzing that sample, e.g., on an oligonucleotide array, it will often be desirable to perform one or more sample preparation operations upon the εample. Typically, theεe sample preparation operations will include such manipulations as extraction of intracellular material, e.g., nucleic acids from whole cell samples, viruseε and the like, amplification of nucleic acids, fragmentation, transcription, labeling and/or extension reactions. One or

more of these various operations may be readily incorporated into the device of the present invention. C. DNA Extraction

For those embodiments where whole cellε, viruses or other tissue samples are being analyzed, it will typically be necessary to extract the nucleic acids from the cells or viruses, prior to continuing with the various εample preparation operationε. Accordingly, following sample collection, nucleic acids may be liberated from the collected cells, viral coat, etc., into a crude extract, followed by additional treatments to prepare the sample for subsequent operations, e.g., denaturation of contaminating (DNA binding) proteinε, purification, filtration, deεalting, and the like.

Liberation of nucleic acidε from the sample cells or viruεes, and denaturation of DNA binding proteins may generally be performed by physical or chemical methods. For example, chemical methodε generally employ lysing agents to disrupt the cells and extract the nucleic acids from the cells, followed by treatment of the extract with chaotropic salts such as guanidinium isothiocyanate or urea to denature any contaminating and potentially interfering proteins. Generally, where chemical extraction and/or denaturation methods are used, the appropriate reagents may be incorporated within the extraction chamber, a separate accessible chamber or externally introduced.

Alternatively, physical methods may be used to extract the nucleic acids and denature DNA binding proteins. U.S. Patent No. 5,304,487, incorporated herein by reference in its entirety for all purposes, discusseε the use of physical protrusions within microchannels or sharp edged particleε within a chamber or channel to pierce cell membranes and extract their contents. Combinations of such structures with piezoelectric elements for agitation can provide εuitable shear forceε for lyεiε. Such elements are described in greater detail with respect to nucleic acid fragmentation, below.

More traditional methodε of cell extraction may also be used, e.g., employing a channel with restricted crosε- sectional dimension which causeε cell lyεis when the sample is passed through the channel with sufficient flow pressure. Alternatively, cell extraction and denaturing of contaminating proteins may be carried out by applying an alternating electrical current to the sample. More specifically, the sample of cells is flowed through a microtubular array while an alternating electric current is applied across the fluid flow. A variety of other methodε may be utilized within the device of the preεent invention to effect cell lysis/extraction, including, e.g., subjecting cells to ultrasonic agitation, or forcing cells through microgeometry apertures, thereby subjecting the cellε to high shear εtreεs resulting in rupture.

Following extraction, it will often be desirable to separate the nucleic acids from other elementε of the crude extract, e.g., denatured proteins, cell membrane particles, salts, and the like. Removal of particulate matter is generally accomplished by filtration, flocculation or the like. A variety of filter types may be readily incorporated into the device. Further, where chemical denaturing methodε are used, it may be desirable to desalt the sample prior to proceeding to the next step. Desalting of the sample, and isolation of the nucleic acid may generally be carried out in a single step, e.g., by binding the nucleic acids to a solid phase and washing away the contaminating εaltε or performing gel filtration chromatography on the sample, pasεing εaltε through dialysis membranes, and the like. Suitable solid supports for nucleic acid binding include, e.g. , diatomaceous earth, silica (i.e., glass wool), or the like. Suitable gel exclusion media, also well known in the art, may also be readily incorporated into the devices of the present invention, and iε commercially available from, e.g., Pharmacia and Sigma Chemical.

The isolation and/or gel filtration/desalting may be carried out in an additional chamber, or alternatively, the

particular chromatographic media may be incorporated in a channel or fluid pasεage leading to a εubεequent reaction chamber. Alternatively, the interior εurfaceε of one or more fluid paεsages or chambers may themselves be derivatized to provide functional groups appropriate for the desired purification, e.g., charged groupε, affinity binding groupε and the like, i.e., poly-T oligonucleotideε for mRNA purification.

Alternatively, deεalting methods may generally take advantage of the high electrophoretic mobility and negative of DNA compared to other elements. Electrophoretic methods may alεo be utilized in the purification of nucleic acidε from other cell contaminantε and debriε. In one example, a εeparation channel or chamber of the device iε fluidly connected to two separate "field" channels or chambers having electrodes, e.g., platinum electrodes, dispoεed therein. The two field channels are separated from the separation channel using an appropriate barrier or "capture membrane" which allows for pasεage of current without allowing paεsage of nucleic acids or other large molecules. The barrier generally serves two basic functions: first, the barrier acts to retain the nucleic acids which migrate toward the poεitive electrode within the εeparation chamber; and εecond, the barrierε prevent the adverεe effectε aεsociated with electrolyεis at the electrode from entering into the reaction chamber (e.g., acting aε a salt junction). Such barriers may include, e.g., dialysiε membranes, dense gels, PEI filters, or other suitable materials. Upon application of an appropriate electric field, the nucleic acids present in the sample will migrate toward the positive electrode and become trapped on the capture membrane. Sample impurities remaining free of the membrane are then washed from the chamber by applying an appropriate fluid flow. Upon reversal of the voltage, the nucleic acidε are releaεed from the membrane in a εubstantially purer form. The field channelε may be diεposed on the same or opposite sides or ends of a separation chamber or channel, and may be used in conjucton with mixing elements described herein, to

ensure maximal efficiency of operation. Further, coarse filters may also be overlaid on the barriers to avoid any fouling of the barriers by particulate matter, proteins or nucleic acidε, thereby permitting repeated uεe. In a similar aspect, the high electrophoretic mobility of nucleic acids with their negative charges, may be utilized to εeparate nucleic acidε from contaminantε by utilizing a short column of a gel or other appropriate matrix or gel which will slow or retard the flow of other contaminants while allowing the faster nucleic acids to pasε. For a number of applications, it may be deεirable to extract and εeparate messenger RNA from cells, cellular debris, and other contaminants. Aε εuch, the device of the preεent invention may, in εome caεes, include an mRNA purification chamber or channel. In general, such purification takeε advantage of the poly-A tailε on mRNA. In particular and aε noted above, poly-T oligonucleotides may be immobilized within a chamber or channel of the device to serve as affinity ligands for mRNA. Poly-T oligonucleotides may be immobilized upon a solid support incorporated within the chamber or channel, or alternatively, may be immobilized upon the surface(s) of the chamber or channel itself. Immobilization of oligonucleotides on the surface of the chambers or channels may be carried out by methods described herein including, e.g., oxidation and silanation of the surface followed by standard DMT synthesis of the oligonucleotides.

In operation, the lyεed εample is introduced into thiε chamber or channel in a high εalt εolution to increaεe the ionic εtrength for hybridization, whereupon the mRNA will hybridize to the immobilized poly-T. Hybridization may also be enhanced through incorporation of mixing elements, also as described herein. After enough time has elapsed for hybridization, the chamber or channel is washed with clean salt solution. The mRNA bound to the immobilized poly-T oligonucleotides is then washed free in a low ionic strength buffer. The surface area upon which the poly-T

oligonucleotides are immobilized may } a increased through the use of etched structures within the chamber or channel, e.g., ridges, grooves or the like. Such structures also aid in the agitation of the contents of the chamber or channel, as described herein. Alternatively, the poy-T oligonucleotides may be immobiliized upon poroussurfaces, e.g. , porous silicon, zeolites silica xerogels, scintered particleε, or other εolid supports.

D. Amplification and In Vitro Transcription Following sample collection and nucleic acid extraction, the nucleic acid portion of the sample is typically subjected to one or more preparative reactions. These preparative reactions include in vitro transcription, labeling, fragmentation, amplification and other reactions. Nucleic acid amplification increases the number of copies of the target nucleic acid sequence of interest. A variety of amplification methods are suitable for uεe in the methodε and device of the preεent invention, including for example, the polymeraεe chain reaction method or (PCR) , the ligaεe chain reaction (LCR) , εelf εuεtained εequence replication (3SR) , and nucleic acid baεed εequence amplification (NASBA) .

The latter two amplification methodε involve isothermal reactions based on isothermal tranεcription, which produce both εingle stranded RNA (εsRNA) and double stranded DNA (dsDNA) aε the amplification productε in a ratio of approximately 30 or 100 to 1, reεpectively. Aε a reεult, where these latter methods are employed, εeguence analysis may be carried out using either type of εubstrate, i.e., complementary to either DNA or RNA. In particularly preferred aspectε, the amplification step is carried out using PCR techniques that are well known in the art. See PCR Protocolε : A Guide to Methods and Applications (Innis, M. , Gelfand, D., Sninsky, J. and White, T., eds.) Academic Presε (1990), incorporated herein by reference in its entirety for all purposeε. PCR amplification generally involves the use of one strand of the target nucleic acid sequence as a template for producing a large number of

complementε to that sequence. Generally, two primer sequenceε complementary to different endε of a segment of the complementary strands of the target sequence hybridize with their respective strands of the target sequence, and in the presence of polymerase enzymes and nucleoside triphosphates, the primers are extended along the target sequence. The extenεionε are melted from the target εequence and the proceεε is repeated, this time with the additional copies of the target sequence synthesized in the preceding stepε. PCR amplification typically involveε repeated cycles of denaturation, hybridization and extension reactions to produce sufficient amounts of the target nucleic acid. The first step of each cycle of the PCR involves the separation of the nucleic acid duplex formed by the primer extension. Once the strandε are separated, the next step in PCR involveε hybridizing the separated strands with primers that flank the target sequence. The primers are then extended to form complementary copies of the target strandε. For εucceεεful PCR amplification, the primerε are deεigned εo that the poεition at which each primer hybridizes along a duplex sequence is such that an extension product syntheεized from one primer, when separated from the template (complement) , serves as a template for the extension of the other primer. The cycle of denaturation, hybridization, and extension iε repeated as many times as necesεary to obtain the deεired amount of amplified nucleic acid.

In PCR methods, strand separation iε normally achieved by heating the reaction to a εufficiently high temperature for a εufficient time to cauεe the denaturation of the duplex but not to cause an irreversible denaturation of the polymerase enzyme (see U.S. Patent No. 4,965,188, incorporated herein by reference) . Typical heat denaturation involves temperatures ranging from about 80°C to 105°C for times ranging from secondε to minuteε. Strand εeparation, however, can be accompliεhed by any εuitable denaturing method including phyεical, chemical, or enzymatic meanε. Strand separation may be induced by a helicase, for example, or an

enzyme capable of exhibiting helicase activity. For example, the enzyme RecA has helicase activity in the presence of ATP. The reaction conditions suitable for strand separation by helicases are known in the art (see Kuhn Hoffman-Berling, 1978, CSH-Quantitative Biology, 43:63-67; and Radding, 1982, Ann . Rev. Genetics 16:405-436, each of which is incorporated herein by reference) . Other embodiments may achieve strand separation by application of electric fields acrosε the sample. For example. Published PCT Application Nos. WO 92/04470 and WO 95/25177, incorporated herein by reference, describe electrochemical methods of denaturing double stranded DNA by application of an electric field to a sample containing the DNA. Structures for carrying out this electrochemical denaturation include a working electrode, counter electrode and reference electrode arranged in a potentiostat arrangement across a reaction chamber (See, Published PCT Application Noε. WO 92/04470 and WO 95/25177, each of which iε incorporated herein by reference for all purposes) . Such devices may be readily miniaturized for incorporation into the devices of the present invention utilizing the microfabrication techniques described herein.

Template-dependent extension of primers in PCR is catalyzed by a polymerizing agent in the presence of adequate amounts of at least 4 deoxyribonucleotide triphosphateε (typically εelected from dATP, dGTP, dCTP, dUTP and dTTP) in a reaction medium which compriεeε the appropriate εaltε, metal cationε, and pH buffering εyεtem. Reaction componentε and conditions are well known in the art (See PCR Protocols : A Guide to Methods and Applications (Innis, M. , Gelfand, D., Sninsky, J. and White, T. , eds.) Academic Presε (1990), previously incorporated by reference) . Suitable polymerizing agents are enzymes known to catalyze template-dependent DNA synthesis.

Published PCT Application No. WO 94/05414, to Northrup and White, discusεeε the uεe of a microPCR chamber which incorporateε microheaters and micropumps in the thermal cycling and mixing during the PCR reactionε.

The amplification reaction chamber of the device may comprise a sealable opening for the addition of the various amplification reagents. However, in preferred aspects, the amplification chamber will have an effective amount of the various amplification reagents described above, predisposed within the amplification chamber, or within an asεociated reagent chamber whereby the reagentε can be readily transported to the amplification chamber upon initiation of the amplification operation. By "effective amount" is meant a quantity and/or concentration of reagents required to carry out amplification of a targeted nucleic acid sequence. These amounts are readily determined from known PCR protocols. See, e.g., Sambrook, et al. Molecular Cloning: A Laboratory Manual , (2nd ed.) Vols. 1-3, Cold Spring Harbor Laboratory, (1989) and PCR Protocols : A Guide to Methods and Applications (Innis, M. , Gelfand, D. , Sninsky, J. and White, T. , eds.) Academic Presε (1990) , both of which are incorporated herein by reference for all purpoεeε in their entirety. For thoεe embodimentε where the variouε reagentε are prediεpoεed within the amplification or adjacent chamber, it will often be deεirable for theεe reagents to be in lyophilized formε, to provide maximum εhelf life of the overall device. Introduction of the liguid εample to the chamber then reconstitutes the reagents in active form, and the particular reactions may be carried out. In εome aεpectε, the polymerase enzyme may be present within the amplification chamber, coupled to a suitable solid support, or to the walls and surfaceε of the amplification chamber. Suitable solid supports include those that are well known in the art, e.g., agarose, cellulose, silica, divinylbenzene, polystyrene, etc. Coupling of enzymes to solid supports has been reported to impart stability to the enzyme in question, which allowε for εtorage of dayε, weekε or even monthε without a εubεtantial loεε in enzyme activity, and without the neceεεity of lyophilizing the enzyme. The 94 kd, single subunit DNA polymerase from Thermus aquaticus (or tag polymerase) is particularly εuited for the PCR baεed amplification methods used in the present invention, and iε

generally commercially available from, e.g., Promega, Inc., Madison, WI. In particular, monoclonal antibodies are available which bind the enzyme without affecting its polymerase activity. Conseguently, covalent attachment of the active polymeraεe enzyme to a solid support, or the walls of the amplification chamber can be carried out by using the antibody as a linker between the enzyme and the εupport.

