Other applications of this invention relates to the use of antisense oligonucleotides based on arabinonucleo- tides or modified arabinonucleotides in combination with RNaseH as laboratory reagents for the sequence specific cleavage and mapping of RNA. This invention also relates to the use of oligonucleotides based on arabinonucleotides or modified arabinonucleotides, par- ticularly those comprised of 2'F-arabinonucleic acid strands to hybridize duplex DNA to form a triple heli- cal complex and thereby block DNA transcription.

(b) Description of Prior Art The Antisense Strategy Antisense oligonucleotides (AON) are novel therapeutic agents which can inhibit specific gene expression in a sequence-specific manner. Many AON are currently in clinical-trial for the treatment of cancer and viral diseases (for reviews see: (i) Uhlmann, E.; Peyman, A. Chem. Rev. (ii) Cook, P. D.

Anti-Cancer Drug Design (iii) Crooke, S. T. Annu. Rev. Pharmacol. Toxicol. 1992,32,329.

(iv) Crooke, S. T.; Lebleu, B. Antisense Research and Applications; 1993, pp. 579, CRC Press, Boca Raton, FL.

(v) Agrawal, S.; Iyer, R. P. Cur. Op. Biotech. 1995,6, 12.). (vi) DeMesmaeker, A.; Haner, R.; Martin, P.; Moser, H. Acc. Chem. Res. 1995,28,366. (vii) Crooke, S. T.; Bennett, C. F. Annu. Rev. Pharmacol. Toxicol.

For potential clinical utility, AON should exhibit stability against degradation by serum and cellular nucleases, show low non-specific binding to serum and cell proteins (this binding would diminish the amount of antisense oligonucleotide available to base-pair with the target RNA), exhibit enhanced recog- nition of the target RNA sequence (in other words, pro- vide increased stability of the antisense-target RNA duplex at physiological temperature), and to some extent, demonstrate cell-membrane permeability. The formation of a duplex between the antisense oligomer and its target RNA blocks the translation of that RNA, by a mechanism termed"translation arrest". This mecha- nism may however be a minor contributor to the overall antisense effect. More important is the ability of the

antisense oligonucleotide to induce the activation of ribonuclease H (RNaseH), an endogenous enzyme that spe- cifically degrades RNA when duplexed with a complemen- tary DNA oligonucleotide (or antisense oligonucleotide) component (Walder, R. T.; Walder, J. A. Proc. Natl. Acad.

Sci. USA 1988,85,5011). For example, when an antisense DNA oligonucleotide hybridizes to a mRNA transcript, RNase H then cuts the mRNA at that site.

Antisense oligomers that modulate gene expression by more than one mechanism of action are highly desirable as this increases the potential efficacy of the antisense compound in vivo.

Oligonucleotide Analogs Oligonucleotides containing natural sugars (D- ribose and D-2-deoxyribose) and phosphodiester (PO) linkages are rapidly degraded by serum and intracellu- lar nucleases, which limits their utility as effective therapeutic agents. Chemical strategies to improve nuclease stability include modification of the sugar moiety, the base moiety, and/or modification or replacement of the internucleotide phosphodiester link- age. To date, the most widely studied analogues are the phosphorothioate (PS) oligodeoxynucleotides, in which one of the non-bridging oxygen atoms in the phos- phodiester backbone is replaced with a sulfur (Eckstein, F. Ann. Rev. Biochem. 1985,54,367).

Oligonucleotides that activate RNaseH 0 Base Base 0 Base 0 Base 0 0 OH00 H O O O=P-O S P O=P-O O P-O \-/YYYyy X H O O 04-0 S-P-O O=P-O O=P-O ''k S-\ BHf \ O-\ PS_DNA PS2-DNA Borano. DNA ANA X = OH, F (present invention)

Several phosphorothioate oligonucleotide ana- logues are undergoing clinical trial evaluation in the treatment of cancer and viral diseases, and some are moving rapidly towards New Drug Application (NDA) fil- <BR> <BR> <BR> <BR> <BR> ings (Akhtar, S.; Agrawal, S."In vivo studies with antisense oligonucleotides"TiPS 1997,18,12). Phos- phorothioates retain the ability to induce RNaseH deg- radation of the target RNA and exhibit good stability to degradation by nucleases. However, the PS oligode- oxynucleotides form less stable duplexes with the tar- get nucleic acid than do PO oligodeoxynucleotides, and also exhibit significant nonspecific binding to cellu- lar proteins, which can reduce the probability of find- ing and interacting with the target nucleic acid; these characteristics can limit the therapeutic utility of PS-AON (for a review see: Brach, A. D.;"A good antisense molecule is hard to find", TIBS, 1998,23, 45). Furthermore, PS-AONs are less efficient at induc- ing RNaseH degradation of the target RNA than are the

corresponding PO-AONs (Agrawal, S.; Mayrand, S. H.; Zamenick, P.; Pederson, T. Proc. Natl. Acad. Sci. USA 1990,87,1401).

Specificity of action may be improved by devel- oping novel oligonucleotide analogues. Current strate- gies to generate novel oligonucleotides are to alter the internucleotide phosphate backbone, the heterocy- clic base, and the sugar ring, or a combination of these. Alteration or complete replacement of the internucleotide linkage has been the most popular approach, with over 60 types of modified phosphate backbones studied since 1994 (Sanghvi, Y. DNA in "Altered Backbones in Antisense Applications", in Com- prehensive Natural Product Chemistry, Barton, D. H. R.; Nakanishi, K.; Meth-Coth, O. (eds), 1998, Elsevier Sci- ence, Oxford, UK). Apart from the phosphorothioate backbone, only two others have been reported to acti- vate RNaseH activity, i. e., the phosphorodithioate (PS) (Seeberger, P. H.; Yen, E.; Caruthers, M. H. J. Am. Chem.

Soc. and the boranophosphonate back- bones (Sergueev, D. et al., Poster 269, XIII Interna- tional Round Table, Montpellier, France, Sept. 6-10, 1998; Higson, A. P. et al. Tetrahedron Letters 1998,39, 3899). Because of the higher sulfur content of phos- phorodithioate-linked (PS2) oligodeoxynucleotides, they appear to bind proteins tighter than the phosphorothio- ate (PS) oligomers, and to activate RNaseH mediated cleavage with reduced efficiency compared to the PS analogue. Boranophosphonate-linked oligodeoxynucleo- tides activate RNaseH mediated cleavage of RNA targets,

but less well than PO-or PS-linked oligodeoxynucleo- tides.

Among the reported sugar-modified oligonucleo- tides most of them contain a five-membered ring, closely resembling the sugar of DNA (D-2-deoxyribose) and RNA (D-ribose). Example of these are a-oligodeoxy- nucleotide analogs, wherein the configuration of the 1' (or anomeric) carbon has been inverted as shown below (Morvan, F.; Rayner, B.; Imbach, J.-L., Chang, D. K.; Lown, J. W. Nucleic Acids Res. 1987,15,7027).

These analogues are nuclease resistant, form stable duplexes with DNA and RNA sequences, and are capable of inhibiting P-globin mRNA translation via an RNaseH-independent antisense mechanism (Boiziau, C; Kurfurst, R.; Cazanave, C; Roig, V.; Thuong, N. T.

Nucleic Acids Res. Other examples shown also below are xylo-DNA, 2'-O-Me RNA and 2'-F RNA (reviewed in Sanghvi, Y. S.; Cook, P. D. in"Carbohydrate Modifications in Antisense Research", Sanghvi, Y. S.; Cook, P. D. (eds), ACS Symposium Series, vol. 580, pp.

1, American Chemical Society, Washington DC, 1994).

Sugar modified oligonucleotide analogs that do not activate RNaseH Base Base O O vase \ CH3 O 6\ o bcHgo F ase Base O base ys. CH3 0 F -/ase O=P-O O=p-O so-6- .--DNA)

These analogues form stable duplexes with RNA targets, however, these duplexes are not substrates for RNaseH. To overcome this limitation, mixed-backbone oligonucleotides ("MBO") composed of either phosphodiester (PO) and phosphorothioate (PS) oligodeoxynucleotide segments flanked on both sides by sugar-modified oligonucleotide segments have been synthesized (Zhao, G. et al., Biochem. Pharmacol. 1996, <BR> <BR> <BR> <BR> <BR> 51,173; Crooke, S. T. et al. J. Pharmcol. Exp. Ther.

1996,277,923). Among the MBOs most studied to date <BR> <BR> <BR> <BR> <BR> is the [2'-OMe RNA]- [PS DNA]- [2'OMe RNA] chimera. The PS segment in the middle of the chain serves as the RNaseH activation domain, whereas the flanking 2'-OMe RNA regions increase affinity of the MBO strand for the target RNA. MBOs have increased stability in vivo, and appear to be more effective than phosphorothioate analogues in their biological activity both in vitro and in vivo. Examples of this approach incorporating 2'-OMe and other alkoxy substituents in the flanking regions of an oligonucleotide have been demonstrated by Monia et al. by enhanced antitumor activity in vivo (Monia, P. B.; Johnston, J. F.; Geiger, T.; Muller, M.; Fabbro, D. Nature Med. 1996,2,668). Several pre- clinical trials with these analogues are ongoing (Akhtar, S.; Agrawal, S."In vivo studies with antisense oligonucleotides"TiPS 1997,18,12).

The synthesis of oligonucleotides containing hexopyranoses instead of pentofuranose sugars has also <BR> <BR> <BR> <BR> <BR> been reported (Herdewijn, P. et al., in"Carbohydrate Modifications in Antisense Research", Sanghvi, Y. S.; Cook, P. D. (eds), ACS Symposium Series, vol. 580, pp.

80, American Chemical Society, Washington DC, 1994). A

few of these analogues have increased enzymatic stabil- ity but generally suffer from a reduced duplex forming capability with the target sequence. A notable excep- tion are 6'e4'linked oligomers constructed from 1,5- anhydrohexitol units which, due to their highly pre- organized sugar structure, form very stable complexes with RNA (van Aeroschot, A. C. et al., Nucleosides &<BR> <BR> <BR> <BR> Nucleotides However, none of these hexopyranose oligonucleotide analogues have been shown to elicit RNaseH activity. Recently, oligonucleotides containing completely altered backbones have been syn- thesized. Notable examples are the peptide nucleic acids ("PNA") with an acyclic backbone (Nielsen, P. E. in"Perspectives in Drug Discovery and Design", vol. 4, pp. 76, Trainor, G. L. (ed.), ESCOM, Leiden, 1996).

These compounds have exceptional hybridization proper- ties, and stability towards nucleases and proteases.

