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Title:
NUCLEIC ACID BASE ANALOG WITH QUENCHING CHARACTERISTICS AND FLUORESCENCE AND APPLICATION THEREOF
Document Type and Number:
WIPO Patent Application WO/2011/132801
Kind Code:
A1
Abstract:
Disclosed is a nucleic acid base analog with quenching characteristics and fluorescence and application thereof. Specifically disclosed is a quencher characterized by having a 2-nitropyrrole structure shown by formula (I). [In formula (I), R1 and R2 are groups selected independently from a group formed from ribose and deoxyribose; hydrogen, hydroxyl groups, SH groups, and halogens; optionally substituted C2-10 alkyl groups, alkenyl groups, and alkynyl groups; one or a plurality of 5-member heterocycles, one or a plurality of 6-member heterocycles, one or a plurality of polycyclic heterocycles and one or a plurality of aromatic rings, containing nitrogen atoms or sulfur atoms; sugars, sugar chains, amino acids, and peptides; and florescent molecules bound through linkers.]

Inventors:
HIRAO ICHIRO (JP)
HIRAO MICHIKO (JP)
YOKOYAMA SHIGEYUKI (JP)
MITSUI TSUNEO (JP)
YAMASHIGE RIE (JP)
Application Number:
PCT/JP2011/060343
Publication Date:
October 27, 2011
Filing Date:
April 21, 2011
Export Citation:
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Assignee:
RIKEN (JP)
TAGCYX BIOTECHNOLOGIES (JP)
HIRAO ICHIRO (JP)
HIRAO MICHIKO (JP)
YOKOYAMA SHIGEYUKI (JP)
MITSUI TSUNEO (JP)
YAMASHIGE RIE (JP)
International Classes:
C12N15/09; C07H19/044; C07H19/073; C12Q1/68; G01N33/53; G01N33/542
Domestic Patent References:
WO2009123216A12009-10-08
Foreign References:
JP2004506431A2004-03-04
JP2009232776A2009-10-15
JP2007061087A2007-03-15
JP2009232851A2009-10-15
Other References:
ICHIRO HIRAO ET AL.: "An Efficient Unnatural Base Pair for PCR Amplification", JACS, vol. 129, 2007, pages 15549 - 15555, XP008145067
MICHIKO KIMOTO ET AL.: "Site-specific incorporation of functional components into RNA by transcription using unnatural base pair systems", NUCLEIC ACIDS SYMPOSIUM SERIES, no. 53, 2009, pages 73 - 74, XP008161979
MICHIKO KIMOTO ET AL.: "A Unique Fluorescent Base Analogue for the Expansion of the Genetic Alphabet", JACS, vol. 132, 24 March 2010 (2010-03-24), pages 4988 - 4989, XP008159272
LAIBIN ZHANG ET AL.: "Absorption and Fluorescence Emission Spectroscopic Characters of Size-Expanded yDNA Bases and Effect of Deoxyribose and Base Pairing", J.PYS.CHEM.B, vol. 113, 2009, pages 1173 - 1181, XP008161980
HAIBO LIU ET AL.: "Size-Expanded Analogues of dG and dC:Synthesis and Pairing Properties in DNA", J. ORG.CHEM., vol. 70, 2005, pages 639 - 647, XP008143019
CHANG ZHAO ET AL.: "Synthesis of HIV-1 T-site RNA sequences with site specific incorporation of the fluorescent base analog 2-aminopurine", TETRAHEDRON, vol. 63, 2007, pages 3575 - 3584, XP005929589
MICHIKO KIMOTO ET AL.: "A New Unnatural Base Pair System between Fluorophore and Quencher Base Analogues for Nucleic Acid-Based Imaging Technology", JACS, vol. 132, 12 October 2010 (2010-10-12), pages 15418 - 15426, XP055052833
I. HIRAO; T. MITSUI; M. KIMOTO; S. YOKOYAMA, J. AM. CHEM. SOC., vol. 129, 2007, pages 15549 - 15555
M. KIMOTO; R. KAWAI; T. MITSUI; S. YOKOYAMA; I. HIRAO: "An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules", NUCLEIC ACIDS RES., vol. 37, 2009, pages EL4
T. MITSUI; M. KIMOTO; R. KAWAI; S. YOKOYAMA; I. HIRAO: "Characterization of fluorescent, unnatural base pairs", TETRAHEDRON, vol. 63, 2007, pages 3528 - 3537, XP005929584, DOI: doi:10.1016/j.tet.2006.11.096
M. KIMOTO; T. MITSUI; Y. HARADA; A. SATO; S. YOKOYAMA; I. HIRAO: "Fluorescent probing for RNA molecules by an unnatural base-pair system,", NUCLEIC ACIDS RES., vol. 35, 2007, pages 5360 - 5369, XP008159271, DOI: doi:10.1093/nar/gkm508
D. LOAKES; D. W. BROWN; S. LINDE; F. HILL: "3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR", NUCLEIC ACIDS RES., vol. 23, 1995, pages 2361 - 2366, XP002109690
I. HIRAO; M. KIMOTO; T. MITSUI; T. FUJIWARA; R. KAWAI; SATO, Y. HARADA; S. YOKOYAMA: "An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA", NATURE METHODS, vol. 3, 2006, pages 729 - 735
J. AM. CHEM. SOC., vol. 132, 2010, pages 4988 - 4989
I. HIRAO; M. KIMOTO; T. MITSUI; T. FUJIWARA; R. KAWAI; A. SATO; Y. HARADA; S. YOKOYAMA: "An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA.", NATURE METHODS, vol. 3, 2006, pages 729 - 735
M. KIMOTO; R. KAWAI; T. MITSUI; S. YOKOYAMA; I. HIRAO: "An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules. M", NUCLEIC ACIDS RES., vol. 37, 2009, pages E14
KIMOTO, M.; YOKOYAMA, S.; HIRAO, I., BIOTECHNOL. LETT., vol. 26, 2004, pages 999 - 1005
PETRUSKA, J.; GOODMAN, M. F.; BOOSALIS, M. S.; SOWERS, L. C.; CHEONG, C.; TINOCO, I., PROC. NATL. ACAD. SCI. USA, vol. 85, 1988, pages 6252 - 6256
GOODMAN, M. F.; CREIGHTON, S.; BLOOM, L. B.; PETRUSKA, J., CRIT. REV. BIOCHEM. MOL. BIOL., vol. 28, 1993, pages 83 - 126
MORALES, J. C.; KOOL, E. T., NAT. STRUCT. BIOL., vol. 5, 1998, pages 950 - 954
See also references of EP 2562255A4
Attorney, Agent or Firm:
ONO, Shinjiro et al. (JP)
Ono Shinjiro (JP)
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