In addition to PCR and IVT reactionε, the methods and devices of the preεent invention are alεo applicable to a number of other reaction typeε, e.g., reverεe tranεcription, nick translation, and the like.

E. Labeling and Fragmentation

The nucleic acids in a sample will generally be labeled to facilitate detection in subεequent steps. Labeling may be carried out during the amplification, in vitro transcription or nick translation processes. In particular, amplification, in vitro transcription or nick translation may incorporate a label into the amplified or transcribed sequence, either through the use of labeled primers or the incorporation of labeled dNTPs into the amplified sequence. Alternatively, the nucleic acids in the sample may be labeled following amplification. Post amplification labeling typically involveε the covalent attachment of a particular detectable group upon the amplified εequenceε. Suitable labelε or detectable groupε include a variety of fluorescent or radioactive labeling groups well known in the art. These labels may also be coupled to the sequenceε using methods that are well known in the art. See, e.g., Sambrook, et al. In addition, amplified sequenceε may be εubjected to other post amplification treatments. For example, in some cases, it may be desirable to fragment the seguence prior to hybridization with an oligonucleotide array, in order to provide segments which are more readily acceεεible to the probeε, which avoid looping and/or hybridization to multiple probes. Fragmentation of the nucleic acids may generally be carried out by phyεical, chemical or enzymatic methods that

are known in the art. These additional treatmentε may be performed within the amplification chamber, or alternatively, may be carried out in a εeparate chamber. For example, physical fragmentation methods may involve moving the sample containing the nucleic acid over pits or spikes in the surface of a reaction chamber or fluid channel. The motion of the fluid sample, in combination with the surface irregularities produces a high shear rate, resulting in fragmentation of the nucleic acids. In one aspect, this may be accompliεhed in a miniature device by placing a piezoelectric element, e.g., a PZT ceramic element adjacent to a εubstrate layer that covers a reaction chamber or flow channel, either directly, or through a liquid layer, as deεcribed herein. The εubεtrate layer haε pitε, spikes or apertures manufactured in the surface which are within the chamber or flow channel. By driving the PZT element in the thickness mode, a standing wave is set up within the chamber. Cavitation and/or streaming within the chamber resultε in εubεtantial εhear. Similar shear rates may be achieved by forcing the nucleic acid containing fluid sample through restricted εize flow passages, e.g., apertures having a crosε-εectional dimenεion in the micron or submicron scale, thereby producing a high shear rate and fragmenting the nucleic acid.

A number of sample preparation operationε may be carried out by adjuεting the pH of the sample, such as cell lysis, nucleic acid fragmentation, enzyme denaturation and the like. Similarly, pH control may also play a role in a wide variety of other reactions to be carried out in the device, i.e., for optimizing reaction conditions, neutralizing acid or base additions, denaturing exogenously introduced enzymes, quenching reactions, and the like. Such pH monitoring and control may be readily accomplished uεing well known methodε. For example, pH may be monitored by incorporation of a pH sensor or indicator within a particular chamber. Control may then be carried out by titration of the chamber contents with an appropriate acid or base.

In an alternative aspect, the device may include an electronically controlled pH system. In operation, an electrode iε placed adjacent, e.g., in fluid contact, to a reaction chamber wehile a counter electrode iε poεitioned within a second chamber or channel fluidly connected to the first. Upon application of current to these electrodes, the pH of the reaction chamber is altered through the electrolysiε of water at the surface of the electrode, producing 0 ₂ and hydrogen. A pH sensor may also be included within the reaction chamber to provide for monitoring and/or feedback control of the precise pH within the chamber.

One example of a reaction chamber employing an electronic pH control syεtem is shown in Figure 11. As shown, a device 1100 fabricated from two planar memberε 1102 and 1104, includeε three diεtinct chamberε, a reference chamber

1106, a reaction chamber 1108, and a counter-electrode chamber 1110. Each of the reference chamber 1106 and counter- electrode chamber 1110 are fluidly connected to the reaction chamber 1108, e.g., via fluid paεεageε 1112 and 1114. Theεe paεεages are typically blocked by an appropriate barrier 1116, e.g., dialysiε membrane, gel plug or the like, to prevent the electrophoretic paεsage of sample elements between the chambers. The reference chamber 1106 typically includes a reference electrode 1118. The reference electrode may be fabricated, e.g., from a platinum, gold or nickel screen pressed with a mixture of teflon and platinum black (producing a hydrogen electrode) . The reaction chamber 1108 typically includes an electrolysis electrode 1120, e.g., a platinum, gold or nickel screen coated with an appropriate barrier, e.g., polyacrylamide gel layer, and a hydrogen electrode 1122, also protected with an appropriate barrier. The reference electrode 1118 and hydrogen electrode 1122 are connected to an electrometer 1126 for monitoring the pH within the reaction chamber. The counter-electrode chamber 1110 typically includes the counter-electrode 1123, e.g., a single platinum, gold or nickel screen electrode. Tlu electrolysis electrode

and counter-electrode are connected to an appropriate current cource 1124.

Upon introduction of the sample, e.g., a cell suspension or nucleic acid containing sample, a current is applied by the current source. Electrolysiε at the electrolyεiε electrode alters the pH within the reaction chamber 1108. The electrometer compareε the pH εensed by the voltage between the reference and hydrogen electrodes. This signal may be compared to a set-point by appropriate meanε, e.g., an appropriately programmed computer or other microproceεsor 1128, and used to control the application of current. The resulting syεtem allowε the automated control of pH within the reaction chamber by varying the εet-point signal. F. Sample Analvsiε

Following the variouε sample preparation operations, the sample will generally be εubjected to one or more analyεiε operationε. Particularly preferred analyεiε operations include, e.g. , seguence based analyεeε uεing an oligonucleotide array and/or εize baεed analyεeε uεing, e.g., microcapillary array electrophoreεiε.

1. Oligonucleotide Probe Array

In one aspect, following sample preparation, the nucleic acid sample is probed using an array of oligonucleotide probes. Oligonucleotide arrays generally include a substrate having a large number of positionally diεtinct oligonucleotide probeε attached to the εubstrate. These oligonucleotide arrays, also described as "Genechip™ arrays," have been generally described in the art, for example, U.S. Patent No. 5,143,854 and PCT patent publication Nos. WO 90/15070 and 92/10092. These pioneering arrays may be produced using mechanical or light directed syntheεiε methodε which incorporate a combination of photolithographic methodε and solid phase oligonucleotide syntheεiε methodε. See Fodor et al.. Science , 251:767-777 (1991), Pirrung et al., U.S. Patent No. 5,143,854 (see alεo PCT Application No. WO 90/15070) and Fodor et al., PCT Publication No. WO 92/10092,

all incorporated herein by reference. Theεe referenceε disclose methods of forming vast arrays of peptides, oligonucleotides and other polymer sequenceε uεing, for example, light-directed εyntheεis techniques. Techniques for the synthesis of these arrays uεing mechanical εyntheεiε strategies are described in, e.g., PCT Publication No. 93/09668 and U.S. Patent No. 5,384,261, each of which is incorporated herein by reference in its entirety for all purpoεes. Incorporation of these arrays in injection molded polymeric casingε has been described in Published PCT Application No. 95/33846.

The basic strategy for light directed synthesis of oligonucleotide arrays is as follows. The εurface of a solid support, modified with photosensitive protecting groups is illuminated through a photolithographic mask, yielding reactive hydroxyl groups in the illuminated regions. A selected nucleotide, typically in the form of a 3 '-O- phosphoramidite-activated deoxynucleoside (protected at the 5' hydroxyl with a photosenεitive protecting group) , iε then preεented to the εurface and coupling occurε at the εiteε that were expoεed to light. Following capping and oxidation, the substrate is rinsed and the surface is illuminated through a second mask, to expose additional hydroxyl groups for coupling. A second selected nucleotide (e.g., 5 '-protected, 3 '-O-phosphoramidite-activated deoxynucleoside) is preεented to the surface. The selective deprotection and coupling cycles are repeated until the desired set of products is obtained. Since photolithography is used, the procesε can be readily miniaturized to generate high denεity arrays of oligonucleotide probes. Furthermore, the seguence of the oligonucleotides at each site iε known. See, Pease, et al. Mechanical syntheεiε methodε are εimilar to the light directed methodε except involving mechanical direction of fluidε for deprotection and addition in the εynthesis stepε. Typically, the arrayε uεed in the preεent invention will have a εite density of greater than 100 different probes per cm ² . Preferably, the arrays will have a site denεity of

greater than 500/cm ² , more preferably greater than about 1000/cm ² , and most preferably, greater than about 10,000/cm ² . Preferably, the arrays will have more than 100 different probes on a single substrate, more preferably greater than about 1000 different probes still more preferably, greater than about 10,000 different probes and most preferably, greater than 100,000 different probes on a single substrate.

For some embodiments, oligonucleotide arrayε may be prepared having all poεεible probes of a given length. Such arrays may be used in such areas aε εequencing or εequence checking applicationε, which offer εubεtantial benefitε over traditional methodε. The uεe of oligonucleotide arrays in such applications is described in, e.g., U.S. Patent application Serial No. 08/515,919, filed July 24, 1995, and U.S. Patent Application Serial No. 08/284,064, filed August 2, 1994, each of which is incorporated herein by reference in its entirety for all purposeε. Theεe methods typically use a set of short oligonucleotide probes of defined sequence to search for complementary sequences on a longer target strand of DNA. The hybridization pattern of the target sequence on the array is used to reconstruct the target DNA sequence. Hybridization analysis of large numbers of probes can be used to sequence long stretches of DNA.

One strategy of de novo sequencing can be illustrated by the following example. A 12-mer target DNA sequence is probed on an array having a complete set of octanucleotide probeε. Five of the 65,536 octamer probeε will perfectly hybridize to the target εequence. The identity of the probeε at each εite iε known. Thuε, by determining the locationε at which the target hybridizes on the array, or the hybridization pattern, one can determine the sequence of the target seguence. While these strategies have been proposed and utilized in some applications, there has been difficulty in demonstrating seguencing of larger nucleic acids using these same strategies. Accordingly, in preferred aspects, SBH methods utilizing the devices deεcribed herein uεe data from miεmatched probes, as well as perfectly matching probeε, to

supply useful sequence data, as described in U.S. Patent Application No. 08/505,919, incorporated herein by reference. While oligonucleotide probes may be prepared having every possible sequence of length n, it will often be deεirable in practicing the preεent invention to provide an oligonucleotide array which iε εpecific and complementary to a particular nucleic acid sequence. For example, in particularly preferred aspectε, the oligonucleotide array will contain oligonucleotide probeε which are complementary to specific target sequences, and individual or multiple mutations of these. Such arrays are particularly useful in the diagnosiε of εpecific diεorderε which are characterized by the preεence of a particular nucleic acid sequence. For example, the target sequence may be that of a particular exogenous disease causing agent, e.g., human immunodeficiency virus (see, U.S. Application Serial No. 08/284,064, previously incorporated herein by reference) , or alternatively, the target sequence may be that portion of the human genome which is known to be mutated in instances of a particular disorder, i.e., sickle cell anemia (see, e.g., U.S. Application Serial No.08/082,937, previously incorporated herein by reference) or cystic fibrosis.

In such an application, the array generally comprises at leaεt four εetε of oligonucleotide probes, usually from about 9 to about 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in the target sequence. A probe iε related to itε corresponding nucleotide by being exactly complementary to a subsequence of the target sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that iε occupied by a complementary nucleotide to the corresponding nucleotide in the target sequence. The three additional probe setε each have a corresponding probe for each probe in the first probe set, but substituting the interrogation position with the three other nucleotides. Thus, for each nucleotide in the target sequence, there are four corresponding probeε, one from

each of the probe εetε. The three correεponding probes in the three additional probe setε are identical to the correεponding probe from the first probe or a subεequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four correεponding probeε.

Some arrayε have fifth, εixth, seventh and eighth probe sets. The probes in each set are selected by analogouε principleε to thoεe for the probeε in the firεt four probe setε, except that the probes in the fifth, sixth, seventh and eighth sets exhibit complementarity to a second reference sequence. In some arrayε, the firεt εet of probes is complementary to the coding strand of the target sequence while the second εet iε complementary to the noncoding εtrand. Alternatively, the second reference sequence can be a subsequence of the first reference εequence having a substitution of at least one nucleotide.

In some applications, the target sequence has a subεtituted nucleotide relative to the probe εequence in at least one undetermined position, and the relative specific binding of the probeε indicateε the location of the poεition and the nucleotide occupying the poεition in the target sequence.

Following amplification and/or labeling, the nucleic acid sample is incubated with the oligonucleotide array in the hybridization chamber. Hybridization between the εample nucleic acid and the oligonucleotide probes upon the array is then detected, uεing, e.g., epifluoreεcence confocal microscopy. Typically, sample is mixed during hybridization to enhance hybridization of nucleic acids in the sample to nucleoc acid probes on the array. Again, mixing may be carried out by the methods described herein, e.g., through the use of piezoelectric elements, electrophoretic methods, or physical mixing by pumping fluids into and out of the hybridization chamber, i.e., into an adjoining chamber.

Generally, the detection operation will be performed using a reader device external to the diagnostic device. However, it

may be desirable in some caεes, to incorporate the data gathering operation into the diagnostic device itself.

The hybridization data is next analyzed to determine the presence or absence of a particular seguence within the sample, or by analyzing multiple hybridizations to determine the sequence of the target nucleic acid using the SBH techniques already described.

In some caseε, hybridized oligonucleotideε may be labeled following hybridization. For example, wghere biotin labeled dNTPε are used in, e.g. , amplification or transcription, streptavidin linked reporter groups may be used to label hybridized complexes. Such operations are readily integratable into the syεtemε of the preεent invention. 2. Capillary Electrophoreεiε In εome embodimentε, it may be deεirable to provide an additional, or alternative meanε for analyzing the nucleic acidε from the sample. In one embodiment, the device of the invention will optionally or additionally comprise a micro capillary array for analysis of the nucleic acids obtained from the εample.