However, efforts to use PNA oligomers as antisense con- structs have been hampered by poor water solubility, self-aggregation properties, poor cellular uptake, and inability to activate RNaseH. Very recently, PNA- [PS- DNA]-PNA chimeras have been designed to maintain RNaseH mediated cleavage via the PS-DNA portion of the chimera (Bergman, F; Bannworth, W.; Tam, S. Tetrahedron Lett.

1995,36,6823; Van der Laan, A. C. et al. Trav. Chim Pays-Bas 1995, 114,295).

Arabinonucleosides and Arabinonucleic Acids (ANA) Arabinonucleosides are stereoisomers of ribonu- cleosides, differing only in the configuration at the 2'-position of the sugar ring. They have had a sub-

stantial impact on chemotherapy and as such they have been extensively used as antiviral and anticancer drugs (for a review, see: Wright, G. E.; Brown, N. C. Pharma- col. Ther. 1990,47,447). p-D-Arabinofuranosylcyto- sine (ara-C) is the most successful nucleoside antileu- kemic agent and is widely used in combination therapy or at high doses as a single agent to treat patients with acute lymphoblastic and myeloblastic leukemias (Kufe, D. W.; Spriggs, D. R. Semin. Oncol. 1985,12,34; Lauer et al. Cancer 1987,60,2366).

Oligonucleotides constructed from arabinonu- cleotides ("arabinonucleic acids"or ANA, have been under investigation from various different aspects.

ANA oligomers have been synthesized as pro-drugs in an attempt to improve the solubility of arabinonucleoside therapeutics. Incorporation of ara-C into DNA strands has also been the focus of research to understand the mechanism of action of this anticancer drug (Mikita, T.; Beardsley, G. P. Biochemistry 1988,27,4698; Mikita, T.; Beardsley, G. P. Biochemistry 1994,33, 9195).

DNA strands containing arabinonucleosides have also been a subject of a number of structural studies.

In the crystal, DNA duplexes containing araC adopt a normal B-type double helix with only small conforma- tional perturbations at the araC-dG base pair (Chwang, A. K.; Sundaralingam, M. Nature 1973,243,78; Teng, M. et al. Biochemistry 1989,28,4923; Gao, Y.-G. et al., Biochemistry 1991,30,9922). Mikita and Beardsley prepared DNA/DNA and DNA/RNA duplexes containing a sin- gle araC-G base pair to investigate the structural dis-

tortions caused by arabinonucleotides. They found that both the DNA duplex and the DNA/RNA hybrid can accommo- date araC-dG (rG) base pair with only a moderate and equivalent loss of stability (Mikita, T.; Beardsley, G. P. Biochemistry 1994,33,9195). Pfleiderer and co- workers synthesized an all-arabinose oligonucleotide mimicking a transfer RNA molecule (Resmini, M; Pfleiderer, W. Helv. Chim. Acta 1993,76,158).

The association properties of uniformly modi- fied oligoarabinonucleotides (ANA) were investigated by Giannaris and Damha and independently by Watanabe and co-workers (Giannaris, P. A.; Damha, M. J. Can. J. Chem.

1994,72,909; Kois, P.; Watanabe, K. A. Nucleic Acids Symposium Series Kois, P. et al. Nucleo- sides & Nucleotides 1993,12,1093). Giannaris and Damha showed that oligomers of either purine or pyrimi- dine P-arabinonucleosides generally associate with com- plementary DNA and RNA with thermal stabilities compa- rable with those of the corresponding DNA strands (Giannaris, P. A.; Damha, M. J. Can. J. Chem. 1994,72, 909). For example, they showed that (a) an octaarabino- adenylate, ara-A8 associated with poly ribo-U and poly deoxy-T; the melting temperature of the resulting com- plex was slightly higher than the corresponding com- <BR> <BR> <BR> <BR> plexes formed by the normal ribo-A8 and deoxy-A8<BR> strands; (b) ara-C and ara (UCU UCC CUC UCC C) associ- 8 ated with their complementary RNA strand, albeit with lower affinity relative to the corresponding unmodified strands; (c) ara-U8 did not bind with poly rA under con- ditions where ribo-U8 and deoxy-U8 formed a complex with poly rA. Giannaris and Damha also reported that

replacement of the normal phosphodiester (PO) linkage in ANA oligomers with phosphorothioate (PS) linkages had a severe destabilizing effect; the destabilization was greater than that observed when the PO linkages of a normal DNA strand were replaced with PS internucleo- tide linkages (Giannaris, P. A.; Damha, M. J. Can. J.

Chem. 1994,72,909). ANA oligomers displayed some stability against cleavage by snake-venom phosphodi- esterase; however, they were rapidly degraded by nucle- ase P1, ribonuclease S1 and spleen-phosphodiesterase (Giannaris, P. A.; Damha, M. J. Can. J. Chem. 1994,72, 909).

Watanabe and co-workers incorporated 2'-deoxy- 2'-fluoro-ß-D-arabinofuranosylpyrimidine nucleosides (2'F-ara-N, where N=C, U and T) at multiple positions within a normal DNA chain and evaluated the hybridiza- tion properties of such (2'-F) ANA-DNA"chimeras" towards complementary DNA (Kois, P. et al. Nucleosides & Nucleotides 1993,12,1093). They found that substi- tutions with 2'F-araU and 2'F-araC had a destabilizing effect on duplex stability, whereas substitution with 2'F-araT was stabilizing compared to unmodified oligo- deoxynucleotide strands. The authors also reported that 2'F-araT and 2'F-araU oligomers were able to m m bind to the complementary DNA with equal or slightly <BR> <BR> <BR> <BR> better affinity compared to the control dT11 (DNA) oli-<BR> gomer. Marquez and co-workers recently evaluated the self-association of a DNA strand in which two internal thymidines were replaced by 2'F-araT's (Ikeda et al.

Nucleic Acids Res. They confirmed the findings of Watanabe and co-workers that internal 2'F-

araT residues stabilize significantly the DNA double helix. The association of these (2'-F) ANA-DNA"chime- ras"with complementary RNA (the typical antisense tar- get) was not reported.

Recently, Noronha and Damha tested oligonucleo- tides based on P-D-arabinose for their ability to rec- ognize duplex DNA, duplex RNA and DNA/RNA hybrids (Noronha, A.; Damha, M. J. Nucleic Acids Res. 1998,26, 2665). A pyrimidine oligoarabinonucleotide was shown to form triple-helical complexes with duplex DNA and hybrid DNA (purine)/RNA (pyrimidine). However, this oli- goarabinonucleotide was found to bind with an affinity that was lower relative to the natural pyrimidine oli- godeoxynucleotide or oligoribonucleotide controls.

Oligomers constructed from a-arabinofurano- sylthymine (a-ara-T) exhibited a large decrease in melting temperature towards complement DNA when com- pared to the control DNA (P-dT) strand (Adams, A. D.; Petrie, C. R.; Meyer Jr., R. B. Nucleic Acids Res. 1991, 19,3647). On the other hand, the duplexes formed between either a-ara-T15 or dTls and complementary RNA (poly-rA) were of similar strength. More recently, Wengel and co-workers reported the synthesis and asso- ciation properties of DNA oligomers containing one and two ß-2'-OMe-araT inserts (Gotfredsen, C. H.; Spielmann, P.; Wengel, J.; Jacobsen, J. P. Bioconjugate Chem. 1996, 7,680). These oligomers showed moderately lowered thermal stabilities towards both single stranded DNA and RNA, compared to unmodified DNA controls. The same authors reported that oligomers constructed from a-2'- OMe-araT units exhibited increased affinity towards the

riboadenylate (RNA) target compared to normal DNA con- trols; however, a-2'-OMe araT strands did not display any advantage relative to the known a-dT oligomers. The susceptibility of the above duplexes to RNase H-medi- ated cleavage was not investigated.

Activation of RNase H by Antisense Oligonucleotides As described above, an important mechanism of action of antisense oligonucleotides is the induction of cellular enzymes such as RNaseH to degrade the tar- get RNA (Walder, R. T.; Walder, J. A. Proc. Natl. Acad.

Sci. USA 1988,85,5011; Chiang et al. J. Biol Chem.

1991,266,18162; Monia et al. J. Biol. Chem. 1993, 268,14514; Giles, R. V.; Spiller, D. G.; Tidd, D. M.

Antisense Res. & Devel. 1994,5,23; Giles et al.

Nucleic Acids Res. 1995,23,954). RNase H selectively hydrolyzes the RNA strand of a DNA/RNA heteroduplex (Hausen, P.; Stein, H. Eur. J. Biochem. 1970,14,279).

RNase Hl from the bacterium Escherichia coli is the most readily available and the best characterized enzyme. Studies with eukaryotic cell extracts contain- ing RNase H suggest that both prokaryotic and eukary- otic enzymes exhibit similar cleavage properties (Monia et al. J. Biol. Chem. 1993,268,14514; Crooke et al.

Biochem J. 1995,312,599; Lima, W. F.; Crooke, S. T.

Biochemistry 1997,36,390). Escherichia coli RNase H is thought to bind in the minor groove of the DNA/RNA double helix and to cleave the RNA by both endonuclease and processive 3'-to-5'exonuclease activities <BR> <BR> <BR> <BR> (Nakamura, H. et al. Proc. Natl. Acad. Sci. USA 1991, Federoff, O. Y.; Salazar, M.; Reid, B. R. J.

Mol. Biol. 1993,233,509; Daniher, A. T. et al. Bioorg.

& Med. Chem. 1997; 5,1037). The efficiency of RNase H degradation displays minimal sequence dependence and is quite sensitive to chemical changes in the antisense oligonucleotide. For example, RNaseH degrades RNA in PS-DNA/RNA hybrids (Gao et al. Mol. Pharmacol. 1991, 41,223), but not in hybrids containing methylphospho- nate-DNA, a-DNA, or 2'-OMe RNA antisense strands (For a review, see: Sanghvi, Y. S.; Cook, P. D. (eds), ACS Sym- posium Series, vol. 580, pp. 1, American Chemical Soci- ety, Washington DC, 1994). Furthermore, while E. coli RNaseH binds to RNA/RNA duplexes, it cannot cleave them, despite the fact that the global helical confor- mation of RNA/RNA duplexes is similar to that of DNA/RNA substrate duplexes ("A"-form helices) (Oda et al. Nucleic Acids Res. 1993,21,4690). These results suggest that local structural differences between DNA/RNA (substrate) and RNA/RNA duplexes is responsi- ble, at least in part, for substrate discrimination (Oda et al. Nucleic Acids Res. 1993,21,4690; Lima, W. F.; Crooke, S. T. Biochemistry 1997,36,390). In this regard it is interesting to note that HIV-1 reverse transcriptase (RT)-associated RNaseH cleaves both DNA/RNA and RNA/RNA duplexes; however, cleavage of the latter is at least 30-fold slower and occurs only when RT is artificially arrested (Gotte et al., EMBO J.

