3′-OH unblocked, nucleotides and nucleosides, base...

Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C536S025320, C536S026100, C536S026200

Reexamination Certificate

active

07897737

ABSTRACT:
Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3′-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.

REFERENCES:
patent: 4318846 (1982-03-01), Khanna et al.
patent: 4439356 (1984-03-01), Khanna et al.
patent: 4657897 (1987-04-01), Bristol et al.
patent: 4704381 (1987-11-01), Schaumann et al.
patent: 5151507 (1992-09-01), Hobbs, Jr. et al.
patent: 5188934 (1993-02-01), Menchen et al.
patent: 5614386 (1997-03-01), Metzker et al.
patent: 5684142 (1997-11-01), Mishra et al.
patent: 5728529 (1998-03-01), Metzker et al.
patent: 5763594 (1998-06-01), Hiatt et al.
patent: 5773423 (1998-06-01), Jacobson et al.
patent: 5808045 (1998-09-01), Hiatt et al.
patent: 5861287 (1999-01-01), Metzker et al.
patent: 5872244 (1999-02-01), Hiatt et al.
patent: 5994063 (1999-11-01), Metzker et al.
patent: 6214987 (2001-04-01), Hiatt et al.
patent: 6664079 (2003-12-01), Ju et al.
patent: 6762048 (2004-07-01), Williams
patent: 6818395 (2004-11-01), Quake et al.
patent: 6833246 (2004-12-01), Balasubramanian
patent: 6869764 (2005-03-01), Williams et al.
patent: 6995841 (2006-02-01), Scott et al.
patent: 7125660 (2006-10-01), Stanton et al.
patent: 7355036 (2008-04-01), Guimil et al.
patent: 7476734 (2009-01-01), Liu
patent: 2003/0180769 (2003-09-01), Metzker
patent: 2004/0014096 (2004-01-01), Anderson et al.
patent: 2005/0048601 (2005-03-01), Dellinger et al.
patent: 2005/0049407 (2005-03-01), Dellinger et al.
patent: 2005/0049411 (2005-03-01), Dellinger et al.
patent: 2008/0131952 (2008-06-01), Wu et al.
patent: 2009/0081686 (2009-03-01), Wu et al.
patent: 0 272 007 (1988-06-01), None
patent: 0 866 071 (1998-09-01), None
patent: WO91/05060 (1991-04-01), None
patent: WO97/000967 (1997-01-01), None
patent: WO 97/00967 (1997-01-01), None
patent: WO 03/021212 (2003-03-01), None
patent: WO 2004/018497 (2004-03-01), None
patent: WO2004/058791 (2004-07-01), None
Seo et al., Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry, pp. 5488-5493—PNAS—Apr. 13, 2004—vol. 101—No. 15.
Adzamli et al., “Development of phosphonate derivatives of gadolinium chelates for NMR imaging of calcified soft tissues,”J. Med. Chem., 32(1):139-144, 1989.
Bartholomew and Broom, “One-step chemical synthesis of ribonucleosides bearing a photolabile ether protecting group,”J. Chem. Soc. Chem. Commun., 38, 1975.
Berlier et al. “Quantitative comparison of long-wavelength alexa fluor dyes to cy dyes: fluorescence of the dyes and their bioconjugates,”The Journal of Histochemistry&Cytochemistry, 51(12):1699-1712, 2003.
Brandis, “Dye structure affectsTaqDNA polymerase terminator selectivity,”Nucleic Acids Research, 27(8):1912-1918, 1999.
Chaulk and MacMillan, “Caged RNA: photo-control of a ribozyme reaction,”Nucleic Acids Res., 26:3173-3178, 1998.
Dewey et al., “New uridine derivatives for systematic evolution of RNA ligands by exponential enrichment,”J. Am. Chem. Soc., 117:8474-8475, 1995.
Gardner and Jack, “Acyclic and dideoxy terminator preferences denote divergent sugar recognition by archaaeon andTaqDNA polymerases,”Nucleic Acids Research, 30(2):605-613, 2002.
Gardner and Jack, “Determinants of nucleotide sugar recognition in an archaeon DNA polymerase,”Nucleic Acids Research, 27(12):2545-2553, 1999.
Gebeyehu et al., “Novel biotinylated nucleotide—analogs for labeling and colorimetric detection of DNA,”Nucleic Acids Research, 15(11):4513-4534, 1987.