Microcapillary array electrophoreεis generally involves the use of a thin capillary or channel which may or may not be filled with a particular separation medium. Electrophoresiε of a sample through the capillary provides a size based separation profile for the sample. The use of microcapillary electrophoresis in size εeparation of nucleic acidε haε been reported in, e.g., Woolley and Mathieε, Proc . Nat ' l Acad . Sci . USA (1994) 91:11348-11352. Microcapillary array electrophoreεis generally provides a rapid method for size based sequencing, PCR product analysiε and reεtriction fragment sizing. The high surface to volume ratio of theεe capillarieε allows for the application of higher electric fields across the capillary without substantial thermal variation acrosε the capillary, consequently allowing for more rapid separations. Furthermore, when combined with confocal imaging methods, these methods provide sensitivity in the

range of attomoleε, which iε comparable to the εenεitivity of radioactive εequencing methodε.

Microfabrication of microfluidic devices including microcapillary electrophoretic devices has been discuεεed in detail in, e.g., Jacobεen, et al., Anal . Chem . (1994) 66:1114- 1118, Effenhauεer, et al., Anal. Chem . (1994) 66:2949-2953, Harrison, et al.. Science (1993) 261:895-897, Effenhauser, et al. Anal. Chem . (1993) 65:2637-2642, and Manz, et al., J. Chromatog. (1992) 593:253-258. Typically, theεe methodε comprise photolithographic etching of micron scale channelε on a silica, silicon or other rigid subεtrate or chip, and can be readily adapted for uεe in the miniaturized deviceε of the present invention. In some embodiments, the capillary arrayε may be fabricated from the εame polymeric materialε deεcribed for the fabrication of the body of the device, uεing the injection molding techniques described herein. In such caεes, the capillary and other fluid channels may be molded into a first planar element. A second thin polymeric member having ports corresponding to the termini of the capillary channels disposed therethrough, is laminated or sonically welded onto the first to provide the top surface of these channels. Electrodes for electrophoretic control are dispoεed within theεe portε/wells for application of the electrical current to the capillary channels. Through use of a relatively this sheet as the covering member of the capillary channels, heat generated during electrophoreεiε can be rapidly diεεipated. Additionally, the capillary channelε may be coated with more thermally conductive material, e.g., glaεs or ceramic, to enhance heat disεipation. In many capillary electrophoreεiε methods, the capillaries, e.g., fuεed εilica capillarieε or channelε etched, machined or molded into planar εubεtrateε, are filled with an appropriate εeparation/εieving matrix. Typically, a variety of εieving matriceε are known in the art may be used in the microcapillary arrays. Examples of such matrices include, e.g., hydroxyethyl cellulose, polyacrylamide, agarose and the like. Gel matrices may be introduced and polymerized

within the capillary channel. However, in some caεeε, thiε may result in entrapment of bubbles within the channels which can interfere with sample separationε. Accordingly, it iε often desirable to place a preformed separation matrix within the capillary channel(s), prior to mating the planar elements of the capillary portion. Fixing the two parts, e.g., through sonic welding, permanently fixes the matrix within the channel. Polymerization outside of the channels helpε to ensure that no bubbles are formed. Further, the preεsure of the welding proceεs helps to ensure a void-free syεtem. Generally, the specific gel matrix, running buffers and running conditions are selected to maximize the separation characteristicε of the particular application, e.g., the εize of the nucleic acid fragments, the required resolution, and the presence of native or undenatured nucleic acid moleculeε. For example, running bufferε may include denaturantε, chaotropic agentε such as urea or the like, to denature nucleic acdε in the εample.

In addition to its use in nucleic acid "fingerprinting" and other sized based analyses, the capillary arrays may also be used in sequencing applications. In particular, gel based sequencing techniques may be readily adapted for capillary array electrophoresiε. For example, capillary electrophoreεiε may be combined with the Sanger dideoxy chain termination εequencing methods as discuεsed in Sambrook, et al. (See alεo Brenner, et al., Proc . Nat ' l Acad . Sci . (1989) 86:8902-8906). In theεe methods, the sample nucleic acid is amplified in the presence of fluorescent dideoxynucleoside triphoεphateε in an extenεion reaction. The random incorporation of the dideoxynucleotideε terminateε tranεcription of the nucleic acid. Thiε resultε in a range of tranεcription productε differing from another member by a single baεe. Comparative size based separation then allows the sequence of the nucleic acid to be determined based upon the last dideoxy nucleotide to be incorporated.

G. Data Gathering and Analysiε

Gathering data from the variouε analyεis operations, e.g., oligonucleotide and/or microcapillary arrays, will typically be carried out using methods known in the art. For example, the arrays may be scanned using lasers to excite fluorescently labeled targets that have hybridized to regions of probe arrays, which can then be imaged using charged coupled deviceε ("CCDs") for a wide field scanning of the array. Alternatively, another particularly useful method for gathering data from the arrayε iε through the uεe of laser confocal microscopy which combines the ease and speed of a readily automated procesε with high resolution detection. Particularly preferred scanning devices are generally described in, e.g., U.S. Patent Nos. 5,143,854 and 5,424,186. Following the data gathering operation, the data will typically be reported to a data analysis operation. To facilitate the sample analysiε operation, the data obtained by the reader from the device will typically be analyzed using a digital computer. Typically, the computer will be appropriately programmed for receipt and storage of the data from the device, aε well aε for analyεiε and reporting of the data gathered, i.e., interpreting fluoreεcence data to determine the εequence of hybridizing probeε, normalization of background and single base mismatch hybridizations, ordering of sequence data in SBH applicationε, and the like, aε deεcribed in, e.g., U.S. Patent Application Serial No. 08/327,525, filed October 21, 1994, and incorporated herein by reference.

III. The Nucleic Acid Diagnoεtic System A. Analytical System

A schematic of a representative analytical system based upon the device of the invention is shown in Figure 1. The system includes the diagnostic device 2 which performs one or more of the operationε of εample ' ollection, preparation and/or analyεiε uεing, e.g., hybridization and/or εize based separation. The diagnostic device iε then placed in a reader

device 4 to detect the hybridization and or εeparation information preεent on the device. The hybridization and/or separation data is then reported from the reader device to a computer 6 which is programmed with appropriate software for interpreting the data obtained by the reader device from the diagnostic device. Interpretation of the data from the diagnostic device may be uεed in a variety of ways, including nucleic acid εequencing which iε directed toward a particular diεeaεe causing agent, such as viral or bacterial infectionε, e.g., AIDS, malaria, etc., or genetic diεorders, e.g., sickle cell anemia, cyεtic fibrosis. Fragile X syndrome, Duchenne muscular dystrophy, and the like. Alternatively, the device can be employed in de novo sequencing applications to identify the nucleic acid sequence of a previously unknown sequence. B. The Diagnostic Device 1. Generally

Aε deεcribed above, the device of the preεent invention iε generally capable of carrying out a number of preparative and analytical reactionε on a εample. To achieve thiε end, the device generally compriεeε a number of diεcrete reaction, εtorage and/or analytical chamberε diεpoεed within a εingle unit or body. While referred to herein as a "diagnostic device," those of skill in the art will appreciate that the device of the invention will have a variety of applications outεide the εcope of diagnoεtics, alone. Such applications include sequencing applicationε, εample identification and characterization applications (for, e.g., taxonomic studies, forensic applications, i.e., criminal investigationε, and the like) . Typically, the body of the device defines the various reaction chambers and fluid passages in which the above described operations are carried out. Fabrication of the body, and thus the various chamberε and channelε diεpoεed within the body may generally be carried out uεing one or a combination of a variety of well knc ^* n manufacturing techniqueε and materialε. Generally, the material from which the body iε fabricated will be εelected εo aε to provide

maximum resistance to the full range of conditions to which the device will be exposed, e.g., extremes of temperature, salt, pH, application of electric fields and the like, and will also be selected for compatibility with other materials used in the device. Additional components may be later introduced, as necesεary, into the body. Alternatively, the device may be formed from a plurality of diεtinct partε that are later aεεembled or mated. For example, εeparate and individual chamberε and fluid passageε may be aεεembled to provide the variouε chamberε of the device.

As a miniaturized device, the body of the device will typically be approximately 1 to 20 cm in length by about 1 to 10 cm in width by about 0.1 to about 2 cm thick. Although indicative of a rectangular shape, it will be readily appreciated that the devices of the invention may be embodied in any number of shapeε depending upon the particular need. Additionally, theεe dimenεionε will typically vary depending upon the number of operationε to be performed by the device, the complexity of these operations and the like. As a result, theεe dimenεionε are provided aε a general indication of the size of the device. The number and size of the reaction chambers included within the device will also vary depending upon the specific application for which the device is to be used. Generally, the device will include at least two distinct reaction chambers, and preferably, at leaεt three, four or five diεtinct reaction chamberε, all integrated within a single body. Individual reaction chambers will also vary in size and shape according to the specific function of the reaction chamber. For example, in εome caεeε, circular reaction chamberε may be employed. Alternatively, elongate reaction chamberε may be uεed. In general however, the reaction chamberε will be from about 0.05 to about 20 mm in width or diameter, preferably from about 0.1 or 0.5 to about 20 mm in width or diameter and about 0.05 to about 5 mm deep, and preferably 0.05 to about 1 mm deep. For elongate chambers, length will also typically vary along these same ranges. Fluid channelε, on the other hand, are typically

distinguished from chambers in having smaller dimenεionε relative to the chamberε, and will typically range from about 10 to about 1000 μm wide, preferably, 100 to 500 μm wide and about 1 to 500 μm deep. Although deεcribed in termε of reaction chambers, it will be appreciated that these chambers may perform a number of varied functions, e.g., as storage chamberε, incubation chamberε, mixing chamberε and the like.

In εome cases, a separate chamber or chambers may be used as volumetric chambers, e.g., to precisely measure fluid volumeε for introduction into a εubsequent reaction chamber. In such cases, the volume of the chamber will be dictated by volumetric needs of a given reaction. Further, the device may be fabricated to include a range of volumetric chamberε having varied, but known volumes or volume ratios (e.g., in comparison to a reaction chgamber or other volumetric chambers) .

As described above, the body of the device is generally fabricated using one or more of a variety of methods and materials εuitable for microfabrication techniqueε. For example, in preferred aεpectε, the body of the device may comprise a number of planar members that may individually be injection molded parts fabricated from a variety of polymeric materials, or may be silicon, glaεε, or the like. In the caεe of substrates like silica, glass or silicon, methods for etching, milling, drilling, etc. , may be used to produce wells and depreεεionε which make up the variouε reaction chamberε and fluid channels within the device. Microfabrication techniques, such as those regularly used in the semiconductor and microelectronics induεtries are particularly suited to these materials and methodε. Theεe techniques include, e.g., electrodeposition, low-pressure vapor deposition, photolithography, wet chemical etching, reactive ion etching (RIE) , laser drilling, and the like. Where these methods are used, it will generally be desirable to fabricate the planar members of the device from materials similar to thoεe uεed in the semiconductor industry, i.e., silica, silicon, gallium arsenide, polyimide substrates. U.S. Patent No. 5,252,294, to

Kroy, et al., incorporated herein by reference in its entirety for all purposes, reports the fabrication of a silicon based multiwell apparatus for sample handling in biotechnology applications. Photolithographic methods of etching εubstrates are particularly well suited for the microfabrication of these substrates and are well known in the art. For example, the first sheet of a substrate may be overlaid with a photoresist. An electromagnetic radiation source may then be shone through a photolithographic maεk to expoεe the photoreεist in a pattern which reflects the pattern of chambers and/or channels on the surface of the sheet. After removing the exposed photoresist, the exposed substrate may be etched to produce the desired wells and channels. Generally preferred photoresists include those used extensively in the semiconductor industry. Such materials include polymethyl methacrylate (PMMA) and its derivatives, and electron beam resists such as poly(olefin sulfones) and the like (more fully discussed in, e.g., Ghandi, "VLSI Fabrication Principleε, " Wiley (1983) Chapter 10, incorporated herein by reference in its entirety for all purposeε) .

As an example, the wells manufactured into the surface of one planar member make up the various reaction chambers of the device. Channels manufactured into the surface of this or another planar member make up fluid channels which are used to fluidly connect the various reaction chambers. Another planar member is then placed over and bonded to the first, whereby the wells in the first planar member define cavities within the body of the device which cavities are the various reaction chamberε of the device.

Similarly, fluid channelε manufactured in the surface of one planar member, when covered with a second planar member define fluid passages through the body of the device. These planar members are bonded together or laminated to produce a fluid tight body of the device. Bonding of the planar members of the device may generally be carried out using a variety of methods known in the art and which may vary depending upon the

materialε uεed. For example, adheεives may generally be used to bond the planar members together. Where the planar members are, e.g., glass, silicon or combinationε thereof, thermal bonding, anodic/electroεtatic or silicon fusion bonding methods may be applied. For polymeric parts, a similar variety of methods may be employed in coupling εubεtrate partε together, e.g., heat with preεεure, solvent based bonding. Generally, acoustic welding techniques are generally preferred. In a related aspect, this adhesive tapes may be employed as one portion of the device forming a thin wall of the reaction chamber/channel structures.

Although primarily described in terms of producing a fully integrated body of the device, the above described methods can also be used to fabricate individual discrete componentε of the device which are later assembled into the body of the device.

In additional embodiments, the body may comprise a combination of materials and manufacturing techniques described above. In some caseε, the body may include εome parts of injection molded plasticε, and the like, while other portionε of the body may compriεe etched silica or silicon planar memberε, and the like. For example, injection molding techniqueε may be uεed to form a number of diεcrete cavitieε in a planar εurface which define the various reaction chambers, whereas additional components, e.g., fluid channels, arrays, etc, may be fabricated on a planar glasε, silica or silicon chip or substrate. Lamination of one set of parts to the other will then result in the formation of the variouε reaction chamberε, interconnected by the appropriate fluid channels.