1995,14,838).

Arabinonucleic Acids as Activators of RNaseH Activity An essential requirement in the antisense approach is that an oligonucleotide or its analogue recognize and bind tightly to its complementary target

RNA. The ability of the resulting antisense oli- gomer/RNA hybrid to serve as a substrate of RNaseH is likely to have therapeutic value by enhancing the antisense effect relative to oligomers that are unable to activate this enzyme. Apart from PS-DNA (phosphoro- thioates), PS-DNA (phosphorodithioates), boranophospho- nate-linked DNA, and MBO oligos containing an internal PS-DNA segment, there are no other examples of fully modified oligonucleotides that elicit RNaseH activity.

For this reason, and because of the problems encoun- tered with PS-oligonucleotides (e. g., non-antisense effects and potential risk of toxicity), we have designed alternative oligonucleotide analogues that selectively block gene expression through the activa- tion of RNaseH activity. As a starting point, we felt that such analogues should (a) retain the natural P-D- furanose configuration, (b) possess the unmodified phosphate groups for solubility purposes, and (c) be able to mimic the conformation of DNA strands (e. g., with sugars puckered in the C2'-endo conformation).

The latter requirement stems from the fact that the antisense strand of natural substrates is DNA, and as indicated above, its primary structure (and/or confor- mation) appears to be essential for RNaseH/substrate cleavage. Since the DNA sugars of DNA/RNA hybrids adopt primarily the C2'-endo conformation (Salazar, M.; Champoux, J. J.; Reid, B. R. Biochemistry 1993,32,739; Salazar, M.; Federoff, O. Y.; Reid, B. R. Biochemistry 1996,35,8126), we were interested in an oligonucleo- tide analog that favored this conformation. Analogues mimicking the RNA structure (i. e., those that adopt the

C3'-endo rather than the C2'-endo conformation) would not be suitable for evoking RNase H activity since it is known that RNA/RNA duplexes are generally not sub- strates of RNaseH. This prompted us to consider oli- gomers constructed from arabinonucleotides (i. e., the arabinonucleic acids or ANA). ANA is an stereoisomer of RNA differing only in the stereochemistry at the 2'- position of the sugar ring. ANA/RNA duplexes adopt a helical structure that is very similar to that of DNA/RNA substrates ("A"-form), as shown by similar cir- cular dichroism spectra of these complexes. In addi- tion, X-ray crystallographic studies on ara-C nucleo- sides and on DNA duplexes containing ara-C indicated that the arabinose sugar adopts the C1'-exo or the C2'- endo conformation; the latter conformation is found in the DNA sugars of DNA/RNA substrates. Furthermore, examination of molecular models of an A-type ANA/RNA duplex suggested that the P-2'-OH group of the arabi- nose strand is positioned within the major groove of the hybrid and thus should not interfere with RNase H's binding and catalytic processes. We also considered replacing the P-2'-OH by other electronegative sub- <BR> <BR> <BR> <BR> stituents, e. g., (3-2'-fluorine, since strong stereoe- lectronic effects are expected to stabilize the C2'- endo form (Saenger, W. Principes of Nucleic Acids Structure, Cantor, C. R. (ed.), Springer-Verlag, N. Y., 1984; Marquez, V. E.; Lim, B. B.; Barchi, J. J., Jr.; Nicklaus, M. C.,"Conformational studies of anti-HIV activity of mono-and difluorodideoxynucleosides", in Nucleosides and Nucleotides as Antitumor and Antiviral Agents, Chu, C. K.; Baker, D. C. (eds.), pp. 265-284,

Plenum Press, N. Y., 1993). The possibility of an ANA oligomer activating RNaseH has not been reported.

It would be highly desirable to be provided with ANA oligomers and their analogues for sequence specific inhibition of gene expression via association to (and RNaseH mediated cleavage of) complementary mes- senger RNA.

It would be highly desirable to be provided with ANA oligomers and their analogues that modulate gene expression by binding directly to gene sequences (duplex DNA).

SUMMARY OF THE INVENTION It is the purpose of this invention to provide ANA oligomers and their analogues for sequence specific inhibition of gene expression via association to (and RNaseH mediated cleavage of) complementary messenger RNA. It is also the purpose of this invention to pro- vide ANA oligomers and their analogues that modulate gene expression by binding directly to gene sequences (duplex DNA).

In one aspect, the present invention provides sugar-modified oligonucleotides that form a duplex with its target RNA sequence. The resulting duplex is a substrate for RNaseH, an enzyme that recognizes this duplex and degrades the RNA target portion. RNaseH mediated cleavage of RNA targets is considered to be a major mechanism of action of antisense oligonucleo- tides. The sugar-modified oligomers are composed of P- D-arabinonucleotides (i. e., ANA oligomers) and 2'- deoxy-2'-fluoro-ß-D-arabinonucleosides (i. e., 2'F-ANA oligomers).

Prior to this invention, only the natural DNA (deoxyribonucleic acid phosphodiester) or deoxyribonu- cleic acid oligonucleotides based on phosphorothioate (PS-DNA), dithioate, and boranophosphonate backbones, had been reported to elicit RNaseH degradation of the target RNA. The present invention relates to the dis- <BR> <BR> <BR> <BR> covery that certain uniformly sugar-modified oligonu- cleotides, namely those based on P-D-arabinonucleotides (i. e., ANA oligomers) and 2'-deoxy-2'-fluoro-ß-D-arabi- nonucleotides (i. e., 2'F-ANA oligomers), can activate RNaseH activity when duplexed to the target RNA sequences.

Also provided are oligonucleotides based on 2'- deoxy-2'-fluoro-p-D-arabinonucleosides (i. e., 2'F-ANA oligomers) that bind to duplex DNA with higher affinity relative to unmodified oligodeoxynucleotides.

In another aspect of the invention, defined sequence oligoarabinonucleotides (ANA and 2'F-ANA) were prepared and found to inhibit the expression of a spe- cific target mRNA that codes for the expression of a specific protein (luciferase). This inhibition was noted both in experiments that assessed inhibition of target protein expression in in vitro transcrip- tion/translation of the target (in the presence of a large excess of non-specific exogenous protein contrib- uted by the in vitro transcription/translation system) and in experiments assessing target protein expression in intact cells.

In summary, our experiments establish that ANA oligomers serve as excellent models of antisense agents that have enhanced resistance to the action of degrada- tive nucleases, bind to RNA through duplex formation, elicit RNase H activity, and inhibit in vitro and intracellular specific gene expression. Accordingly, ANA and its analogues have potential utility as thera- peutics agents and/or tools for the study and control of specific gene expression in cells and organisms.

BRIEF DESCRIPTION OF THE DRAWINGS Figs. 1A-1B illustrate thermal melting curves of 18-bp heteroduplexes; Figs. 2A-2C illustrate circular dichroic (CD) spectra of duplexes; Fig. 3 illustrates thermal melting curves of triple helical complexes formed by the association of oligoarabinonucleotide SEQ ID NO: 13 with DNA/DNA ("DD") and DNA/RNA ("DR") hairpin duplexes;

Fig. 4 illustrates gel mobility shift triplex assay under non-denaturing conditions; Fig. 5 illustrates oligonucleotides with P-D- arabinose as sugar component elicit RNaseH degradation of complementary target RNA; Fig. 6 illustrates homopolymeric oligonucleo- tides with 2'-F-P-D-arabinose as sugar component elicit RNaseH degradation of complementary target RNA; Fig. 7 illustrates heteropolymeric oligonucleo- tides with 2'-F-P-D-arabinose as sugar component elicit RNaseH degradation of complementary target RNA; Fig. 8 illustrates stability of oligonucleo- tides with 2'-F-P-D-arabinose as sugar component to degradation by serum nucleases; Fig. 9 illustrates stability of oligonucleo- tides with 2'-F- (3-D-arabinose as sugar component to degradation by snake venom phosphodiesterase I; Fig. 10 illustrates oligonucleotides based on P-D-arabinose and 2'-deoxy-2'-fluoro-ß-D-arabinose show low nonspecific binding to cellular proteins; Fig. 11 illustrates oligonucleotide inhibition of specific gene expression in an in vitro protein translation system; and Fig. 12 illustrates oligonucleotide inhibition of luciferase gene expression in Hela X1/5 cells.

DETAILED DESCRIPTION OF THE INVENTION The present invention relates to oligonucleo- tides based on P-D-arabinose and its derivatives and the therapeutic use of such compounds. It is the object of the present invention to provide a new oligo-

nucleotide analogue that hybridizes to complementary nucleic acids which may be mRNA, viral RNA (including retroviral RNA), or duplex DNA for the purpose of inhibiting gene transcription and expression. More particularly this invention relates to the use of ara- binonucleic acid strands and their analogues to cleave complementary RNA via RNaseH activation. Other appli- cations of this invention relates to the use of antisense oligonucleotides based on arabinonucleotides in combination with RNaseH as laboratory reagents for the sequence specific cleavage and mapping of RNA.

The oligonucleotides of this invention may be represented by the following Formula (I): where B includes but it is not necessarily limited to a common purine or pyrimidine base such as adenine, gua- nine, cytosine, thymine, and uracil. The sugar is P-D- arabinofuranose, its mirror image enantiomer ß-L-arabi- nofuranose, and the corresponding carbocyclic sugars (i. e., in which the ring oxygen at position 4'is replaced by a methylene or CH2 group). The substituent at the 2'position of the sugar ring includes but it is not necessarily limited to a halogen (fluorine, chlo-

rine, bromine, iodine), hydroxy, alkyl, alkylhalide (e. g. CH2F), alkylsulfhydryl (e. g.-SCH3), allyl, amino, aryl, alkoxy, and azido. Y at the internucleotide phosphate linkage includes but it is not necessarily limited to oxygen, sulfur, methyl, amino, alkylamino, dialkylamino, methoxy, and ethoxy. The ANA oligomers may also include modified sugars in part of the oli- gomer. The oligonucleotides may also include the 2'- deoxy-2', 2"-difluoro- (3-ribofuranose sugar (D or L con- figuration) in part or all of the oligomer (this struc- ture is obtained by replacing the 2'-H atom in formula I with a fluorine atom, thus providing an oligonucleo- tide containing two fluorine atoms at carbon 2'). The oligonucleotides may also include stretches of ssDNA flanked by ANA segments (e. g., ANA-DNA-ANA, 2'F-ANA- DNA-2'F-ANA chimeras), or combination of ANA and 2'F- ANA segments (e. g., ANA-2'F-ANA chimeras). The ANA oligomers of this invention contains a sequence that is complementary to a specific sequence of a mRNA, or genomic viral RNA, such that the oligonucleotide can specifically inhibit protein biosynthesis, or virus replication (reverse transcription), respectively. A complementary target may also be duplex or single stranded DNA, such that the arabinonucleotide strand can specifically inhibit DNA replication and/or tran- scription. Partial modifications to the oligonucleo- tide directed to the 5'and/or 3'-terminus, or the phosphate backbone or sugar residues to enhance their antisense properties (e. g. nuclease resistance) are within the scope of the invention.