Gibbs, “Identification of mutations leading to the Lesch-Nyhan syndrome by automated direct DNA sequencing of in vitro amplified cDNA,”Proc. Natl. Acad. Sci. USA, 86:1919-1923, 1989.
Gommers-Ampt and Borst, “Hypermodified bases in DNA,”FASEB J., 9(11):1034-1042, 1995.
Hampton et al., “Species- or isozyme-specific enzyme inhibitors. 4. Design of a two-site inhibitor of adenylate kinase with isozyme selectivity,”J. Med. Chem., 25:638-644, 1982.
International Search Report issued in International Application No. PCT/US07/86559, mailed Aug. 21, 2008.
Ju et al., “Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis,”Proc. Natl. Acad. Sci USA, 92:4347-4351, 1995.
Kahl and Greenberg, “Introducing structural diversity in oligonucleotides via photolabile, convertible C5-substituted nucleotides,”Journal of the American Chemical Society, 121(4):597-604, 1999.
Kong et al., “Characterization of a DNA polymerase from the hyperthermophile archaeaThermococcus litoralis,” The Journal of Biological Chemistry, 268(3):1965-1975, 1993.
Kornher and Livak, “Mutation detection using nucleotide analogs that alter electrophoretic mobility,”Nucleic Acids Research, 17(19):7779-7784, 1989.
Kulikowski et al., “Structure-activity relationships and conformational features of antiherpetic pyrimidine and purine analogues. A review,”Pharmacy World&Science, 16(2):127-138, 1994.
Lee et al., “New energy transfer dyes for DNA sequencing,”Nucleic Acids Research, 25(14):2816-2822, 1997.
Lewis et al., “Color-blind fluorescence detection for four-color DNA sequencing,”PNAS, 102(15):5346-5351, 2005.
Malecki et al., “Mutations in NEUROD1 are associated with the development of type 2 diabetes mellitus,”Nature Genetics, 23:323-328, 1999.
McMinn and Greenberg, “Novel solid phase synthesis supports for the preparation of oligonucleotides containing 3′-alkyl amines,”Tetrahedron, 52(11):3827-3840, 1996.
Metzker et al., “Electrophoretically uniform fluorescent dyes for automated DNA sequencing,”Science, 271:1420-1422, 1996.
Metzker et al., “Elimination of residual natural nucleotides from 3′-O-modified-dNTP syntheses by enzymatic mop-up,”BioTechniques, 25:814-817, 1998.
Metzker et al., “Emerging technologies in DNA sequencing,”Genome Research, 15:1767-1776, 2005.
Metzker et al., “Termination of DNA synthesis by novel 3′-modified-deoxyribonucleoside 5′-triphosphates,”Nucleic Acids Res., 22:4259-4267, 1994.
Molecular Probes™ invitrogen detection technologies, “Alexa Fluor® Dyes—Simply the Best and Brightest, Fluorescent dyes and conjugates,” 2005.
Office Action issued in U.S. Appl. No. 11/567,193, mailed Nov. 24, 2008.
Office Action issued in U.S. Appl. No. 11/567,193, mailed Sep. 26, 2008.
Ohtsuka et al., “Studies on transfer ribonucleic acids and related compounds. IX. Ribooligonucleotide synthesis using a photosensitive o-nitrobenzyl protection at the 2′-hydroxyl group,”Nucleic Acids Res., 1:1351-1357, 1974.
Panchuk-Voloshina et al., “Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates,”The Journal of Histochemistry&Cytochemistry, 47(9):1179-1188, 1999.
Pease et al., “Light-generated oligonucleotide arrays for rapid DNA sequence analysis,”Proc. Natl. Acad. Sci. USA, 91:5022-5026, 1994.
Perler et al., “Intervening sequences in an A

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

3′-OH unblocked, nucleotides and nucleosides, base... does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with 3′-OH unblocked, nucleotides and nucleosides, base..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and 3′-OH unblocked, nucleotides and nucleosides, base... will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-2746076

All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.