In particularly preferred embodiments, the body of the device iε made from at leaεt one injection molded, preεε molded or machined polymeric part that haε one or more wellε or depressionε manufactured into its surface to define several of the walls of the reaction chamber or chamberε. Moldε or mold faceε for producing these injection molded parts may generally be fabricated using the methods described herein

for, e.g., εilicon moldε. Examples of suitable polymers for injection molding or machining include, e.g., polycarbonate, polystyrene, polypropylene, polyethylene, acrylic, and commercial polymers such as Kapton, Valox, Teflon, ABS, Delrin and the like. A second part that is similarly planar in shape is mated to the surface of the polymeric part to define the remaining wall of the reaction chamber(s) . Published PCT Application No. 95/33846, incorporated herein by reference, describes a device that is used to package individual oligonucleotide arrays. The device includes a hybridization chamber disposed within a planar body. The chamber is fluidly connected to an inlet port and an outlet port via flow channels in the body of the device. The body includes a plurality of injection molded planar parts that are mated to form the body of the device, and which define the flow channels and hybridization chamber.

The surfaces of the fluid channels and reaction chambers which contact the samples and reagents may alεo be modified to better accomodate a deεired reaction. Surfaces may be made more hydrophobic or more hydrophilic depending upon the particular application. Alternatively, surfaceε may be coated with any number of materialε in order to make the overall system more compatible to the reactions being carried out. For example, in the case of nucleic acid analyεes, it may be desireable to coat the surfaceε with, e.g., a teflon or other non-stick coating, to prevent adhesion of nucleic acidε to the surface. Additionally, insulator coatings may also be desirable in those instances where electrical leads are placed in contact with fluids, to prevent shorting out, or excess gas formation from electrolyεiε. Such inεulatorε may include those well known in the art, e.g., silicon oxide, ceramics or the like. Additional surface treatments are deεcribed in greater detail below.

Figureε 2A and 2B εhow a εchematic representation of one embodiment of a reaction chamber for inclusion in the device of the invention. The reaction chamber includes a machined or injection molded polymeric part 102 which has a

well 104 manufactured, i.e., machined or molded, into its . surface. This well may be closed at the end opposite the well opening as shown in Figure 2A, or optionally, may be supplied with an additional opening 118 for inclusion of an optional vent, as shown in Figure 2B.

The reaction chamber is also provided with additional elements for transporting a fluid sample to and from the reaction chamber. These elements include one or more fluid channelε (122 and 110 in Figureε 2A and 2B, respectively) which connect the reaction chamber to an inlet/outlet port for the overall device, additional reaction chambers, storage chambers or one or more analytical chambers. A second part 124, typically planar in structure, is mated to the polymeric part to define a closure for the reaction chamber. This second part may incorporate the fluid channels, as εhown in Figureε 2A and 2B, or may merely define a further wall of the fluid channelε provided in the εurface of the firεt polymeric part (not εhown) . Typically, this second part will comprise a serieε of fluid channels manufactured into one of its surfaces, for fluidly connecting the reaction chamber to an inlet port in the overall device or to another reaction or analytical chamber. Again, this second part may be a second polymeric part made by injection molding or machining techniques. Alternatively, this second part may be manufactured from a variety of other materials, including glass, silica, silicon or other crystalline subεtrates. Microfabrication technigueε suited for these subεtrates are generally well known in the art and are described above. In a first preferred embodiment, the reaction chamber is provided without an inlet/outlet valve structure, as shown in Figure 2A. For these embodiments, the fluid channels 122 may be provided in the εurface of the second part that is mated with the surface of the polymeric part such that upon mating the εecond part to the firεt polymeric part, the fluid channel 122 iε fluidly connected to the reaction chamber 104.

Alternatively, in a second preferred embodiment, the reaction chamber may be provided with an inlet/outlet valve structure for sealing the reaction chamber to retain a fluid sample therein. An example of such a valve structure iε shown in Figure 2B. In particular, the second part 124 mated to the polymeric part may compriεe a plurality of mated planar members, wherein a first planar member 106 is mated with the first polymeric part 102 to define a wall of the reaction chamber. The first planar member 106 has an opening 108 disposed therethrough, defining an inlet to the reaction chamber. This first planar member also includes a fluid channel 110 etched in the surface oppoεite the εurface that iε mated with the firεt polymeric part 102. The fluid channel terminates adjacent to, but not within the reaction chamber inlet 108. The first planar member will generally be manufactured from any of the above deεcribed materials, using the above-deεcribed methodε. A εecond planar member 112 iε mated to the first and includes a diaphragm valve 114 which extends acroεε the inlet 108 and overlapε with the fluid channel 110 εuch that deflection of the diaphragm reεultε in a gap between the firεt and εecond planar memberε, thereby creating a fluid connection between the reaction chamber 104 and the fluid channel 110, via the inlet 108. Deflection of the diaphragm valve may be carried out by a variety of methods including, e.g., application of a vacuum, electromagnetic and/or piezoelectric actuators coupled to the diaphragm valve, and the like. To allow for a deflectable diaphragm, the second planar member will typically be fabricated, at least in part, from a flexible material, e.g., silicon, silicone, latex, mylar, polyimide, Teflon or other flexible polymers. As with the reaction chambers and fluid channels, these diaphragmε will alεo be of miniature εcale. Specifically, valve and pump diaphragms used in the device will typically range in size depending upon the size of the chamber or fluid passage to which they are fluidly connected. In general, however, these diaphragms will be in the range of from about 0.5 to about 5 mm for valve diaphragmε, and from about 1 to

about 20 mm in diameter for pumping diaphragms. As shown in Figure 2B, second part 124 includes an additional planar member 116 having an opening 126 for application of pressure or vacuum for deflection of valve 114. Where reagentε involved in a particular analyεiε are incompatible with the materialε used to manufacture the device, e.g., silicon, glasε or polymeric parts, a variety of coatings may be applied to the surfaceε of theεe partε that contact theεe reagents. For example, components that have silicon elements may be coated with a silicon nitride layer or a metallic layer of, e.g., gold or nickel, may be εputtered or electroplated on the surface to avoid adverse reactions with these reagents. Similarly, inert polymer coatingε, e.g., Teflon and the like, pyraline coatingε, or εurface silanation modifications may also be applied to internal surfaces of the chambers and/or channels.

The reaction/εtorage chamber 104 εhown in Figure 2B iε alεo shown with an optional vent 118, for release of displaced gas present in the chamber when the fluid is introduced. In preferred aspects, this vent may be fitted with a gas permeable fluid barrier 120, which permits the paεsage of gaε without allowing for the paεsage of fluid, e.g., a poorly wetting filter plug. A variety of materials are suitable for use as poorly wetting filter plugs including, e.g., porous hydrophobic polymer materials, such aε εpun fibers of acrylic, polycarbonate, teflon, pressed polypropylene fiberε, or any number commercially available filter plugε (American Filtrona Corp., Richmond, VA, Gelman Scienceε, and the like) . Alternatively, a hydrophobic membrane can be bonded over a thru-hole to εupply a εimilar structure. Modified acrylic copolymer membranes are commercially available from, e.g., Gelman Sciences (Ann Arbor, MI) and particle-track etched polycarbonate membranes are available from Poretics, Inc. (Livermore, CA) . Venting of heated chambers may incorporate barriers to evaporation of the sample, e.g., a reflux chamber or a mineral oil layer dispoεed within the chamber, and over the top εurface of the εample, to

permit the evolution of gaε while preventing exceεεive evaporation of fluid from the εample.

Aε deεcribed herein, the overall geometry of the device of the invention may take a number of formε. For example, the device may incorporate a plurality of reaction chamberε, storage chambers and analytical chambers, arranged in series, whereby a fluid sample is moved serially through the chambers, and the reεpective operationε performed in theεe chambers. Alternatively, the device may incorporate a central fluid distribution channel or chamber having the various reaction/storage/analytical chambers arranged around and fluidly connected to the central channel or chamber, which central channel or chamber actε as a conduit or hub for εample rediεtribution to the variouε chamberε. An example of the εerial geometry of the device iε shown in Figure 3. In particular, the illustrated device includes a plurality of reaction/storage/analytical chambers for performing a number of the operations described above, fluidly connected in serieε. The εchematic repreεentation of the device in

Figure 3 shows a device that compriseε εeveral reaction chamberε arranged in a εerial geometry. Specifically, the body of the device 200 incorporateε reaction chamberε 202, 206, 210, 214 and 218. Theεe chamberε are fluidly connected in series by fluid channels 208, 212 and 216, reεpectively. In carrying out the variouε operationε outlined above, each of theεe reaction chamberε iε aεεigned one or more different functionε. For example, reaction chamber 202 may be a sample collection chamber which iε adapted for receiving a fluid sample, i.e., a cell containing sample. For example, this chamber may include an opening to the outside of the device adapted for receipt of the sample. The opening will typically incorporate a sealable closure to prevent leakage of the sample, e.g., a valve, check-valve, or septum, through which the sample iε introduced or ir ected. In some embodiments, the apparatus may incluαe a hypodermic needle or other sample conduit, integrated into the body of the device

and in fluid connection with the sample collection chamber, for direct transfer of the sample from the host, patient, sample vial or tube, or other origin of the sample to the sample collection chamber. Additionally, the sample collection chamber may have disposed therein, a reagent or reagents for the stabilization of the sample for prolonged storage, aε deεcribed above. Alternatively, theεe reagentε may be diεpoεed within a reagent storage chamber adjacent to and fluidly connected with the sample collection chamber.

The sample collection chamber is connected via a first fluid channel 204 to second reaction chamber 210 in which the extraction of nucleic acids from the cellε within the sample may be performed. This is particularly suited to analytical operations to be performed where the sampleε include whole cellε. The extraction chamber will typically be connected to εample collection chamber, however, in εome cases, the extraction chamber may be integrated within and exist as a portion of the sample collection chamber. As previouεly deεcribed, the extraction chamber may include phyεical and or chemical meanε for extracting nucleic acids from cells.

The extraction chamber is fluidly connected via a second fluid channel 208, to third reaction chamber 210 in which amplification of the nucleic acids extracted from the sample is carried out. The amplification proceεε begins when the sample is introduced into the amplification chamber. Aε described previously, amplification reagents may be exogenously introduced, or will preferably be predispoεed within the reaction chamber. However, in alternate embodimentε, these reagents will be introduced to the amplification chamber from an optional adjacent reagent chamber or from an external source through a sealable opening in the amplification chamber. For PCR amplification methods, denaturation and hybridization cycling will preferably be carried out by repeated heating and cooling of the sample. Accordingly, PCR

based amplification chambers will typically include a a temperature controller for heating the reaction to carry out the thermal cycling. For example, a heating element or temperature control block may be dispoεed adjacent the external surface of the amplification chamber thereby transferring heat to the amplification chamber. In this case, preferred devices will include a thin external wall for chambers in which thermal control is desired. This thin wall may be a thin cover element, e.g., polycarbonate sheet, or high temperature tape, i.e. silicone adhesive on Kapton tape (commercially available from, e.g., 3M Corp.). Micro-scale PCR devices have been previouεly reported. For example, published PCT Application No. WO 94/05414, to Northrup and White reports a miniaturized reaction chamber for use as a PCR chamber, incorporating microheaters, e.g., resiεtive heaterε. The high surface area to volume ratio of the chamber allows for very rapid heating and cooling of the reagentε diεposed therein. Similarly, U.S. Patent No. 5,304,487 to Wilding et al., previously incorporated by reference, also discuεεeε the use of a microfabricated PCR device.

In preferred embodiments, the amplification chamber will incorporate a controllable heater disposed within or adjacent to the amplification chamber, for thermal cycling of the sample. Thermal cycling is carried out by varying the current supplied to the heater to achieve the desired temperature for the particular stage of the reaction. Alternatively, thermal cycling for the PCR reaction may be achieved by transferring the fluid εample among a number of different reaction chamberε or regions of the same reaction chamber, having different, although constant temperatures, or by flowing the sample through a serpentine channel which travels through a number of varied temperature 'zones'. Heating may alternatively be supplied by exposing the amplification chamber to a laεer or other light or electromagnetic radiation εource.

The amplification chamber iε fluidly connected via a fluid channel, e.g., fluid channel 212, to an additional

reaction chamber 214 which can carry out additional preparative operations, such as labeling or fragmentation.

A fourth fluid channel 216 connects the labeling or fragmentation chamber to an analytical chamber 218. Aε shown, the analytical chamber includes an oligonucleotide array 220 aε the bottom surface of the chamber. Analytical chamber 218 may optionally, or additionally comprise a microcapillary electrophoresis device 226 and additional preparative reaction chambers, e.g., 224 for performing, e.g., extension reactions, fluidly connected to, e.g., chamber 210. The analytical chamber will typically have as at leaεt one εurface, a transparent window for observation or scanning of the particular analysis being performed.

Figureε 4A-C illuεtrate an embodiment of a microcapillary electrophoreεiε device. In this embodiment, the sample to be analyzed is introduced into sample reservoir 402. Thiε sample reservoir may be a separate chamber, or may be merely a portion of the fluid channel leading from a previous reaction chamber. Reservoirε 404, 406 and 414 are filled with sample/running buffer. Figure 4A illustrateε the loading of the sample by plug loading, where the sample iε drawn acroεs the intersection of loading channel 416 and capillary channel 412, by application of an electrical current across buffer reservoir 406 and sample reservoir 402. In alternative embodiments, the εample iε "stack" loaded by applying an electrical current acrosε εample reεervoir 402 and waste reservoir 414, as shown in Figure 4B. Following sample loading, an electrical field is applied across buffer reservoir 404 and waste reservoir 414, electrophoresing the sample through the capillary channel 412. Running of the sample is εhown in Figure 4C. Although only a εingle capillary is shown in Figures 4A-C, the device of the preεent invention may typically compriεe more than one capillary, and more typically, will compriεe an array of four or more capillarieε, which are run in parallel. Fabrication of the microcapillary electrophoreεiε device may generally be carried uεing the methodε deεcribed herein and as described in e.g.,

Woolley and Mathies, Proc. Nat'l Acad. Sci. USA 91:11348-11352 (1994) , incorporated herein by reference in its entirety for all purposeε. Typically, each capillary will be fluidly connected to a separate extension reaction chamber for incorporation of a different dideoxynucleotide.