A preferred group of oligonucleotides useful in this invention, are those wherein B is a natural base (adenine, guanine, cytosine, thymine, uracil); the sugar moiety is ß-D-arabinofuranose; X is fluorine; Y is oxygen since these modifications give rise to oli- gomers that exhibit high affinity for single stranded RNA, single stranded DNA, and duplex DNA. In addition, these oligomers have been shown to meet the require- ments necessary for antisense therapeutics. For exam- ple, they activate RNaseH activity, show resistance to cellular and serum nucleases, inhibit the expression of a specific target mRNA that codes for the expression of a specific protein in intact cells; and exhibit little (if any) nonspecific binding to cellular proteins; as such they may be potentially more effective in vivo.

The free R-D-arabinose pyrimidine (araU, araC) nucleoside monomers may be prepared from the corre- sponding ribonucleosides in good yields, and can be further elaborated to the corresponding 5'-0-mono- methoxytrityl-2'-O-acetyl-3'-O- (P-cyanoethylphospho- ramidite) derivatives suitable for solid-phase oligonu- cleotide synthesis (Giannaris, P. A.; Damha, M. J. Can.

J. Chem. 1994,72,909). The corresponding araA nucleo- side is commercially available, and can be prepared readily from riboadenosine (via oxidation of the 2'-OH group and reduction of the 2'-keto group with a hydride source, e. g., Robins, M. J. et al. in"Nucleosides, Nucleotides and their Biological Applications", Rideaut, J. L.; Henry, D. W.; Beacham III, L. M. (eds.), pp. 279, Academic Press, Inc., 1993). The correspond- ing ara-G monomer can be prepared by the method of

Pfleiderer and co-workers (Resmini, M.; Pfleiderer, W.

Helv. Chim. Acta 1994,77,429). The 3'-0- (P-cyano- ethyl-N, N-diisopropylphosphoramidite) derivatives of 5'-MMT-2'-deoxy-2'-fluoro-ß-D-arabinonucleosides (2'F- ara-C, 2'F-ara-A, 2'F-ara-G and 2'F-ara-T) may be syn- thesized following published procedures (Tann, C. H.; Brodfuehrer, P. R.; Brundidge, S. P.; Sapino, C. Jr.; Howell, H. G. J. Org. Chem. 1985,50,3644; Howell; H. G.; Brodfuehrer, P. R.; Brundidge, S. P.; Benigni, D. A.; Sapino, C., Jr. J. Org. Chem. 1988,53,85; Kois, P.; Tocik, Z.; Spassova, M.; Ren, W.-Y.; Rosenberg, I.; Farras Soler, J.; Watanabe, K. A. Nucleosides & Nucleo- tides 1993,12,1093; Chou, T.-C.; Burchenal, J. H.; Fox, J. J.; Watanabe, K. A. Chem. Pharm. Bull. 1989,37, 336).

The protected arabinonucleoside monomers can be attached to the solid support by known methods. In a preferred embodiment, the solid support is long-chain alkylamine controlled pore glass, and the procedure of Damha et al. is used for its derivatization (Damha et al. Nucleic Acids Res. 1990,18,3813).

The oligomers of this invention (constructed from either P-D-arabinose or 2-deoxy-2-fluoro-D-D-ara- binose) exhibit a number of desirable properties: (1) They were found to bind to and cleave sin- gle stranded RNA by activating RNaseH. Circular dichroism studies in solution showed that DNA/RNA hybrids (the natural substrate of RNase H) and ANA/RNA duplexes adopt a very similar helical structure that falls within the"A"-conformational family. The abil- ity of RNaseH to degrade RNA in the ANA: RNA duplexes

may be due, at least in part, to (a) the similarity of the structure of ANA/RNA to that of DNA/RNA duplexes, and (b) the fact that the 2'-substituent of the sugar ring is located in the major groove, where it does not interfere in RNase H's binding and catalytic processes.

The 2'-fluorinated ANA derivatives in particular were found to have excellent affinity towards RNA targets, compared to normal DNA and phosphorothioate oligodeoxy- nucleotide strands.

(2) An oligonucleotides based on P-D-arabinose and containing four nucleobases (U, C, A and G) was found to hybridize to complementary RNA but not comple- mentary single stranded DNA. This property suggests that these oligomers may be useful for targeting retro- viral genomic RNA to inhibit early stages of virus rep- lication, including reverse transcription. This high level of RNA specificity has previously been reported for other types of oligonucleotide analogs (e. g., 2', 5'-linked RNA and 2', 5'-linked DNA; Giannaris, P. A.; Damha, M. J., Nucleic Acids Res. 1993,20,4742; Alul, R.; Hoke, G. D. Antisense Res. Dev. 1995,5,3), how- ever, none of these oligonucleotides elicit RNaseH activity.

(3) Pyrimidine oligonucleotides constructed from 2'-deoxy-2'-fluoro-ß-D-arabinonucleoside units were also found to hybridize to duplex DNA and DNA/RNA hybrids via triplex helix formation. The thermal sta- bility of these triplexes are significantly higher than those formed by normal oligodeoxynucleotides. These results were unexpected given that the P-D-arabinose series produces triplexes with only modest stability

(Noronha, A.; Damha, M. J. Nucleic Acids Res. 1998,26, 2665).

(4) Results from metabolic stability studies indicate that the arabinose modification, particularly the (3-D-arabinose (2'-OH) derivatives, confers greater resistance to degradation by both serum and cellular nucleases compared with natural strands (PO-DNA), although less than to phosphorothioate (PS-DNA) deriva- tives. Partial modifications to the ANA or 2'F-ANA oligonucleotide directed to the 5'and/or 3'-terminus, or the phosphate backbone or sugar residues to further enhance nuclease resistance are within the scope of the invention.

(5) ANA and 2'F-ANA show little (if any) non- specific binding to cellular proteins and serum pro- teins. This property results in a significantly improved interaction of arabinooligonucleotides with target RNA in the presence of cell proteins compared to the phosphorothioate analogs.

These properties combined establish that ANA and 2'F-ANA oligomers serve as excellent models of antisense agents that have resistance to the action of degradative nucleases, bind to RNA and single stranded DNA through duplex formation, bind to duplex DNA through triplex formation, and elicit RNase H activity.

Consequently, antisense oligonucleotide constructs con- taining arabinose and their analogues should serve as therapeutics and/or valuable tools for studying and controlling gene expression in cells and organisms.

The following examples are given by way of illustration of the present invention. The examples

are not intended in any way to limit the scope of the invention.

EXAMPLE 1 Preparation of Oligonucleotides containing ß-D- Arabinofuranoses Oligoarabinonucleotides (Formula I; X= OH, Y= O-) were synthesized using standard phosphoramidite chemistry and 3'-ara-C (Bz)-long-chain alkylamine con- trolled pore glass solid support (lcaa-CPG; 500 A; 1 pmol scale). The required monomers, namely 5'-MMT-2'- OAc-3'-O- (P-cyanoethyl-N, N-diisopropylphosphoramidite) derivatives of ara-A (Bz), ara-C (Bz) and ara-U were syn- thesized by the method of Damha et al. (Damha, M. J.; Usman, N.; Ogilvie, K. K., Can. J. Chem. 1988,67,831; Giannaris, P. A.; Damha, M. J.; Can. J. Chem. 1994,72, 909). The corresponding ara-G (N2-i-Bu, 06-NPE) mono- mer was prepared by a modification of the procedure of Resmini et al. (Resmini, M.; Pfleiderer, W. Helv. Chim.

Acta 1994,77,429). Thus, the monomers were dissolved to 0.12 M in anhydrous acetonitrile. Prior to chain assembly, the support (1 jj. mol) was treated with the capping reagents, acetic anhydride/N-methylimidazole/4- dimethylaminopyridine (Damha, M. J.; Ogilvie, K. K. in Methods in Molecular Biology, 20, Protocols for Oligo- nucleotides and Analogs: Synthesis and Properties, Agrawal, S. (ed.), pp. 81, The Humana Press, Inc.

Totawa, N. J., 1993). Chain assembly of sequences was carried out using an Applied Biosystem DNA synthesizer (Model 381A) as follows: (i) detritylation: 3% trichlo- roacetic acid in dichloroethane delivered in 100 s (+ 40 s burst') steps. The eluate from this step was col-

lected and the absorbance at 478 nm (MMT+, arabino sequences) measured to determine the average coupling reaction yield (ca. 60-90%); (b) nucleoside phospho- ramidite coupling time of 7.5 min; (c) capping: 1: 1 (v/v) of acetic anhydride/collidine/THF 1: 1: 8 (solution A) and 1-methyl-lH-imidazole/THF 16: 84 (solution B) delivered in 15 s + 35 s"wait"steps; (d) oxidation: 0.1M iodine in THF/water/pyridine 7: 2: 1, delivered in 20 s + 35 s"wait"step. The 5'-terminal trityl group was removed by the synthesizer and the oligomers were then removed from the support and deprotected by treat- ment of the CPG with a solution containing concentrated ammonium hydroxide/ethanol (3: 1 v/v, 1 mL) for two days at room temperature. The ammonium hydroxide/ethanol solution was evaporated and the crude product purified by preparative polyacrylamide gel electrophoresis (PAGE) followed by gel filtration (desalting) on a Sephadex G-25 column. For sequences containing ara-G units, it was necessary to subject the partially pro- tected oligomer to an additional step; that is, follow- ing the ammonia treatment and evaporation step, the oligomer was treated with a solution of 1M tetra-n- butylammonium fluoride (50 L, r. t., 16 h) in THF.

This step cleaves the p-nitrophenylethyl protecting group at the 06-position of guanine residues. This solution is then quenched with water (1 mL) and desalted via size exclusion chromatography (Sephadex G- 25 column). Purification is then carried out by gel electrophoresis as described above, and its molecular weight confirmed by MALDI-TOF mass spectrometry. The yield, base sequence, hybridization properties of the oligomers synthesized are given in Table 1.

