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)
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:
Assignee:
RIKEN (JP)
TAGCYX BIOTECHNOLOGIES (JP)
HIRAO ICHIRO (JP)
HIRAO MICHIKO (JP)
YOKOYAMA SHIGEYUKI (JP)
MITSUI TSUNEO (JP)
YAMASHIGE RIE (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:
WO2009123216A1 | 2009-10-08 |
Foreign References:
JP2004506431A | 2004-03-04 | |||
JP2009232776A | 2009-10-15 | |||
JP2007061087A | 2007-03-15 | |||
JP2009232851A | 2009-10-15 |
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
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)
Ono Shinjiro (JP)
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