An alternate layout of the reaction chambers within the device of the invention, as noted above, includes a centralized geometry having a central chamber for gathering and distribution of a fluid sample to a number of separate reaction/storage/analytical chamberε arranged around, and fluidly connected to the central chamber. An example of thiε centralized geometry iε εhown in Figure 5. In the particular device shown, a fluid sample is introduced into the device through sample inlet 502, which is typically fluidly connected to a sample collection chamber 504. The fluid sample is then tranεported to a central chamber 508 via fluid channel 506. Once within the central chamber, the εample may be tranεported to any one of a number of reaction/εtorage/analytical chamberε (510, 512, 514) which are arranged around and fluidly connected to the central chamber. Aε εhown, each of reaction chamberε 510, 512 and 514, includeε a diaphragm 516, 518 and 520, reεpectively, aε εhown in Figure 2B, for opening and closing the fluid connection between the central chamber 508 and the reaction chamber. Additional reaction chambers may be added fluidly connected to the central chamber, or alternatively, may be connected to any of the above described reaction chambers.

In certain aspects, the central chamber may have a dual function as both a hub and a pumping chamber. In particular, this central pumping chamber can be fluidly connected to one or more additional reaction and/or storage chambers and one or more analytical chambers. The central pumping chamber again functionε aε a hub for the variouε operationε to be carried out by the device aε a whole aε described above. Thiε embodiment provideε the advantage of a single pumping chamber to deliver a sample to numerous operations, as well as the ability to readily incorporate

additional εample preparation operationε within the device by opening another valve on the central pumping chamber. In particular, the central chamber 508 may incorporate a diaphragm pump aε one εurface of the chamber, and in preferred aεpectε, will have a zero diεplacement when the diaphragm iε not deflected. The diaphragm pump will generally be εimilar to the valve εtructure deεcribed above for the reaction chamber. For example, the diaphragm pump will generally be fabricated from any one of a variety of flexible materialε, e.g., silicon, latex, teflon, mylar and the like. In particularly preferred embodiments, the diaphragm pump is silicon.

With reference to both Figureε 5A and 5B, central chamber 508 is fluidly connected to sample collection chamber 504, via fluid channel 506. The sample collection chamber end of fluid channel 506 includes a diaphragm valve 524 for arresting fluid flow. A fluid sample is typically introduced into sample collection chamber through a εealable opening 502 in the body of the device, e.g., a valve or εeptum. Additionally, sample chamber 504 may incorporate a vent to allow displacement of gas or fluid during εample introduction.

Once the εample iε introduced into the εample collection chamber, it may be drawn into the central pumping chamber 508 by the operation of pump diaphragm 526. Specifically, opening of εample chamber valve 524 openε fluid channel 506. Subεeguent pulling or deflection of pump diaphragm 526 createε negative preεεure within pumping chamber 508, thereby drawing the εample through fluid channel 506 into the central chamber. Subεequent cloεing of the εample chamber valve 524 and relaxation of pump diaphragm 526, createε a positive presεure within pumping chamber 508, which may be used to deliver the sample to additional chambers in the device. For example, where it is desired to add specific reagents to the sample, these reagents may be stored in liquid or solid form within an adjacent storage chamber 510. Opening valve 516 openε fluid channel 528, allowing delivery of the sample into storage chamber 510 upon relaxation of the

diaphragm pump. The operation of pumping chamber may further be employed to mix reagents, by repeatedly pulling and pushing the sample/reagent mixture to and from the storage chamber. This has the additional advantage of eliminating the necesεity of including additional mixing componentε within the device. Additional chamber/valve/fluid channel εtructures may be provided fluidly connected to pumping chamber 508 as needed to provide reagent storage chambers, additional reaction chamberε or additional analytical chamberε. Figure 5A illuεtrateε an additional reaction/εtorage chamber 514 and valve 520, fluidly connected to pumping chamber 508 via fluid channel 530. Thiε will typically vary depending upon the nature of the εample to be analyzed, the analyεiε to be performed, and the deεired sample preparation operation. Following any sample preparation operation, opening valve 520 and closure of other valves to the pumping chamber, allows delivery of the sample through fluid channels 530 and 532 to reaction chamber 514, which may include an analytical device such as an oligonucleotide array for determining the hybridization of nucleic acids in the sample to the array, or a microcapillary electrophoresiε device for performing a εize baεed analyεiε of the sample.

The tranεportation of fluid within the device of the invention may be carried out by a number of varied methodε. For example, fluid tranεport may be affected by the application of preεsure differentialε provided by either external or internal sources. Alternatively, internal pump elements which are incorporated into the device may be used to transport fluid samples through the device. In a first embodiment, fluid samples are moved from one reaction/storage/analytical chamber to another chamber via fluid channelε by applying a poεitive pressure differential from the originating chamber, the chamber from which the sample is to be transported, to the receiving chamber, the chamber to which the fluid εample is to be transported. In order to apply the preεεure differentials, the various reaction chamberε of the device will typically incorporate

pressure inlets connecting the reaction chamber to the presεure εource (positive or negative) . For ease of discussion, the application of a negative pressure, i.e., to the receiving chamber, will generally be deεcribed herein. However, upon reading the instant discloεure, one of ordinary skill in the art will appreciate that application of poεitive pressure, i.e., to the originating chamber, will be as effective, with only slight modifications, which will be illustrated aε they arise herein. In one method, application of the pressure differential to a particular reaction chamber may generally be carried out by selectively lowering the preεsure in the receiving chamber. Selective lowering of the presεure in a particular receiving chamber may be carried out by a variety of methods. For example, the presεure inlet for the reaction chambers may be equipped with a controllable valve structure which may be selectively operated to be opened to the pressure source. Application of the presεure source to the εample chamber then forceε the sample into the next reaction chamber which is at a lower pressure.

Typically, the device will include a presεure/vacuum manifold for directing an external vacuum source to the various reaction/storage/analytical chamberε. A particularly elegant example of a preferred vacuum preεsure manifold iε illustrated in Figures 6A, 6B and 6C.

The vacuum/presεure manifold produceε a εtepped preεsure differential between each pair of connected reaction chambers. For example, assuming ambient presεure iε defined aε having a value of 1, a vacuum iε applied to a firεt reaction chamber, which may be written l-3x, where x iε an incremental preεεure differential. A vacuum of l-2x iε applied to a εecond reaction chamber in the εeries, and a vacuum of 1-x is applied to a third reaction chamber. Thuε, the first reaction chamber is at the lowest preεεure and the third is at the highest, with the second being at an intermediate level. All chamberε, however, are below ambient pressure, e.g., atmospheric. The sample is drawn into the

first reaction chamber by the pressure differential between ambient pressure (1) and the vacuum applied to the reaction chamber (l-3x) , which differential is -3x. The sample doeε not move to the second reaction chamber due to the pressure differential between the first and second reaction chambers (l-3x vs. l-2x, respectively) . Upon completion of the operation performed in the first reaction chamber, the vacuum is removed from the first chamber, allowing the first chamber to come to ambient pressure, e.g., 1. The sample is then drawn from the first chamber into the second by the pressure difference between the ambient pressure of the first reaction chamber and the vacuum of the second chamber, e.g., 1 vs. 1- 2x. Similarly, when the operation to be performed in the second reaction chamber is completed, the vacuum to thiε chamber is removed and the sample moves to the third reaction chamber.

A schematic representation of a pneumatic manifold configuration for carrying out this presεure differential fluid tranεport system is shown in Figure 6A. The pneumatic manifold includes a vacuum source 602 which is coupled to a main vacuum channel 604. The main vacuum channel is connected to branch channels 606, 608 and 610, which are in turn connected to reaction chambers 612, 614 and 616, reεpectively, which reaction chamberε are fluidly connected, in series. The first reaction chamber in the series 616 typically includes a sample inlet 640 which will typically include a sealable closure for retaining he fluid sample and the presεure within the reaction chamber. Each branch channel is provided with one or more fluidic resistorε 618 and 620 incorporated within the branch channel. These fluidic resiεtorε result in a transformation of the presεure from the pressure/vacuum source, i.e., a step down of the gas preεεure or vacuum being applied acroεε the reεiεtance. Fluidic resiεtorε may employ a variety of different εtructureε. For example, a narrowing of the diameter or croεs-sectional area of a channel will typically result in a fluidic reεistance through the channel. Similarly, a plug within the channel which has one or more

holes disposed therethrough, which effectively narrow the channel through which the presεure iε applied, will reεult in a fluidic reεiεtance, which reεiεtance can be varied depending upon the number and/or εize of the holeε in the plug. Additionally, the plug may be fabricated from a porouε material which provideε a fluidic reεiεtance through the plug, which resistance may be varied depending upon the porosity of the material and/or the number of plugs used. Variations in channel length can also be used to vary fluidic resiεtance. Each branch channel will typically be connected at a preεsure node 622 to the reaction chamber via presεure inletε 624. Preεεure inletε 624 will typically be fitted with poorly wetting filter plugs 626, to prevent drawing of the sample into the pneumatic manifold in the caεe of vacuum baεed methodε. Poorly wetting filter plugε may generally be prepared from a variety of materialε known in the art and as described above. Each branch channel is connected to a vent channel 628 which is opened to ambient presεure via vent 630. A differential fluidic reεiεtor 632 iε incorporated into vent channel 628. The fluidic reεiεtance εupplied by fluidic reεistor 632 will be less than fluidic resiεtance εupplied by fluidic resistor 634 which will be leεε than fluidic resistance supplied by fluidic resiεtor 636. Aε deεcribed above, thiε differential fluidic reεistance may be accompliεhed by varying the diameter of the vent channel, varying the number of channelε included in a εingle vent channel, varying channel length, or providing a plug in the vent channel having a varied number of holeε disposed therethrough. The varied fluidic resistanceε for each vent channel will result in a varied level of vacuum being applied to each reaction chamber, where, as described above, reaction chamber 616 may have a presεure of l-3x, reaction chamber 614 may have a pressure of l-2x and reaction chamber 612 may have a pressure of 1-x. The presεure of a c ven reaction chamber may be raised to ambient preεεure, thuε allowing the drawing of the sample into the εubεequent chamber, by opening the chamber

to ambient pressure. This is typically accomplished by providing a sealable opening 638 to ambient preεεure in the branch channel. This sealable opening may be a controllable valve structure, or alternatively, a rupture membrane which may be pierced at a desired time to allow the particular reaction chamber to achieve ambient presεure, thereby allowing the sample to be drawn into the subseguent chamber. Piercing of the rupture membrane may be carried out by the inclusion of solenoid operated pins incorporated within the device, or the device's base unit (discuεεed in greater detail below). In some cases, it may be desirable to prevent back flow from a previouε or εubεequent reaction chamber which iε at a higher pressure. This may be accomplished by equipping the fluid channels between the reaction chambers 644 with one-way check valves. Examples of one-way valve structureε include ball and seat structureε, flap valveε, duck billed check valveε, sliding valve structures, and the like.

A graphical illustration of the presεure profileε between three reaction chambers employing a vacuum based pneumatic manifold is shown in Figure 6C. The solid line indicates the εtarting pressure of each reaction chamber/pressure node. The dotted line indicates the presεure profile during operation. The piercing of a rupture membrane results in an increase in the pressure of the reaction chamber to ambient presεure, reεulting in a preεεure drop being created between the particular chamber and the subsequent chamber. This pressure drop draws the εample from the firεt reaction chamber to the subsequent reaction chamber.

In a similar aspect, a positive pressure source may be applied to the originating chamber to push the sample into subsequent chambers. A pneumatic presεure manifold uεeful in thiε regard is shown in Figure 6B. In this aspect, a presεure source 646 provides a positive presεure to the main channel 604. Before a εample iε introduced to the first reaction chamber, controllable valve 648 is opened to vent the presεure from the preεεure εource and allow the firεt reaction chamber in the series 650 to remain at ambient presεure for the

introduction of the εample. Again, the firεt chamber in the series typically includes a sample inlet 640 having a sealable cloεure 642. After the εample iε introduced into the first reaction chamber 650, controllable valve 648 is cloεed, bringing the system up to presεure. Suitable controllable valves include any number of a variety of commercially available solenoid valves and the like. In this application, each subsequent chamber is kept at an incrementally higher pressure by the presence of the appropriate fluidic resiεtorε and vents, as described above. A base presεure iε applied at originating preεεure node 652. When it iε deεired to deliver the sample to the second chamber 654, sealable opening 656 is opened to ambient presεure. Thiε allowε εecond chamber 654, to come to ambient preεεure, allowing the preεεure applied at the origin pressure node 652 to force the sample into the second chamber 654. Thus, illustrated as above, the firεt reaction chamber 650 iε maintained at a preεεure of 1+x, by application of thiε preεsure at originating preεεure node 652. The εecond reaction chamber 654 iε maintained at preεεure l+2x and the third reaction chamber 658 iε maintained at a preεsure of 1 +3x. Opening εealable valve 656 results in a drop in the presεure of the εecond reaction chamber 654 to 1 (or ambient preεεure) . The preεεure differential from the firεt to the εecond reaction chamber, x, puεhes the sample from the first to the second reaction chamber and eventually to the third.

Fluidic resistor 660 iε provided between preεεure node 662 and sealable valve 656 to prevent the escape of excesε preεεure when sealable valve 656 is opened. This allows the syεtem to maintain a poεitive preεεure behind the εample to puεh it into subsequent chambers.

In a related aspect, a controllable preεsure εource may be applied to the originating reaction veεεel to puεh a sample through the device. The preεεure εource iε applied intermittently, aε needed to move the sample from chamber to chamber. A variety of devices may be employed in applying an intermittent presεure to the originating reaction chamber, e.g., a syringe or other positive displacement pump, or the

like. Alternatively, for the size scale of the device, a thermopneumatic pump may be readily employed. An example of such a pump typically includes a heating element, e.g., a small scale resistive heater dispoεed in a preεεure chamber. Also disposed in the chamber is a quantity of a controlled vapor preεεure fluid, εuch aε a fluorinated hydrocarbon liquid, e.g., fluorinert liquidε available from 3M Corp. These liquids are commercially available having a wide range of available vapor pressures. An increase in the controllable temperature of the heater increaseε preεεure in the preεεure chamber, which iε fluidly connected to the originating reaction chamber. Thiε increaεe in preεεure reεultε in a movement of the εample from one reaction chamber to the next. When the sample reaches the subsequent reaction chamber, the temperature in the pressure chamber is reduced.