TABLE 1

Base composition, yield and properties of oligoarabinonucleotides (ANA) Melting Temperature Base sequence of Oligonucleotidea SEQ ID Yieldb RNA target DNA target NO: ara (AGC UCC CAG GCU CAG AUC) 1 5 44 26d ara (AAA AAA AAA AAA AAA AAA) 2 10 26 45 ara (UUU UUU UUU UUU UUU UUU) 3 9 n. o. e n. o. e ara (UUA UAU UUU UUC UUU CCC) 10 32 <15d ara (AUA UCC UUG UCG UAU CCC) 8 47 n. m. f a Sequence is written in the 5'- 3'direction;<BR> <BR> b Optical density units (A260 nm); c Buffer containing 140 mM KCI, 1 mM MgCI2,5 mM Na2HPO4 (pH 7.2); d weak and broad transition e no melt curve or sharp transition observed; 'not measured.

Presently only the 5'-DMT, 2'-OAc, ara-C (Bz) 3'-phosphoramidite derivative and 3'-ara-C (Bz) long- chain alkylamino controlled pore glass (lcaa-CPG) are commercially available. Of the free (unprotected) nucleosides, only ara-C, ara-U and ara-A are commer- cially available.

EXAMPLE 2 Preparation of Oligonucleotides containing 2-Deoxy-2- Fluoro-ß-D-Arabinose sugars Oligoarabinonucleotide synthesis (Formula I; X= F, Y = 0-) was performed on an Applied Biosystem DNA synthesizer (model 381A) using the phosphoramidite approach. Oligomers were prepared on a 1.0 jJLmol scale using lcaa-CPG solid support bearing 3'-terminal 2'- deoxy-2'-fluoro-ß-D-arabinonucleosides. Coupling yields ranged from 60 to 100% (average ca. 80%) as

monitored by the release of the MMT cation. The required 3'-O-(ß-cyanoethyl-N, N-diisopropylphospho- ramidite) derivatives of 5'-MMT-2'-deoxy-2'-fluoro-ß-D- arabinonucleosides (2'F-ara-C, 2'F-ara-A, 2'F-ara-G and 2'F-ara-T) were synthesized by published procedures (Tann, C. H.; Brodfuehrer, P. R.; Brundidge, S. P.; Sapino, C. Jr.; Howell, H. G. J. Org. Chem. 1985,50, 3644; Howell; H. G.; Brodfuehrer, P. R.; Brundidge, S. P.; Benigni, D. A.; Sapino, C., Jr. J. Org. Chem. 1988,53, 85; Kois, P.; Tocik, Z.; Spassova, M.; Ren, W.-Y.; Rosenberg, I.; Farras Soler, J.; Watanabe, K. A. Nucleo- sides & Nucleotides 1993,12,1093; Chu, C. K.; Matulic- Adamic, J.; Huang, J.-T.; Chou, T.-C.; Burchenal, J. H.; Fox, J. J.; Watanable, K. A. Chem. Pharm. Bull. 1989,37, 336). Thus, the monomers were dissolved to 0.10 M in anhydrous acetonitrile. Prior to chain assembly, the support (1 pmol) was treated with the capping reagents, acetic anhydride/N-methylimidazole/4-dimethylamino pyridine (Damha, M. J.; Ogilvie, K. K. in Methods in Molecular Biology, 20, Protocols for Oligonucleotides and Analogs : Synthesis and Properties, Agrawal, S.

(ed.), pp. 81, The Humana Press, Inc. Totawa, N. J., 1993). Chain assembly of sequences was carried out as follows: (i) detritylation: 3% trichloroacetic acid in dichloroethane delivered in 140 s (+ 80 s'burst') steps. (b) nucleoside phosphoramidite coupling time of 10 min; (c) capping of 5'-hydroxyl groups: 1: 1 (v/v) of acetic anhydride/collidine/THF 1: 1: 8 (solution A) and 1-methyl-lH-imidazole/THF 16: 84 (solution B) delivered in 15 s + 35 s"wait"steps; (d) oxidation of phosphite triester linkage: 0.1M iodine in THF/water/pyridine

7: 2: 1, delivered in 20 s + 35 s"wait"step. The 5'- terminal trityl group was removed by the synthesizer and the oligomers were then removed from the support and deprotected by treatment of the CPG with a solution containing concentrated ammonium hydroxide/ethanol (3: 1 v/v, 1 mL) for two days at room temperature. The ammo- nium hydroxide/ethanol solution was evaporated and the crude product purified by preparative polyacrylamide gel electrophoresis (PAGE) followed by gel filtration (desalting) on a Sephadex G-25 column. Molecular weight of oligomers were confirmed by MALDI-TOF mass spec- trometry. The yield, base sequence, and hybridization of the oligomers synthesized are given in TABLE 2.

TABLE 2 Base composition, yield and properties of 2'-F- oligoarabinonucleotides (2'F-ANA) Melting Temperature Base sequence of Oligonucleotidea SEQ ID Yieldb RNA target DNA target NO: 2'F-ara (AGC TCC CAG GCT CAG 6 11 86 68 ATC) 2'F-ara (TTT TTT TTT TTT TTT TTT) 7 15 52 55 2'F-ara (AAA AAA AAA AAA AAA AAA) 8 27 30 63 2'F-ara(TTA TAT TTT TTC TTT CCC) 9 15 64 54 2'F-ara (ATA TCC TTG TCG TAT CCC) 10 21 76 n. m. d a Sequence is written in the 5'-> 3'direction;<BR> <BR> b Optical density units (A260 nm); c Buffer containing 140 mM KCI, 1 mM MgCI2,5 mM Na2HPO4 (pH 7.2); d Not measured.

EXAMPLE 3 Association Properties of Uniformly Modified Oligonucleotides possessing P-D-Arabinose and P-D-2- Fluoro-2-Deoxyarabinose Sugars Binding to single stranded DNA and RNA Targets The ability of oligonucleotides to hybridize to single-stranded nucleic acids to give a double-helical complex is crucial for their use as antisense therapeu- tic agents. The formation of such a complex involves stacking and hydrogen bonding interactions between the base chromophores, a process which is accompanied by a reduction in W absorption ("hypochromicity").. When the temperature of the solution containing the double- helical complex is gradually raised, the hydrogen bonds break and the duplex dissociates into single strands.

This reduces the amount of base-base interactions and hence leads to a sudden increase of the W absorbance.

The temperature at which the double-helical complex dissociates, or more precisely, the point at which half the population exists as complex and the remaining half as single strands, is termed the"melting temperature" (Tm). Thus a common technique used in nucleic acid chemistry to investigate duplex formation (and its strength) involves mixing equimolar amounts of the strand of interest together, incubating at low tempera- ture to allow strands to anneal, and then observing the W-absorption at 260 nm (absorption maxima) as a func- tion of temperature. The result is an absorbance ver- sus temperature plot, or sigmoidal"melt profile"or "melting curve"from which the Tm (the midpoint of the raise of the melt curve) is calculated (Wickstrom, E.; Tinoco, I. Jr. Biopolymers Circular

dichroism (CD) is another powerful optical technique for the study of nucleic acid structure and conforma- tion. The CD spectrum usually includes a region of rapid change (Cotton effects) with respect to wave- length (200-350 nm region). The signs, absolute inten- sity and position of the Cotton effects are particu- larly sensitive to chemical composition and three- dimensional structure of the nucleic acid complexes.

CD measurements can therefore be applied to determine global helical conformation (or helix type) as well as to investigate structural changes (e. g., helix-to-coil transitions) as a function of temperature (Bloomfield, <BR> <BR> <BR> <BR> V. A.; Crothers, D.; Tinoco, Jr., I."Physical Chemistry of Nucleic Acids", Harper and Row, N. Y., 1974; Ts'o, P. O. P. (ed.),"Basic Principles in Nucleic Acid Chemis- try", vol. 1 and 2, Academic Press, N. Y., 1974).

The binding properties of oligonucleotides (SEQ ID NO: 1, and SEQ ID NO: 6) (for base sequences see Tables 1 and 2) with complementary DNA and RNA single strands were evaluated in a buffer containing 140 mM KC1,1 mM MgCl2,5 mM Na2HPO4 (pH 7.2), which is repre- sentative of intracellular conditions (Alberts, B.

Molecular Biology of the Cell, pp. 304, Garland, N. Y., 1989). Molar extinction coefficients for oligoarabino- nucleotide strands were calculated using the nearest- neighbor approximation, and were assumed to be the same as those of normal strands (Puglisi, J. D.; Tinoco, I.

Jr. Methods in Enzymology, Dahlberg, J. E.; Abelson, J. N. (eds.), 180, pp. 304, Academic Press, S. D., 1989).

Thermal denaturation curves were acquired at 260 nm from 5°C to 90°C (rate of heating: 0.5°C/min), at a con-

centration of approximately 2.8 M of each strand.

Melting temperatures (Tm) were calculated from first- derivative plots of absorbance versus temperature.

Thermal denaturation curves of the heteroduplexes are shown in Figs. 1A & 1B. Oligoarabinonucleotides ANA (SEQ ID NO: 1), 2'F-ANA (SEQ ID NO: 6), and control DNA, PS-DNA and RNA oligonucleotides were hybridized to (Fig. 1A) complementary single-stranded RNA, and (Fig.

1B) complementary single-stranded DNA.

The results (Fig. 1A) show that the arabinonu- cleotide of mixed base sequence, ANA (SEQ ID NO: 1), has the ability to form a stable heteroduplex with its RNA complement, exhibiting a Tm of 44°C, compared to 72°C for the corresponding natural DNA/RNA heteroduplex. A 1: 1 mixture of ANA (SEQ ID NO: 1) and its DNA complement showed a much weaker and broader transition suggesting that, under the conditions used, SEQ ID NO: 1 does not bind to single stranded DNA (Fig. 1B). The data shown in Fig. 1A and Table 2 also show that interaction of 2'F-oligoarabinonucleotides with complement RNA results in the formation of heteroduplexes that are of superior thermal stability relative to the complexes formed by the natural (PO-DNA) and thioate (PS-DNA) strands. For example, the Tm of 2'F-araA18 (SEQ ID NO: 8)/ rU hetero- duplex was 30.2°C, compared to 25.4°C for the natural dAl,/rUl8 heteroduplex. Similarly, the Tm of the 2'F- ara-A8 (SEQ ID NO: 7)/rA heteroduplex was 43.9°C, which represents an increase in Tm of ca. 5°C relative to the natural dT/rA heteroduplex (Tm 39°C). Also, the mixed base heteroduplex formed by the association of 2'F-ANA (SEQ ID NO: 6) and its target RNA sequence is thermally

more stable (Tm 86°C) than the corresponding of PO- DNA/RNA and PS-DNA/RNA duplexes (Fig. 1A). In contrast to the behavior observed for ANA sequence (SEQ ID NO: 1) (which exhibited selective binding to RNA), the 2'F-ANA oligonucleotides (e. g. SEQ ID NO: 6) bind strongly to both single stranded complementary DNA and RNA. In fact, 2'F-araA1a (SEQ ID NO: 8) formed a more stable het- eroduplex with single stranded complementary DNA (dT18) than with RNA (rU18), i. e., T. 63.3°C and 30.2°C, respec- tively (Table 2). This amounts to a binding selectiv- ity of ATm = +33°C. The selective binding to single stranded PO-DNA (over RNA) was also observed for the natural dA18 strand, although in this case the selectiv- ity observed was less (ATm = +20°C).