The inclusion of gas permeable fluid barriers, e.g., poorly wetting filter plugs or hydrophobic membranes, in these devices also permits a εenεorleεs fluid direction and control system for moving fluids within the device. For example, as described above, such filter plugε, incorporated at the end of a reaction chamber oppoεite a fluid inlet will allow air or other gaε present in the reaction chamber to be expelled during introduction of the fluid component into the chamber. Upon filling of the chamber, the fluid sample will contact the hydrophobic plug thus stopping net fluid flow. Fluidic resistances, as described previously, may alεo be employed aε gas permeable fluid barriers, to accomplish this same reεult, e.g., using fluid pasεageε that are εufficiently narrow aε to provide an exceεεive fluid reεiεtance, thereby effectively stopping or retarding fluid flow while permitting air or gas flow. Expelling the fluid from the chamber then involves applying a positive pressure at the plugged vent. This permits chambers which may be filled with no valve at the inlet, i.e., to control fluid flow into the chamber. In moεt aspects however, a single valve will be employed at the chamber inlet in order to ensure retention of the fluid sample within the chamber, or to provide a mechanism for directing a

fluid sample to one chamber of a number of chambers connected to a common channel.

A schematic representation of a reaction chamber employing this syεtem is shown in Figure 12A. In brief, the reaction chamber 1202 includes a fluid inlet 1204 which is sealed from a fluid pasεage 1206 by a valve 1208. Typically, this valve can employ a variety of structureε, as described herein, but is preferably a flexible diaphragm type valve which may be displaced pneumatically, magnetically or electrically. In preferred aspects, the valves are controlled pneumatically, e.g., by applying a vacuum to the valve to deflect the diaphragm away from the valve seat, thereby creating an opening into adjoining pasεageε. At the end opposite from the inlet, iε an outlet vent 1210, and disposed across this outlet vent is a hydrophobic membrane 1212. A number of different commercially available hydrophobic membranes may be used as described herein, including, e.g., Versapore 200 R membranes available from Gelman Scienceε. Fluid introduced into the reaction chamber fills the chamber until it contacts the membrane 1212. Cloεure of the valve then allowε performance of reactionε within the reaction chamber without influencing or influence from elementε outεide of the chamber.

In another example, theεe plugε or membraneε may be used for degasεing or debubbling fluidε within the device.

For degassing purposeε, for example, a chamber may be provided with one or more vents or with one wall completely or substantially bounded by a hydrophobic membrane to allow the passage of disεolved or trapped gases. Additionally, vacuum may be applied on the external surface of the membrane to draw gases from the sample fluidε. Due to the εmall cross sectional dimensions of reaction chambers and fluid pasεageε, elimination of such gases takes on greater importance, as bubbles may interfere with fluid flow, and/or result in production of irregular data.

In a related aspect, such membranes may be used for removing bubbles purposely introduced into the device, i.e.,

for the purpose of mixing two fluids which were previously desired to be separated. For example, discrete fluids, e.g. , reagents, may be introduced into a single channel or debubbling chamber, separated by a gas bubble which is sufficient to separete the fluid plugs but not to inhibit fluid flow. These fluid plugs may then be flowed along a channel having a vent dispoεed therein, which vent includeε a hydrophobic membrane. Aε the fluid plugε flow paεt the membrane, the gas will be expelled acrosε the membrane whereupon the two fluids will mix. A schematic illustration of such a debubbling chamber is shown in Figure 12B.

Figure 12C shows a schematic illustration of a device employing a fluid flow syεtem which utilizeε hydrophobic membrane bound ventε for control of fluid flow. As shown, the device 1250 includes a main channel 1252. The main channel is fluidly connected to a serieε of εeparate chamberε 1254-1260. Each of theεe fluid connectionε with the main channel 1252 iε mediated (opened or cloεed) by the incluεion of a separate valve 1262-1268, respectively, at the intersection of these fluid connections with the main channel. Further, each of the various chambers will typically include a vent port 1270-1276 to the outside environment, which vent ports will typically be bounded by a hydrophobic or poorly wetting membrane. The basic design of thiε εystem iε reflected in the device schematic shown in Figure 5, as well, in that it employs a central distribution chamber or channel.

In operation, sampleε or other fluidε may be introduced into the main channel 1252 via a valved or otherwise sealable liguid inlet 1278 or 1280. Application of a positive pressure to the fluid inlet, combined with the selective opening of the elastomeric valve at the fluid connection of a selected chamber with the main channel will force the fluid into that chamber, expelling air or other gaseε through the vent port at the terminuε of the εelected chamber, until that vent iε contacted with the fluid, whereupon fluid flow iε εtopped. The valve to the εelected chamber may then be returned to the cloεed poεition to εeal

the fluid within the chamber. As described above, the requisite presεure differential needed for fluid flow may alternatively or additionally involve the application of a negative preεsure at the vent port to which fluid direction is sought.

As a εpecific example incorporating the device shown in Figure 12C, a sample introduced into the main channel 1252, is first forced into the degassing chamber 1254 by opening valve 1262 and applying a positive presεure at inlet port 1278. Once the fluid haε filled the degaεεing chamber, valve 1262 may then be cloεed. Degassing of the fluid may then be carried out by drawing a vacuum on the sample through the hydrophobic membrane disposed across the vent port 1270. Degassed sample may then be moved from the degassing chamber 1254 to, e.g., reaction chamber 1256, by opening valves 1262 and 1264, and applying a positive pressure to the degasεing chamber vent port 1270. The fluid iε then forced from the degassing chamber 1254, through main channel 1252, into reaction chamber 1256. When the fluid fills the reaction chamber, it will contact the hydrophobic membrane, thereby arresting fluid flow. As shown, the device includes a volumetric or measuring chamber 1258 as well aε a storage chamber 1260, including similar valve:vent port arrangements 1266:1274 and 1268:1276, respectively. The fluid may then be selectively directed to other chambers aε deεcribed.

Figure 12D shows a top view of a portion of an injection molded substrate for carrying out the operations schematically illuεtrated in Figure 12C. As shown, this device includeε liguid loading chamberε 1278a and 1280a which are in fluid communication with the fluid inletε 1278 and 1280 (not shown) . Theεe fluid inletε may typically be fabricated into the injection molded portion, e.g., drilled into the loading chamber, or fabricated into an overlaying planar member (not shown). Also included are reaction chambers 1254, degassing chambers 1256 and 1256a, meaεuring chamberε 1258, and storage chambers 1260. Each of these chambers iε fluidly connected to main channel 1252.

A number of the operationε performed by the variouε reaction chamberε of the device require a controllable temperature. For example, PCR amplification, aε deεcribed above, requireε cycling of the sample among a strand separation temperature, an annealing reaction temperature and an extension reaction temperature. A number of other reactions, including extension, transcription and hybridization reactions are also generally carried out at optimized, controlled temperatures. Temperature control within the device of the invention is generally supplied by thin film resistive heaters which are prepared using methods that are well known in the art. For example, these heaters may be fabricated from thin metal films applied within or adjacent to a reaction chamber uεing well known methodε εuch aε sputtering, controlled vapor deposition and the like. The thin film heater will typically be electrically connected to a power source which delivers a current across the heater. The electrical connections will also be fabricated using methods similar to those described for the heaters. Typically, these heaters will be capable of producing temperatures in excess of 100 degrees without suffering adverse effects as a result of the heating. Examples of resistor heaters include, e.g., the heater discuεsed in Published PCT Application No. WO 94\05414, laminated thin film NiCr/polyimide/copper heaters, as well as graphite heaters. These heaters may be provided as a layer on one surface of a reaction chamber, or may be provided as molded or machined inεertε for incorporation into the reaction chambers. Figure 2B illustrateε an example of a reaction chamber 104 having a heater insert 128, dispoεed therein. The reεiεtive heater iε typically electrically connected to a controlled power source for applying a current across the heater. Control of the power source is typically carried out by an appropriately programmed computer. The above-described heaters may be incorporated within the individual reaction chambers by depositing a resiεtive metal film or insert within the reaction chamber, or alternatively, may be applied to the

exterior of the device, adjacent to the particular reaction chamber, whereby the heat from the heater iε conducted into the reaction chamber.

Temperature controlled reaction chamberε will also typically include a miniature temperature senεor for monitoring the temperature of the chamber, and thereby controlling the application of current acroεε the heater. A wide variety of microεenεorε are available for determining temperatures, including, e.g., thermocouples having a bimetallic junction which produces a temperature dependent electromotive force (EMF) , resistance thermometerε which include material having an electrical resiεtance proportional to the temperature of the material, thermiεtorε, IC temperature sensors, quartz thermometers and the like. See, Horowitz and Hill, The Art of Electronics, Cambridge

University Press 1994 (2nd Ed. 1994) . One heater/sensor design that is particularly suited to the device of the present invention is described in, e.g., U.S. Patent Application Serial No. 08/535,875, filed September 28, 1995, and incorporated herein by reference in its entirety for all purposes. Control of reaction parameters within the reaction chamber, e.g., temperature, may be carried out manually, but is preferably controlled via an appropriately programmed computer. In particular, the temperature measured by the temperature sensor and the input for the power source will typically be interfaced with a computer which is programmed to receive and record this data, i.e., via an analog- digital/digital-analog (AD/DA) converter. The same computer will typically include programming for instructing the delivery of appropriate current for raiεing and lowering the temperature of the reaction chamber. For example, the computer may be programmed to take the reaction chamber through any number of predetermined time/temperature profileε, e.g., thermal cycling for PCR, and the like. Given the εize of the deviceε of the invention, cooling of the reaction chambers will typically occur through exposure to ambient temperature, however additional cooling elementε may be

included if desired, e.g., coolant syεtems, peltier coolers, water bathε, etc.

In addition to fluid tranεport and temperature control elementε, one or more of the reaction chamberε of the device may alεo incorporate a mixing function. For a number of reaction chamberε, mixing may be applied merely by pumping the sample back and forth into and out of a particular reaction chamber. However, in some caεeε conεtant mixing within a single reaction/analytical chamber is desired, e.g., PCR amplification reactions and hybridization reactions.

In preferred aspectε, acouεtic mixing is used to mix the sample within a given reaction chamber. In particular, a PZT element (element composed of lead, zirconium and titanium containing ceramic) is contacted with the exterior surface of the device, adjacent to the reaction chamber, as shown in Figure 7A. For a discuεεion of PZT elementε for uεe in acouεtic baεed methods, see, Phyεical Acoustics, Principles and Methods , Vol. I, (Mason ed. , Academic Press, 1965), and Piezoelectric Technology, Data for Engineers, available from Clevite Corp. As shown, PZT element 702 is contacting the external surface 704 of hybridization chamber 706. The hybridization chamber includes aε one internal εurface, an oligonucleotide array 708. Application of a current to this element generates εonic vibrationε which are translated to the reaction chamber whereupon mixing of the sample diεpoεed therein occurε. The vibrationε of thiε element reεult in substantial convection being generated within the reaction chamber. A symmetric mixing pattern generated within a micro reaction chamber incorporating this mixing system is shown Figure 7B.

Incomplete contact (i.e., bonding) of the element to the device may reεult in an incomplete mixing of a fluid sample. As a reεult, the element will typically have a fluid or gel layer (not shown) dispoεed between the element 702 and the external surface of the device ir \ , e.g., water. This fluid layer will generally be incorporated within a membrane, e.g., a latex balloon, having one surface in contact with the

external surface of the reaction chamber and another surface in contact with the PZT element. An appropriately programmed computer 714 may be used to control the application of a voltage to the PZT element, via a function generator 712 and RF amplifier 710 to control the rate and/or timing of mixing. In alternate aspects, mixing may be supplied by the incorporation of ferromagnetic elements within the device which may be vibrated by εupplying an alternating current to a coil adjacent the device. The oεcillating current creates an oscillating magnetic field through the center of the coil which results in vibratory motion and rotation of the magnetic particles in the device, resulting in mixing, either by direct convection or accoustic streaming.

In addition to the above elements, the devices of the present invention may include additional componentε for optimizing εample preparation or analyεiε. For example, electrophoretic force may be uεed to draw target moleculeε into the surface of the array. For example, electrodes may be disposed or patterned on the surface of the array or on the surface opposite the array. Application of an appropriate electric field will either push or pull the targetε in solution onto the array. A variety of similar enhancements can be included without departing from the εcope of the invention. Although it may often be deεirable to incorporate all of the above deεcribed elementε within a εingle diεpoεable unit, generally, the coεt of εome of these elements and materialε from which they are fabricated, may make it deεirable to provide a unit that is at least partially reusable. Accordingly, in a particularly preferred embodiment, a variety of control elements for the device, e.g., temperature control, mixing and fluid transport elementε may be supplied within a reuεable baεe-unit.

For example, in a particularly preferred embodiment, the reaction chamber portion of the • ^' rvice can be mated with a reusable base unit that iε adapted for receiving the device. As described, the base unit may include one or more heaters

for controlling the temperature within selected reaction chambers within the device. Similarly, the base unit may incorporate mixing elements such as thoεe described herein, as well as vacuum or pressure sources for providing sample mixing and transportation within the device.

As an example, the baεe unit may include a firεt surface having disposed thereon, one or more resiεtive heaterε of the type deεcribed above. The heaterε are positioned on the surface of the base unit such that when the reaction chamber device is mated to that surface, the heaterε will be adjacent to and preferably contacting the exterior εurface of the device adjacent to one or more reaction chambers in which temperature control is desired. Similarly, one or more mixing elementε, εuch aε the acoustic mixing elements described above, may alεo be disposed upon this surface of the base unit, whereby when mated with the reaction chamber device, the mixing elementε contact the outer εurface of the reaction/storage/analytical chambers in which such mixing iε deεired. For thoεe reaction chamberε in which both mixing and heating are deεired, interspersed heaters and mixers may be provided on the surface of the baεe unit. Alternatively, the base unit may include a second surface which contacts the opposite surface of the device from the first surface, to apply heating on one exterior surface of the reaction chamber and mixing at the other.