As shown in Fig. 2A, the CD spectra of the heteroduplexes ANA (SEQ ID NO: 1)/RNA and 2'F-ANA (SEQ ID NO: 6)/RNA, closely resembled those of the corre- sponding DNA/RNA control duplexes (the normal substrate of RNaseH), suggesting that all of these complexes share the same helical conformation. The spectral fea- tures observed are characteristic of a"A"-type helix, a structure that appears to be important in the recog- nition of DNA/RNA substrates by RNase H (Lima, W. F., Crooke, S. T. Biochemistry The fact that ANA/RNA and 2'F-ANA/RNA heteroduplexes are sub- strates of RNaseH (see Examples 5 and 6) is fully con- sistent with this notion. The CD spectra of the DNA/DNA duplex (of the same base sequence) is very dif- ferent, and is characteristic of the"B-form"helical conformation. The CD spectra of the A-form RNA/RNA control duplex is also shown.

Fig. 2B shows the CD spectra of 2'F-araAl8 (SEQ ID NO: 8)/ruile and dA,,/rUl8 duplexes, as well as the cor- responding dA18/dT18 duplex. The first two duplexes exhibit a similar CD profiles (i. e., peak pattern and peak position) that is characteristic of the A-helix conformation, whereas the spectrum of the DNA/DNA duplex (dAl8/dT18) falls into a pattern that is typical of"B-form"helices.

The same conclusions can be reached from the spectra shown in Fig. 2C. The CD spectra of the 2'F- aras18 (SEQ ID NO: 7)/rA18 duplex displays very similar spectral features of the normal dT/rAg hybrid, also typical of the A-form conformation. The spectra of the DNA/DNA duplex, dA18/dTl8 (B-form), is also shown for comparison.

EXAMPLE 4 Association Properties of Oligonucleotides possessing 2-Deoxy-2-Fluoro-ß-D-Arabinose Sugars Binding to DNA Duplexes and DNA/RNA Hybrids To study the interaction between oligomers of 2'-deoxy-2'-fluoroarabinonucleotides and DNA/DNA and DNA/RNA duplexes, the experimental design of Roberts and Crothers was adopted (Roberts, R. W.; Crothers, D. M.

Science 1992,258,1463). The target duplexes are the following purine-pyrimidine hairpins: 5'-GGAGAGGAGGGA T DNA/DNA T (SEQ ID NO: 11) T 3'-CCTCTCCTCCCT T 5'-GGAGAGGAGGGA T DNA/RNA T (SEQ ID NO: 12) T 3'-CCUCUCCUCCCU T

Triplex-helix formation can occur when an oli- gonucleotide binds in the major groove of the targeted duplexes (Le Doan, T. et al. Nucleic Acids Res. 1987, 238,645; Moser; H. E.; Dervan, P. B. Science 1987,238, <BR> <BR> <BR> <BR> 645). The oligopyrimidine strand containing 2'-deoxy- 2'-fluoro-arabinose sugars, i. e., 2'F-ara (CCT CTC CTC CCT) (SEQ ID NO: 13) was used to assess triple helix formation with the above hairpin duplexes. For the pur- pose of comparisons, the association of the correspond- ing oligodeoxyribopyrimidine ("DNA", 2'-deoxy-ß-D- ribose) and oligoarabinopyrimidine ("ANA",-D-arabi- nose) sequences were also examined. The ability of these oligomers to form triple helices was determined from ultraviolet spectroscopic melting experiments (as described in Example 3) and native gel electrophoresis, in a solution containing 100 mM sodium acetate and 1 mM ethylenediamine tetraacetate (EDTA), pH 5.5. Molar extinction coefficients for oligonucleotides were cal- culated from those of the mononucleotides and dinucleo- tides according to nearest-neighbouring approximations (Puglisi, J. D.; Tinoco, I. Jr. Methods in Enzymology, Dahlberg, J. E.; Abelson, J. N. (eds.), 180, pp. 304, Academic Press, S. D., 1989). The values for the hybrid hairpin was assumed to be the sum of their DNA plus RNA components: DNA/DNA, 26.5; DNA/RNA, 27.1; (units= 104 M- 1 cm-1). The molar extinction coefficient for the 2'- fluoroarabinonucleotide strand SEQ ID NO: 13 was assumed <BR> <BR> <BR> <BR> <BR> to be the same as a normal DNA strand (9.6 x 104 M-1 cm-1 units). Complexes were prepared by mixing equimolar amounts of interacting strands, e. g., 2'F-ANA (SEQ ID NO: 13) + hairpin DNA/DNA or DNA/RNA, and lyophilizing

the resulting mixture to dryness. The resulting pellet was then re-dissolved in 100 mM NaOAc/1 mM EDTA buffer (pH 5.5). The final concentration was 2 tM in each strand. The solutions were then heated to 80°C for 15 min, cooled slowly to r. t., and stored at 4°C overnight before measurements. Prior to the thermal run, samples were degassed by placing them in a speed-vac concentra- tor (2 min). Denaturation curves were acquired at 260 nm at a rate of heating of 0.5°C/min. Melting tempera- tures (Tm) were calculated from the first derivative of the melting curves. The results of the melting experi- ments are shown in Fig. 3.

The results show that when 2'F-ANA (SEQ ID NO: 13) was mixed with an equimolar concentration of hairpin DNA/DNA (SEQ ID NO: 11) or DNA/RNA (SEQ ID NO: 12), a biphasic transition was observed upon heating the solution from 10°C to 90°C. The low temperature transition is assigned to the dissociation of 2'F-ANA (SEQ ID NO: 13) from the target hairpins (Roberts, R. W.; Crothers, D. M. Science 1992,258,1463). The high tem- perature transition corresponds to the melting of the hairpin duplexes, since it was also observed when a solution of hairpin duplex alone was heated under iden- tical conditions. The data show that T values for low temperature transitions resulting from mixtures of SEQ ID NO: 13 (2'-deoxy-2'-fluoro-ß-D-arabinose oligomer) + hairpins are considerable higher than Tm values for tran- sitions from the corresponding ANA (ß-D-arabinose oli- gomer) + hairpin, or DNA (2'-deoxy-ß-D-ribose oligomer) + hairpin mixtures. For example, as can be seen from <BR> <BR> <BR> the melting curves shown in Fig. 3, the T. for the disso-

ciation of 2'F-ANA strand SEQ ID NO: 13 from the DNA/DNA hairpin (DD, SEQ ID NO: 11) is 49°C, compared to 34°C and 40°C, for the dissociation of the ANA (P-D-arabinose; not shown) and DNA (2'-deoxy-ß-D-ribose) oligonucleotides, respectively. Similarly, the first transition for the triplex formed by 2'F-ANA (SEQ ID NO: 13) and DNA/RNA hairpin (SEQ ID NO: 12) was 53°C, compared to 43°C and 45°C, for the corresponding triplexes formed by the ANA ((3-D-arabinose; not shown) and DNA (2'-deoxy-p-D-ribose) strands, respectively.

The equilibrium between single-, double-, and triple-stranded species of 2'F-ANA (SEQ ID NO: 13) + hairpin mixtures was also directly monitored by poly- acrylamide gel electrophoresis (Fig. 4). Fig. 4 shows a photograph of a polyacrylamide gel of single stranded oligo-2'F-arabinopyrimidine SEQ ID NO: 13 and target hairpins DNA/DNA (SEQUENCE ID NO: 11) ("DD") and DNA/RNA (SEQUENCE ID NO: 12) ("DR"), and 1: 1 ratios of SEQ ID NO: 13: hairpins. The first lane shows marker dyes xylene cyanol (XC) and bromophenol blue (BPB). The next lane shows the SEQ ID NO: 13 strand, whereas the "DD (-)"lane shows the DNA/DNA hairpin (SEQ ID NO: 11).

The SEQ ID NO: 13: DD triplex is clearly seen in the"DD (+)"lane, which contains a 1: 1 molar mixture of 2'F- ANA (SEQ ID NO: 13) and"DD". The DNA/RNA hairpin (SEQ ID NO: 12) is visible in the"DR (-)"lane. The triplex SEQ ID NO: 13: DR triplex is clearly visible in the"DR (+)"lane, which consists of a 1: 1 mixture of 2'F-ANA (SEQ ID NO: 13) and"DR". Gels were visualized by UV- shadowing. Base sequence of single strand 2'F-ANA (SEQ ID NO: 13) and hairpins DD (SEQ ID NO: 11) and DR (SEQ ID

NO: 12) and experimental conditions are given above in Example 4.

This method provides a convenient way to monitor triplex formation and to qualitative check on the stoi- chiometry of interaction the strands (Kibler-Herzog, L. et al. Nucleic Acids Res. 1990,18,3545). The results in Fig. 4 show that the 2'F-ANA strand (SEQ ID NO: 13), hairpins, and triple-helical complexes can be separated with excellent resolution on a polyacrylamide gel at low temperature. As can be seen from the gel results, the triple-helical complex is nearly quantitatively formed at a 1: 1 molar ratio of 2'F-ANA (SEQ ID NO: 13): hairpin.

This is in contrast to the incubation of ANA (D-arabi- nose strand) and hairpin (1: 1 molar ratio) which, under the same conditions, gave a mixture of ANA + hairpin + triplex (see Noronha, A.; Damha, M. J. Nucleic Acids Res.

This is in complete agreement with the Tm results which indicates that the SEQ ID NO: 13 (2'- deoxy-2'-fluoro-p-D-arabinose) strand has a signifi- cantly higher affinity for the DNA/DNA and DNA/RNA hair- pin duplexes relative to the ANA ( (3-D-arabinose) strand.

EXAMPLE 5 Induction of Ribonuclease H (RNaseH) Activity by Oligonucleotides possessing P-D-Arabinose as Sugar Component Defined-sequence oligonucleotides, 18-units in length, were used in these experiments, i. e., 5'-d (AGCTCCCAGGCTCAGATC)-3'"DNA" (SEQ ID NO: 14) 5'-ara (AGCUCCCAGGCUCAGAUC)-3"ARA" (SEQ ID NO: 1) 5'-ribo (AGCUCCCAGGCUCAGAUC)-3'"3', 5'-RNA" (SEQ ID NO: 15) 5'-ribo (AGCUCCCAGGCUCAGAUC)-3"2', 5'-RNA" (SEQ ID NO: 16)

These oligomers are complementary to a sequence within the R region of HIV-1 genomic RNA. The target RNA used was a synthetic 18 nt 3', 5'-RNA oligonucleo- tide, identical to the sequence within the HIV R region, and exactly complementary to the sequence of the above oligonucleotides.