Along with the various above-described elements, the base unit also typically includes appropriate electrical connections for linking the heating and mixing elementε to an appropriate power source. Similarly, the base unit may also be used to connect the reaction chamber device itself to external power sourceε, preεεure/vacuum εourceε and the like. In particular, the baεe unit can provide manifoldε, portε and electrical connectionε which plug into receiving connectors or ports on the device to provide power, vacuum or presεure for the various control elements that are internal to the device. For example, mating of the device to the base unit may provide a connection from a vacuum source in the base unit to a main

vacuum manifold manufactured into the device, as described above. Similarly, the baεe unit may provide electrical connectors which couple to complementary connectors on the device to provide electrical current to any number of operations within the device via electrical circuitry fabricated into the device. Similarly, appropriate connections are alεo provided for monitoring variouε operationε of the device, e.g., temperature, preεεure and the like. For thoεe embodimentε employing a pneumatic manifold for fluid transport which relies on the piercing of rupture membraneε within the device to move the εample to εubεeguent chamberε, the baεe unit will alεo typically include one or more solenoid mounted rupture pins. The solenoid mounted rupture pinε are disposed within receptacleε which are manufactured into the εurface of the baεe unit, which receptacleε correspond to positionε of the rupture membranes upon the device. The pinε are retained below the εurface of the base unit when not in operation. Activation of the solenoid extends the pin above the surface of the base unit, into and through the rupture membrane.

A schematic representation of one embodiment of a base unit is shown in Figure 8. As εhown in Figure 8, the base unit 800 includes a body structure 802 having a mating surface 804. The body structure houseε the variouε elementε that are to be incorporated into the baεe unit. The baεe unit may also include one or more thermoelectric heating/cooling elements 806 dispoεed within the baεe unit εuch that when the reaction chamber contianing portion of the apparatuε iε mated to the mating surface of the base unit, the reaction chamberε will be in contact or immediatly adjacent to the heating elements. For those embodiments employing a differential presεure baεed system for moving fluids within the device, as described above, the base unit may typically include a pressure source opening to the mating surface via the presεure source port 810. The base unit will also typically include other elements of theεe εyεtemε, εuch aε εolenoid 812 driven

pins 814 for piercing rupture membranes. These pinε are typically within receεsed ports 816 in the mating surface 804. The base unit will also typically include mounting structures on the mating surface to ensure proper mating of the reaction chamber containing portion of the device to the base unit. Such mounting structures generally include mounting pins or holes (not shown) disposed on the mating surface which correspond to complementary structures on the reaction chamber containing portion of the device. Mounting pins may be differentially sized, and/or tapered, to ensure mating of the reaction chamber and base unit in an appropriate orientation. Alternatively, the base unit may be fabricated to include a well in which the reaction chamber portion mounts, which well has a nonsymetrical shape, matching a nonsymetrical εhape of the reaction chamber portion. Such a design is similar to that used in the manufacture of audio tape casεetteε and players.

In addition to the above described components, the device of the present invention may include a number of other components to further facilitate analyses. In particular, a number of the operations of sample transport, manipulation and monitoring may be performed by elements external to the device, per se. These elements may be incorporated within the above-deεcribed base unit, or may be included as further attachments to the device and/or base unit. For example, external pumps or fluid flow devices may be used to move the sample through the various operations of the device and/or for mixing, temperature controls may be applied externally to the device to maximize individual operations, and valve controls may be operated externally to direct and regulate the flow of the sample. In preferred embodiments, however, these various operations will be integrated within the device. Thus, in addition to the above described components, the integrated device of the invention will typically incorporate a number of additional components for sample transporting, direction, manipulation, and the like. Generally, this will include a plurality of micropumps, valves, mixers and heating elements.

Pumping devices that are particularly useful include a variety of micromachined pumps that have been reported in the art. For example, suitable pumps include pumps which having a bulging diaphragm, powered by a piezoelectric stack and two check valveε, such as those described in U.S. Patent Nos. 5,277,556, 5,271,724 and 5,171,132, or powered by a thermopneumatic element, aε deεcribed in U.S. Patent No. 5,126,022 piezoelectric peristaltic pumps using multiple membranes in series, and the like. The disclosure of each of these patents iε incorporated herein by reference. Publiεhed PCT Application No. WO 94/05414 alεo discusεeε the uεe of a lamb-wave pump for tranεportation of fluid in micron εcale channels.

Ferrofluidic fluid transport and mixing εyεtemε may alεo be incorporated into the device of the preεent invention. Typically, theεe εystems incorporate a ferrofluidic εubstance which is placed into the apparatus. The ferrofluidic substance is controlled/directed externally through the use of magnets. In particular, the ferrofluidic subεtance provides a barrier which can be selectively moved to force the sample fluid through the apparatus, or through an individual operation of the apparatus. These ferrofluidic syεtems may be used for example, to reduce effective volumes where the sample occupies insufficient volume to fill the hybridization chamber. Insufficient sample fluid volume may result in incomplete hybridization with the array, and incomplete hybridization data. The ferrofluidic syεtem is uεed to sandwich the εample fluid in a εufficiently εmall volume. This small volume is then drawn acrosε the array in a manner which ensures the εample contactε the entire surface of the array. Ferrofluids are generally commercially available from, e.g., FerroFluidicε Inc., New Hampεhire.

Alternative fluid tranεport mechaniεmε for incluεion within the device of the preεent invention include, e.g. electrohydrodynamic pumpε (εee, e.g., Richter, et al. 3rd IEEE Workshop on Micro Electro Mechanical Systemε, February 12-14, 1990, Napa Valley, USA, and Richter et al., Sensors and

Actuators 29:159-165 (1991), U.S. Patent No. 5,126,022, each of which is incorporated herein by reference in itε entirety for all purposes) . Typically, such pumps employ a serieε of electrodes disposed across one surface of a channel or reaction/pumping chamber. Application of an electric field acroεs the electrodes resultε in electrophoretic movement of nucleic acidε in the εample. Indium-tin oxide filmε may be particularly suited for patterning electrodes on subεtrate surfaces, e.g., a glass or silicon subεtrate. These methods can also be used to draw nucleic acids onto an array. For example, electrodes may paterned on the surface of an array substrate and modified with suitable functional groupε for coupling nucleic acidε to the εurface of the electrodes. Application of a current betwen the electrodes on the surface of an array and an oppoεing electrode reεultε in electrophoretic movement of the nucleic acids toward the surface of the array.

Electrophoretic pumping by application of transient electric fields can also be employed to avoid electrolysis at the surface of the electrodes while εtill cauεing εufficient sample movement. In particular, the electrophoretic mobility of a nucleic acid is not constant with the electric field applied. An increaεe in an electric field of from 50 to 400 v/cm resultε in a 30% increaεe in mobility of a nucleic acid sample in an acrylamide gel. By applying an oεcillating voltage between a pair of electrodeε capacitively coupled to the electrolyte, a net electrophoretic motion can be obtained without a net paεεage of charge. For example, a high electric field is applied in the forward direction of sample movement and a lower field is then applied in the reverse direction. See, e.g., Luckey, et al., Electrophoresiε 14:492-501 (1993). The above deεcribed micropumpε may also be used to mix reagentε and samples within the apparatus, by directing a recirculating fluid flow through the particular chamber to be mixed. Additional mixing methods may also be employed. For example, electrohydrodynamic mixers may be employed within the various reaction chambers. These mixers typically employ a

traveling electric field for moving a fluid into which a charge has been introduced. See Bart, et al., Sensorε and Actuators (1990) A21-A-23:193-197. These mixing elements can be readily incorporated into miniaturized deviceε. Alternatively, mixing may be carried out uεing thermopneumatic pumping mechanism. This typically involves the inclusion of small heaters, disposed behind apertures within a particular chamber. When the liquid in contact with the heater is heated, it expandε through the apertures causing a convective force to be introduced into the chamber, thereby mixing the sample. Alternatively, a pumping mechanism retained behind two one way check valves, εuch aε the pump deεcribed in U.S. Patent No. 5,375,979 to Trah, incorporated herein by reference in itε entirety for all purpoεes, can be employed to circulate a fluid sample within a chamber. In particular, the fluid iε drawn into the pumping chamber through a first one-way check valve when the pump is operated in its vacuum or drawing cycle. The fluid is then expelled from the pump chamber through another one way check valve during the reciprocal pump cycle, resulting in a circular fluid flow within the reaction chamber. The pumping mechanism may employ any number of designs, as described herein, i.e., diaphragm, thermal pressure, electrohydrodynamic, etc.

It will typically be desirable to inεulate electrical componentε of the device which may contact fluid samples, to prevent electrolysiε of the sample at the surface of the component. Generally, any number of non-conducting insulating materials may be used for thiε function, including, e.g., teflon coating, Si0 ₂ , Si ₃ N ₄ , and the like. Preferably, insulating layers will be Si0 ₂ , which may generally be sputtered over the surface of the component to provide an insulating layer.

The device of the present invention will also typically incorporate a number of microvalves for the direction of fluid flow within the device. A variety of microvalve deεignε are particularly well εuited for the inεtant device. Exampleε of valveε that may be uεed in the

device are described in, e.g., U.S. Patent No. 5,277,556 to van Lintel, incorporated herein by reference. Preferred valve structures for use in the present devices typically incorporate a membrane or diaphragm which may be deflected onto a valve seat. For example, the electrostatic valves, silicon/aluminum bimetallic actuated valves or thermopneumatic actuated valves can be readily adapted for incorporation into the device of the invention. Typically, theεe valveε will be incorporated within or at one or both of the termini of the fluid channels linking the various reaction chambers, and will be able to withstand the presεureε or reagents used in the various operations. An illustration of an embodiment of the diaphragm valve/fluid channel construction is illustrated in Figure 3. In alternative aspectε, fluidic valveε may alεo be employed. Such fluidic valveε typically include a "liquid curtain" which compriεeε a fluid that iε immiεcible in the aqueouε systemε used in the device, e.g., silicone oil, ferrofluidic fluids, and the like. In operation, a fluidic valve includeε a shallow valving channel, e.g. 50 μm deep, disposed transverεely across and interrupting a deeper primary channel, e.g., a 200 μm deep channel in a mating planar member. The valving channel is connected to at least one oil port. In operation, the valving channel is first filled with oil (or other appropriate fluid element) , which is drawn into the channel by capillary action. When gas or liquid are forced through the primary channel, the oil, or "fluid curtain" moves aside and allowε paεεage. In the absence of differential presεure along the primary channel, the oil will return to seal the fluid or gas behind a vapor barrier. In such cases, these fluidic valveε are useful in the prevention of evaporation of fluid samples or reagents within the device. Additionally, in the caεe of other fluidε, e.g., ferrofluidε or oils with suspended metallic particles, application of an appropriate magnetic field at the valve position immobilizes the fluidic valve, thereby resisting fluid passage at pressures greater than 3-5 psi. Similarly, electrorheological

effects may also be employed in controlling these fluidic valves. For example, the oil portion of the fluid valve mnay have suspended therein appropriate particles having high dielectric constants. Application of an appropriate electric field then increases the viscosity of the fluid thereby creating an appropriate barrier to fluid flow.

The device may also incorporate one or more filters for removing cell debris and protein solids from the sample. The filters may generally be within the apparatus, e.g., within the fluid pasεageε leading from the εample preparation/extraction chamber. A variety of well known filter media may be incorporated into the device, including, e.g., celluloεe, nitrocelluloεe, polyεulfone, nylon, vinyl/acrylic copolymerε, glass fiber, polyvinylchloride, and the like. Alternatively, the filter may be a structure fabricated into the device similar to that described in U.S. Patent No. 5,304,487 to Wilding et al. , previously incorporated herein. Similarly, separation chamberε having a separation media, e.g., ion exchange resin, affinity resin or the like, may be included within the device to eliminate contaminating proteins, etc.

In addition to sensors for monitoring temperature, the device of the present invention may also contain one or more sensorε within the device itεelf to monitor the progreεε of one or more of the operations of the device. For example, optical sensorε and preεsure εenεors may be incorporated into one or more reaction chamberε to monitor the progress of the various reactions, or within flow channels to monitor the progress of fluids or detect characteristicε of the fluidε, e.g., pH, temperature, fluorescence and the like.

As described previously, reagents used in each operation integrated within the device may be exogenously introduced into the device, e.g., through sealable openings in each respective chamber. However, in preferred aspectε, these reagents will be predisposed within the device. For example, these reagents may be diεpoεed within the reaction chamber which performε the operation for which the reagent will be

used, or within the fluid channels leading to that reaction chamber. Alternatively, the reagents may be dispoεed within storage chambers adjacent to and fluidly connected to their respective reaction chambers, whereby the reagents can be readily transported to the appropriate chamber as needed. For example, the amplification chamber will typically have the appropriate reagents for carrying out the amplification reaction, e.g., primer probe sequenceε, deoxynucleoεide triphosphates ("dNTPs") , nucleic acid polymeraεeε, buffering agents and the like, predisposed within the amplification chamber. Similarly, sample stabilization reagents will typically be predisposed within the sample collection chamber. 2. Generic Sample Preparation Device Figure 13 showε a εchematic illuεtration of a device configuration for performing εample preparation reactionε, generally, utilizing the fluid direction εyεtems described herein, e.g., emploing external preεsures, hydrophobic ventε and pneumatic valveε. In the configuration εhown, four domains of the device are each addresεed by an array of valves, e.g., a 10 valve array, with its own common channel. The four domains may generally be defined as: (1) reagent storage; (2) reaction; (3) sample preparation; and (4) poεt proceεsing, which are fluidically interconnected. The sample preparation domain iε typically used to extract and purify nucleic acids from a sample. Aε εhown, included in the εample preparation domain are 5 reagent inletε that are fluidly connected to larger volume εtorage vesselε, e.g., within the base unit. Examples of such reagentε for extraction reactionε may include, e.g., 4M guanidine iεothiocyanate, 1 X TBE and 50:50 EtOH:H ₂ 0. The two reaction chamberε may include, e.g., affinity media for purification of nucleic acidε such as glasε wool, or beadε coated with poly-T oligonucleotides.

The storage domain is linked to the εample preparation domain, and iε uεed for εtorage of reagentε and mixtures, e.g., PCR mix with FITC-dG^ and dUTP but no template, UNG reaction mix and IVT reaction mix without template. The reaction domain is also linked to the sample

preparation domain as well as the storage domain and includes a number of reaction chambers (5) , measuring chambers (2) and debubbling chambers (1) . Both sample preparation and reaction domains may be addressed by a thermal controller, e.g., heaters or thermoelectric heater/cooler.