The ability of the above oligonucleotides to elicit RNaseH degradation of target RNA was determined in assays (10 tL final volume) that comprised 5 pmol of 5'- [32p] _target RNA and 15 pmol of test oligonucleotide in 60 mM Tris-HCl (pH 7.8,25°C) containing 2mM dithio- threitol, 60 mM KC1, and either 10 mM MgCl2 or 0.1 mM MnCl2. Reactions were started by the addition of HIV-RT or E. coli RNaseH. Incubations were carried out at 25°C for varying times (generally 20 to 30 minutes). Reac- tions were quenched by the addition of loading buffer (98% deionized formamide containing 10 mM EDTA and lmg/mL each of bromophenol blue and xylene cyanol), and heating at 100°C for 5 minutes. The reaction products were resolved by electrophoresis using a 16% polyacry- lamide sequencing gel containing 7 M urea, and visual- ized by autoradiography. The result of such experiments is shown in Fig. 5.

The results show that the oligonucleotide based on 2'-deoxyribose ("DNA" (SEQ ID NO: 14)) or P-D-arabi- nose ("ARA" (SEQ ID NO: 1)) are able to form duplexes with target RNA that serve as substrates for the RNase H activity of either HIV-1 RT or E. coli RNase H, as indicated by the numerous smaller sized degradation products of the target RNA in Fig. 5. This RNase H deg- radation was noted with either Mon2+ (illustrated) or Mg2+

(not shown) as metal. In contrast, oligonucleotides based on D-ribose, either in 3', 5'-linkages (3', 5'-RNA (SEQ ID NO: 15)), or in 2', 5'-linkages (2', 5'-RNA (SEQ ID NO: 16)) were unable to elicit this RNase H degrada- tion of target RNA, even though these test oligonucleo- tides were competent to form duplexes with the target RNA. Similarly, an oligonucleotide based on P-D-2'- deoxyribose, but of a random base sequence (DNA random) not complementary to the target RNA (and therefore unable to form duplexes), was also unable to elicit RNase H activity.

EXAMPLES 6 Induction of Ribonuclease H (RNAseH) Activity by Oligonucleotides possessing 2-Deoxy-2-Fluoro-p-D- Arabinose as Sugar Component One set of experiments (A) made use of test homopolymeric octadecanucleotides with either thymine (T) or uracil (U) as base component, namely PO-araU18 (SEQ ID NO: 3), PO-2'F-araTl8 (SEQ ID NO: 7), PO-dT18, PS- date, PO-2'F-riboTle, PO-riboUle. The target RNA in experiment set A was a synthetic 3', 5'-phosphodiester- linked rA18 oligonucleotide, exactly complementary to the sequence of the test oligonucleotides.

Another set of experiments (B) made use of test heteropolymeric octadecanucleotides of the following sequence: 5'-TTA TAT TTT TTC TTT CCC-3' (SEQ ID NO: 9) for PO-DNA, PS-DNA and 2'F-ANA oligonucleotides 5'-UUA UAU UUU UUC UUU CCC-3'for ANA (SEQ ID NO: 4) and RNA oligonucleotides

The target RNA in experiment set B was a het- eropolymeric octadecaribonucleotide exactly complemen- tary to the sequence of the test oligonucleotides.

Experiments set (A): The ability of homopolymeric oligonucleotides with 2'-deoxy-2'-fluoro-ß-D-arabinose as sugar compo- nent, and other oligonucleotides, to elicit RNaseH deg- radation of target RNA was determined in assays (10 µL <BR> <BR> <BR> <BR> final volume) that comprised 1 pmol of 5'- [32p] _ target RNA and 8 pmol of test oligonucleotide in 60 mM Tris- HC1 (pH 7.8,25°C) containing 2mM dithiothreitol, 60 mM KCl, and 2.5 mM MgCl2. Reactions were started by the addition of E. coli RNaseH. Incubations were at 22°C for 0,5,10 and 20 minutes. Reactions were quenched by the addition of loading buffer (98% deionized formamide containing 10 mM EDTA and lmg/mL each of bromophenol blue and xylene cyanol, and heating at 100°C for 5 min- utes. The reaction products were resolved by electro- phoresis using a 16% polyacrylamide sequencing gel con- taining 7 M urea, and visualized by autoradiography.

The result of such an experiment is shown in Fig. 6.

Each of the oligonucleotides based on ß-D-2'- deoxyribose with phosphodiester bonds (i. e., PO-dT18, abbreviated as"dT"), P-D-2'-deoxyribose with phos- phorothioate bonds (PS-dT18, or"dT,, thioate"), 2'-deoxy- 2'-fluoro-p-D-arabinose (PO-2'F-araTla SEQ ID NO: 7, or <BR> <BR> <BR> <BR> <BR> "aFT18"), P-D-ribose (PO-rU18, or rU18tt) and 2'-deoxy-2'- fluoro-ß-D-ribose (PO-2'F-rT18, or "rFT18") were able to form duplexes with target RNA (rA18). Only duplexes formed with oligonucleotides"dTlB","dTlBthioate"or "aFTle"served as substrates for the RNase H activity of

either HIV-1 RT or E. coli RNase H, as indicated by the numerous smaller sized degradation products of the tar- get RNA in Fig. 6. Duplexes formed with rFT18 or rU18 could not serve as substrates for the RNase H activity of E. coli RNase H. Under these conditions an octade- canucleotide based on P-D-arabinosyluracil (PO-araU18 <BR> <BR> <BR> <BR> SEQ ID NO: 3, or aUl8SS) was unable to form a duplex with target rA, and accordingly was unable to elicit RNase H activity (these findings are consistent with those reported by Giannaris and Damha, who found that arase was unable to form a duplex with poly rA; Giannaris, P. A.; Damha, M. J., Can. J. Chem. 1994,74,909).

Experiments set (B): Heteropolymeric octadecanucleotides of the sequence 5'-TTA TAT TTT TTC TTT CCC-3' (SEQ ID NO: 9) for PO-DNA, PS-DNA and 2'F-ANA oligonucleotides, and 5'-UUA UAU UUU WC WU CCC-3' (SEQ ID NO: 4) for ANA and <BR> <BR> <BR> <BR> RNA oligonucleotides were annealed to 5'- [32p]-labeled target RNA exactly complementary to the test AON sequence. The ability of heteropolymeric oligonucleo- tides with 2'-deoxy-2'-fluoro-ß-D-arabinose as sugar component, and other oligonucleotides, to elicit RNaseH degradation of target RNA was determined in assays (50 <BR> <BR> <BR> <BR> gL final volume) that comprised 100 nM 5'- [32p] _ target RNA and 500 nM test oligonucleotide in 60 mM Tris-HCl (pH 7.8,25°C) containing 2mM dithiothreitol, 60 mM KC1, and 2.5 mM MgCl2. Reactions were started by the addition of E. coli RNaseH (final activity 25U/ml). RNaseH digestions were carried out at either 25°C or 37°C. At various times, 10 pL aliquots were removed and quenched by the addition of loading buffer (98% deionized form-

amide containing 10 mM EDTA and lmg/mL each of bromo- phenol blue and xylene cyanol) followed by heating at 100°C for 5 minutes. The reaction products were resolved by electrophoresis using a 16% polyacrylamide sequenc- ing gel containing 7 M urea, and visualized by autora- diography. The result of such an experiment is shown in Fig. 7. The susceptibility of pre-formed oligonucleo- tide/RNA duplexes to degradation by E. coli RNaseH was assessed at 37°C (left panel) and 25°C (Fig. 7, right panel). For each test compound, the lanes correspond to the absence (-) or the presence (+) of added E. coli RNaseH.

All heteropolymeric oligonucleotides were able to form duplexes with target RNA (UV melting experi- ments). Oligonucleotides based on ß-D-2'-deoxyribose with phosphodiester bonds (PO-DNA), ß-D-2s-deoxyribose with phosphorothioate bonds (PS-DNA), (3-D-arabinose (ANA, SEQ ID NO: 4) and 2'-deoxy-2'-fluoro-ß-D-arabinose (2'F-ANA, SEQ ID NO: 9) were able to elicit degradation of the complementary target RNA in the presence of E. coli RNaseH, as indicated by the numerous smaller sized degradation products of the target RNA in Fig. 7. Oli- gonucleotides based on P-D-ribose (RNA) could not elicit RNaseH degradation of the target RNA.

EXAMPLE 7 Nuclease Stability of Oligoarabinonucleotides Thymine octadecanucleotides based on 2'-deoxy- ribose with phosphodiester bonds (PO-DNA dT18, abbrevi- ated as"dT") and 2'-deoxy-2'-F-P-D-arabinose (2'F- <BR> <BR> <BR> <BR> ara-A8 SEQ ID NO: 7, or"aFTlB") were compared for stabil- ity against degradation by serum nucleases and cellular

nucleases. The antisense oligonucleotides were radioac- <BR> <BR> <BR> <BR> tively labeled at the 5'-terminus using [7_32p]-ATP and and T4 polynucleotide kinase according to standard pro- tocols (Ausubel, F. M. et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., 1994).

Stability against serum nucleases was assessed <BR> <BR> <BR> <BR> by adding 1 pmol of 5'- [32p]-AON to a reaction assay (10 juL final volume) containing 90% horse serum. Reactions were incubated at 20°C for varying times (0,5,10,15, 20 and 30 min.), then aliquots were removed and diluted with gel loading buffer (98% deionized formamide con- taining 10 mM EDTA and 1 mg/mL each of bromophenol blue and xylene cyanol), boiled for 5 minutes then resolved by electrophoresis on a 16% polyacrylamide sequencing gel containing 7 M urea. Separated products were visu- alized by autoradiography. The results of such an experiment is shown in Fig. 8.

The"aFT18"oligonucleotide (SEQ ID NO: 7) was substantially more resistant to degradation by serum nucleases, as indicated by the decreased number of smaller molecular size degradation products compared to that noted with normal"dT.."oligonucleotide. Qualita- tively similar results were obtained in similar experi- ments in which human serum was substituted for horse serum (data not presented). Under these same condi- tions, oligonucleotides based on P-D-2'-deoxyribose with phosphorothioate bonds (PS-dT18) were virtually unaffected by serum nucleases (data not shown), as pre- viously established by many investigators.

Unfractionated mouse liver crude homogenates (prepared by homogenizing mouse livers in an equal vol-

ume of 20 mM Tris-HCl (pH 7.9,20°C) containing 60 mM KC1,1mM dithiothreitol and 12% (v/v) glycerol) were used as a source of cellular nucleases. Stability against cellular nucleases was assessed by adding 1 <BR> <BR> <BR> <BR> pmol of 5'- 32P]-ODN to a reaction assay (10 pL final volume) containing 90% unfractionated mouse liver crude homogenate. After varying times (0,10,20,30 and 60 min.) of incubation at 20°C, aliquots were removed, diluted with gel loading buffer (98% deionized formam- ide containing 10 mM EDTA, lmg/mL each of bromophenol blue and xylene cyanol), boiled for 5 minutes then resolved by electrophoresis on a 16% polyacrylamide sequencing gel containing 7 M urea. Separated products were visualized by autoradiography. The results estab- lished that the"aFTi,"oligonucleotide was signifi- cantly more resistant than the corresponding"dTle"oli- gonucleotide to degradation by cellular nucleases (data not shown).

Snake venom phosphodiesterase I is an aggres- sive enzyme that rapidly degrades single strand nucleic acids. Each of the oligonucleotides based on P-D-2'- deoxyribose with phosphodiester bonds (PO-DNA date, abbreviated as"dT"), ß-D-2'-deoxyribose with phos- phorothioate bonds (PS-DNA dT18, or dT18 thioate"), P-D- <BR> <BR> <BR> <BR> arabinosyluracil (PO-araU18 SEQ ID NO: 3, or"aUlB"), 2'- deoxy-2'-fluoro-ß-D-arabinose (PO-2'-F-araT18 SEQ ID NO: 7, or"aFTlB"), and 2'-deoxy-2'-fluoro- (3-D-ribose (PO-2'-F-rT18, or"rFTlB") was examined for stability against degradation by snake venom phosphodiesterase I in assays (50 iL final volume) that comprised 100 nM 5'- [³²P]-oligonucleotide in 100 mM Tris-HC1 (pH 8.9,

37°C) containing 100 mM NaCl and 10 mM MgCl2. Reactions were started by the addition of snake venom phosphodi- esterase I (final activity 0.4U/ml). Digestions were carried out at or 37°C. At various times, 10 µl aliquots were removed and quenched by the addition of loading buffer (98% deionized formamide containing 10 mM EDTA and lmg/mL each of bromophenol blue and xylene cyanol) followed by heating at 100°C for 5 minutes. The reaction products were resolved by electrophoresis using a 16% polyacrylamide sequencing gel containing 7 M urea, and visualized by autoradiography. The results of such an experiment is shown in Fig. 9. They established that the order of nuclease stability is"dT,, thioate"> "aUig""aFT"»"rFTig">"dT".

EXAMPLE 8 Nonspecific Interaction of Oligoarabinonucleotides with Cellular Proteins The ability of thymine octadecanucleotides based on P-D-2'-deoxyribose with phosphodiester bonds (PO-DNA dTl8, abbreviated as"dTg"), P-D-2'-deoxyribose with phosphorothioate bonds (PS-DNA dTl8, or"dEl8 thio- ate"), P-D-arabinosyluracil (PO-araUl8 SEQ ID NO: 3, or <BR> <BR> <BR> <BR> "aU18"), 2'-deoxy-2'-fluoro-ß-D-arabinose (PO-2'-F-araT18 SEQ ID NO: 7, or "aFT18"), and 2'-deoxy-2'-fluoro-ß-D- ribose (PO-2'-F-rTl8, or"rFTla") to bind nonspecifically to proteins in a Hela cell crude extract was analyzed by a gel shift assay procedure. The antisense oligonu- cleotides were radioactively labeled at the 5'-terminus using [γ-³²P]-ATP and and T4 polynucleotide kinase according to standard protocols (Ausubel, F. M. et al., Current Protocols in Molecular Biology, John Wiley &

Sons, Inc., 1994). Hela cell crude extracts were pre- pared by homogenizing cells in buffer (20 mM Tris-HC1 (pH 7.9,20°C) containing 60 mM KC1,1mM dithiothreitol and 12% (v/v) glycerol), followed by centrifugation to remove membrane particles and cell debris.

The binding experiments comprised 1 pmol of 5'- 32P-labeled AON and 5 g Hela cell extract protein in a total volume of 20 il comprising 10 mM Tris-HCl (pH 7.5,25°C) containing 100 mM KC1,1 mM MgCl2,1 mM EDTA and 5 % glycerol. AON and Hela cell proteins were incu- bated for 10 min at 25°C, then electrophoresed on 6% non-denaturing gels. Following completion of the elec- trophoresis, the gels were dried and the positions of the free and protein-bound oligonucleotides visualized by autoradiography. The results of such an experiment are shown in Fig. 10.

Essentially all of the phosphorothioate dTl8 thioate"was bound to the extract proteins, as indi- cated by the"smear"of radioactive material throughout the extent of electrophoresis. None of the other antisense oligonucleotides showed any appreciable interaction with Hela cell proteins under the same con- ditions.

EXAMPLE 9 Antisense oligonucleotide inhibition of specific gene expression Antisense oligonucleotides have the potential to inhibit expression of virtually any gene, based on the specific base sequence of the chosen target mRNA.

We examined the ability of antisense oligonucleotides based on P-D-arabinose and 2'-deoxy-2t-fluoro-ß-D-ara-

binose to interfere with the expression of a well-char- acterized marker model, namely expression of the enzyme luciferase, in both in vitro cell-free translation experiments (Fig. 11), and in cells stably transfected with the luciferase gene (Fig. 12).

The ability of oligonucleotides complementary to a specific region of mRNA coding for luciferase was tested for inhibition of luciferase protein expression in an in vitro protein translation system. The specific antisense oligonucleotide sequences were 5'-ATA TCC TTG TCG TAT CCC-3' (SEQ ID NO: 10) for 2'F-ANA, ANA (SEQ ID NO: 5) and the corresponding PO-DNA and PS-DNA strands, which are complementary to bases 1511-1528 of the cod- ing region of the luciferase gene (M. Gossen, H. Bujard 1992, Proc. Natl. Acad. Sci. USA. 89,5547-5551; (M. <BR> <BR> <BR> <BR> <P>Gossen, H. Bujard 1992, Proc. Natl. Acad. Sci. USA. 89, 5547-5551; W. M. Flanagan et al. 1996, Nucl. Acids Res.

24,2936-2941). As a control, randomized oligonucleo- tide sequences (5'-TAA TCC CTA TCG TCG CTT-3' (SEQ ID NO: 17) for 2'F-ANA, ANA, PO-DNA and PS-DNA were used; these are of the same base composition as the specific AON sequence, but have no complementarity to any por- tion of the luciferase gene. Translation reaction assays (15 pl total volume) comprised 0.15 pmol lucif- erase mRNA, 10 ju. 1 commercial rabbit reticulocyte lysate supplemented with complete amino acids mixture and excess single strand RNA ribonuclease inhibitor. To this mixture was added varying amounts (0.1-5 pmol) of specific or random oligonucleotide, followed by addition of E. coli RNaseH (20U/ml final concentra- tion). Translation reactions were carried out for 60

min at 37°C, then the amount of full-length active luciferase produced was assayed by luminometry (W. M.

Flanagan et al 1996, Nucl. Acids Res. 24,2936-2941).

The results of such an experiment are shown in Fig. 11.

Panel (A) shows the inhibitory activity of oligonucleo- tides based on ß-D-2'-deoxyribose with phosphodiester bonds (PO-DNA). Panel (B) shows the inhibitory activity of oligonucleotides based on P-D-2'-deoxyribose with phosphorothioate bonds (PS-DNA) Panel (C) shows the inhibitory activity of oligonucleotides based on 2'- deoxy-2'-fluoro-ß-D-arabinose with phosphodiester bonds (2'F-ANA SEQ ID NO: 10); Panel (D) shows the inhibitory activity of oligonucleotides based on P-D-arabinose with phosphodiester bonds (ANA, SEQ ID NO: 5).

The results (Fig. 11) show that 2'F-ANA and PO- DNA oligonucleotides are potent and specific inhibitors of luciferase gene expression in the in vitro protein expression model, at low AON: mRNA ratios. In these experiments, the in vitro inhibitory potency (ICso) of oligonucleotides based on 2'-deoxy-2'-fluoro-ß-D-arabi- nose with phosphodiester bonds (2'F-ANA SEQ ID NO: 10) is at least four-fold greater than that of the same- sequence oligonucleotide based on ß-D-2'-deoxyribose with phosphorothioate bonds (PS-DNA).

Hela X1/5 cells stably express the luciferase gene (W. M. Flanagan et al 1996, Nucl. Acids Res. 24, 2936-2941). Cells were treated with Lipofectin and oli- gonucleotide (1 (J. M final concentration) for 24h, then cells were harvested and cell extracts were assayed for luciferase activity (Fig. 12, panel A) and toxicity (residual cell protein, Fig. 12, panel B). The chemical

character of the oligonucleotides is indicated on Fig.

12. Specific sequences used are as those described above, namely, 2'F-ANA (SEQ ID NO: 10), ANA (SEQ ID NO: 5) and their corresponding PO-DNA and PS-DNA sequences. Random sequences were 2'F-ANA (SEQ ID NO: 17, ANA and corresponding randomized PO-DNA and PS- DNA sequences..

X1/5 Hela cells were plated in 96-well plates and allowed to grow, in DMEM/10% FBS, to 80% conflu- ence, as assessed by microscopy. The medium was removed, and the cells washed several times with phos- phate-buffered saline. The cells were overlaid with serum-free DMEM medium containing 20 Fg/ml Lipofectin, then a small volume aliquot of concentrated test AON stock solution was added with mixing to ensure good distribution. After 24h incubation, the Hela cells were harvested, homogenized and assayed for luciferase.

Panel A of Fig. 12 shows that PS-DNA (sequence specific) completely eliminated intracellular lucifer- ase gene expression. The 2'F-ANA (SEQ ID NO: 10) and ANA (SEQ ID NO: 5) sequence specific oligomers were also potent inhibitors decreasing intracellular luciferase gene expression by about 40-50%. These data were sig- nificantly different from the PO-DNA control as indi- cated in the Panel A (statistical significance is indi- cated as well). Panel B shows that neither 2'F-ANA or ANA were toxic to Hela cells as determined by effect on cell number (i. e., residual cell protein after 24-h exposure). In contrast, PS-DNA (both random and spe- cific sequences) exhibited significant toxicity reduc- ing cell number by ca. 40% after 24-h exposure.

While the invention has been described in con- nection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any varia- tions, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features set forth hereinbe- fore, and as follows in the scope of the appended claims.