The post procesεing domain iε typically linked to the reaction domain and includeε a number of reagent inletε (5) , reaction chamberε (2) , εtorage chamberε (1) and εample inlets (1) . The reagent inlets may be used to introduce buffers, e.g., 6 X SSPE or water into the analytical element, e.g., an oligonucleotide array.

3. Generic Multiple Parallel System Figure 14 iε a εchematic illuεtration of a device configurationfor addreεεing situations where several reactions are to be carried out under the same thermal conditions, e.g. , multiple parallel sample analyseε, duplicating multiplex PCR by carrying out εeveral PCR reactionε with εingle primer pairε in parallel followed by recombining them, or cycle εequencing with a variety of primer pairε and/or templates. In this configuration as shown, two storage domains supply reagents to two reaction domians, each being addressed by an array of 50 valves. The reaction and storage arrays each comprise a 4 X 12 matrix of reactors/chamberε, each from 10 nl to 5 μl in volume. These chambers are addresεed by 4 columnε each of pneumatic portε. Two additional arrayε of 10 valveε address a sample preparation and post procesεing domain. A bank of solenoid valveε may be uεed to drive the pneumatic portε and the valve arrayε.

IV. Applicationε

The device and εyεtem of the preεent invention haε a wide variety of uεeε in the manipulation, identification and/or seguencing of nucleic acid sampleε. Theεe εamples may be derived from plant, animal, viral or bacterial sources. For example, the device and syεtem of the invention may be used in diagnostic applicationε, εuch aε in diagnoεing genetic disorders, as well as diagnoεing the preεence of infectious

agentε, e.g., bacterial or viral infectionε. Additionally, the device and system may be used in a variety of characterization applications, such as forenεic analyεiε, ^' e.g., genetic fingerprinting, bacterial, plant or viral identification or characterization, e.g., epidemiological or taxonomic analyεis, and the like.

Although generally described in terms of individual devices, it will be appreciated that multiple devices may be provided in parallel tb perform analyses on a large number of individual samples, because the devices are miniaturized, reagent and/or space requirements are subεtantially reduced. Similarly, the small size allows automation of sample introduction process using, e.g., robot εa plerε and the like. In preferred aεpects, the device and syεtem of the present invention is used in the analysis of human sampleε. More particularly, the device iε uεed to determine the preεence or absence of a particular nucleic acid sequence within a particular human sample. This includeε the identification of genetic anomalieε aεεociated with a particular disorder, as well as the identification within a sample of a particular infectious agent, e.g., virus, bacteria, yeast or fungus.

The devices of the present invention may also be uεed in de novo sequencing applications. In particular, the device may be used in sequencing by hybridization (SBH) techniqueε. The use of oligonucleotide arrays in de novo SBH applications is described, for example, in U.S. Application Serial No. 08/082,937, filed June 25, 1993.

EXAMPLES

Example 1- Extraction and Purification of Nucleic Acids

In separate experimentε, HIV cloned DNA waε εpiked into either horse blood or a suεpension of murine plaεmacytoma fully differentiated B-cells derived from BALBc mice. Guanidine isothiocyanate was added to a concentration of 4 M, to lyse the material. In separate experiments, the lysate waε passed through a cartridge containing glass wool (20 μl) , a

cartridge with soda glasε walls ( 20 μl) , and a glasε tube. After 30 minutes at room temperature, the remaining lysate was washed away with several volumes of ethanol:water (1:1) and the captured DNA was eluted at 60°C using IX TBE. The yield of eluted DNA was measured using ethidum bromide staining on an agarose gel, and purity was tested by using the eluted material as a template for a PCR reaction. Elution yieldε ranged from 10% to 25% and PCR yieldε ranged from 90 to 100% aε compared to controlε uεing pure template.

Example 2- RNA Preparation Reactionε in Miniaturized Syεtem

A model miniature reactor system was designed to investigate the efficacy of miniaturized devices in carrying out prehybridization preparative reactionε on target nucleic acids. In particular, a dual reaction chamber system for carrying out in vitro transcription and fragmentation was fabricated. The device employed a tube based structure using a polymer tubing aε an in vitro tranεcription reactor coupled to a glass capillary fragmentation reactor. Reagents not introduced with the sample were provided as dried deposits on the internal surface of the connecting tubing. The experiment was designed to investigate the effectε of reaction chamber materials and reaction volume in RNA preparative reaction chambers. The sample including the target nucleic acid, DNA amplicons containing a 1 kb portion of the HIV gene flanked with promoter regions for the T3 and T7 RNA primerε on the sense and antisense strands, reεpectively, RNA polymeraεe, NTPε, fluorinated UTP and buffer, were introduced into the reactor system at one end of the tubing based system. In vitro transcription was carried out in a silicone tubing reactor immersed in a water bath. Following thiε initial reaction, the sample was moved through the syεtem into a glaεε capillary reactor which waε maintained at 94°C, for carrying out the fragmentation reaction. The productε of a representative time-course fragmentation reaction are shown in the gel of Figure 10A. In some cases, the tubing connecting

the IVT reactor to the fragmentation reactor contained additional MgCl ₂ for addition to the εample. The glass capillary was first coated with BSA to avoid interactions between the sample and the glasε. Following fragmentation, the sample was hybridized with an appropriately tiled oligonucleotide array, aε deεcribed above. Preparation uεing this system with 14 mM MgCl ₂ addition resulted in a correct base calling rate of 96.5%. Omisεion of the MgCl ₂ gave a correct baεe calling rate of 95.5%. A similar preparative transcription reaction waε carried out in a micro-reaction chamber fabricated in polycarbonate. A well waε machined in the εurface of a first polycarbonate part. The well was 250 μm deep and had an approximate volume of 5 μl. A second polycarbonate part was then acouεtically welded to the firεt to provide a top wall for the reaction chamber. The εecond part had two holeε drilled through it, which holeε were poεitioned at oppoεite endε of the reaction chamber. Temperature control for the tranεcription reaction waε εupplied by applying external temperature controlε to the reaction chamber, aε deεcribed for the tubing baεed system. 3 μl sampleε were uεed for both transcription and fragmentation experiments.

Transcription reactions performed in the micro- reactor achieved a 70% yield as compared to conventional methods, e.g., same volume in microfuge tube and water bath or PCR thermal cycler. A comparison of in vitro transcription reaction products using a microchamber versuε a larger scale control are shown in Figure 10B.

Example 3- PCR Amplification in Miniaturized System

The miniature polymeric reaction chamber similar to the one described in Example 2 was uεed for carrying out PCR amplification. In particular, the chamber waε fabricated from a planar piece of poycarbonate 4 mm thick, and having a cavity measuring 500 μm deep machined into its surface. A second planar polycarbonate piece was welded over the cavity. Thiε second piece waε only 250 μm thick. Thermal control was

supplied by applying a peltier heater against the thinner second wall of the cavity.

Amplification of a target nucleic acid was performed with Perkin-Elmer GeneAmp® PCR kit. The reaction chamber waε cycled for 20 secondε at 94°C (denaturing) , 40 εeconds at 65°C (annealing) and 50 εecondε at 72°C (extenεion) . A profile of the thermal cycling iε εhown in Figure 9. Amplification of approximately IO ⁹ waε shown after 35 cycles. Figure IOC showε production of amplified product in the microchamber as compared to a control using a typical PCR thermal cycler.

Example 4- Syεtem Demonstration. Integrated Reactions

A microfabricated polycarbonate device was manufactured having the structure shown in Figure 15A. The device included three discrete vented chambers. Two of the chambers (top and middle) were thermally isolated from the PCR chamber (bottom) to prevent any denaturation of the RNA polymeraεe used in IVT reractions at PCR temperatures. Thermal iεolation was accomplished by fabricating the chambers more than 10 mm apart in a thin polycarbonate substrate and controlling the temperatures in each region through the use of thermoelectric temperature controllers, e.g., peltier devices.

The reactor device dimensionε were as follows: channels were 250 μm wide by 125 μm deep; the three reaction chambers were 1.5 mm wide by 13 mm in length by 125 to 500 μm deep, with the reactor volumes ranging from 2.5 to 10 μl. Briefly, PCR was carried out by introducing 0.3 unitε of Taq polymerase, 0.2 mM dNTPε, 1.5 mM MgCl ₂ , 0.2 μM primer sequences, approximately 2000 molecules of template sequence and IX Perkin-Elmer PCR buffer into the bottom chamber. The thermal cycling program included (1) an initial denaturation at 94°C for 60 seconds, (2) a denaturation step at 94°C for 20 seconds, (3) an annealing step at 65°C for 40 secondε, (4) an extension step at 72°C for 50 εecondε, (5) repeated cycling through steps 2-4 35 times, and (6) a final extension step at 72°C for 60 secondε.

Following PCR, 0.2 μl of the PCR product waε tranεferred to the IVT chamber (middle) along with 9.8 μl of IVT mixture (2.5 mM ATP, CTP, GTP and 0.5 mM UTP, 0.25 mM Fluorescein-UTP, 8 mM MgCl ₂ , 50 mM HEPES, IX Promega Transcription Buffer, 10 mM DTT, 1 unit T3 RNA polymerase, 0.5 units RNAguard (Pharmacia) ) that had been stored in a storage chamber (top) . Fluid transfer was carried out by applying pressure to the vents at the termini of the chambers. IVT waε carried out at 37°C for 60 minuteε. The results of PCR and IVT are εhown in Figure 15B, compared with control experimentε, e.g., performed in eppendorf tubeε.

Example 5- Acouεtic Mixing The efficacy of an acouεtic element for mixing the contents of a reaction chamber was tested. A 0.5" X 0.5" X 0.04" crystal of PZT-5H was bonded to the external εurface of a 0.030" thick region of a planar piece of delrin which had cavity machined in the εurface oppoεite the PZT element. An oligonucleotide array synthesized on a flat silica subεtrate, waε sealed over the cavity using a rubber gasket, such that the surface of the array having the oligonucleotide probes synthesized on it was expoεed to the cavity, yielding a 250 μl reaction chamber. The PZT cryεtal waε driven by an ENI200 High Frequency Power Supply, which iε driven by a function generator from Hewlett Packard that waε gated by a εecond function generator operated at 1 Hz.

In an initial teεt, the chamber waε filled with deionized water and a εmall amount of 2% milk waε injected for visualization. The crystal was driven at 2 MHz with an average power of 3 W. Fluid velocities within the chamber were estimated in excesε of 1 mm/εec, indicating significant convection. A photograph showing this convection is εhown in Figure 7B. The efficacy of acouεtic mixing waε alεo teεted in an actual hybridization protocol. For thiε hybridization teεt, a fluoreεcently labeled oligonucleotide target sequence

having the seguence 5 '-GAGATGCGTCGGTGGCTG-3 ' and an array having a checkerboard pattern of 400 μm squareε having complementε to thiε εequence synthesized thereon, were used. Hybridization of a 10 nM solution of the target in 6xSSPE was carried out. During hybridization, the external surface of the array was kept in contact with a thermoelectric cooler set at 15°C. Hybridization was carried out for 20 minutes while driving the crystal at 2 MHz at an average power of 4 W (on time = 0.2 sec, off time = 0.8 sec) . The resulting average intensity was identical to that achieved using mechanical mixing of the chamber (vertical rotation with an incorporated bubble) .

Additional experiments using fluorescently labeled and fragmented 1 kb portion of the HIV virus had a succeεεful base calling rates. In particular, a 1 kb HIV nucleic acid segment was sequenced using an HIV tiled oligonucleotide array or chip. See, U.S. Patent Application Serial No. 08/284,064, filed Auguεt 2, 1994, and incorporated herein by reference for all purpoεeε. Acouεtic mixing achieved a 90.5% correct baεe calling rate as compared to a 95.8% correct base calling rate for mechanical mixing.

Example 5- Demonstration of Fluid Direction Syεtem

A polycarbonate cartridge waε fabricated uεing conventional machining, forming an array of valveε linking a common channel to a εerieε of channelε leading to a εerieε of 10 μl chamberε, each of which was terminated in a hydrophobic vent. The chambers included (1) an inlet chamber #1, (2) inlet chamber #2, (3) reaction chamber, (4) debubbling chamber having a hydrophobic vent in the center, (5) a measuring chamber and (6) a storage chamber. Elaεtomeric valveε were opened and cloεed by application of vacuum or preεεure (approx. 60 pεi) to the space above the individual valves. In a first experiment, water containing blue dye (food coloring) was introduced into inlet chamber #1 while water containing yellow dye (food coloring) was introduced into inlet chamber #2. By opening the appropriate valves and

applying 5 pεi to the appropriate vent, the following series of fluid movements were carried out: the blue water was moved from inlet chamber #1 to the reaction chamber; the yellow water was moved from inlet chamber #2 to the storage chamber # 6; the blue water was moved from the reaction chamber to the measuring chamber and the remaining blue water was exhausted to the inlet chamber #1; The measured blue water (approximately 1.6 μl) was moved from the measuring chamber to the debubbling chamber; the yellow water iε then moved from the storage chamber into the debubbling chamber whereupon it linked with the blue water and appeared to mix, producing a green color; and finally, the mixture was moved from the debubbling chamber to the reaction chamber and then to the storage chamber. Functioning of the debubbling chamber was demonstrated by moving four separate plugε of colored water from the reaction chamber to the debubbling chamber. The discrete plugs, upon pasεing into the debubbling chamber, joined together as a single fluid plug. The functioning of the measuring chamber was demonstrated by repetetively moving portions of a 10 μl colored water sample from the εtorage chamber to the meaεuring chamber, followed by exhauεting thiε fluid from the meaεuring chamber. Thiε fluid transfer was carried out 6 times, indicating repeated aliquoting of approximately 1.6 μl per measuring chamber volume (10 μl in 6 aliguots) .

While the foregoing invention haε been described in some detail for purposeε of clarity and underεtanding, it will be clear to one εkilled in the art from a reading of thiε disclosure that various changes in form and detail can be made without departing from the true scope of the invention. All publicationε and patent documentε cited in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication or patent document were εo individually denoted.