RNA labeling method

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

Reexamination Certificate

active

07541144

ABSTRACT:
Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled substrate to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.

REFERENCES:
patent: 4661450 (1987-04-01), Kempe et al.
patent: 5346994 (1994-09-01), Chomczynski
patent: 5573913 (1996-11-01), Rosemeyer et al.
patent: 5659025 (1997-08-01), Engels et al.
patent: 5665549 (1997-09-01), Pinkel et al.
patent: 5721436 (1998-02-01), Boeve et al.
patent: 5763870 (1998-06-01), Sadler et al.
patent: 5830645 (1998-11-01), Pinkel et al.
patent: 5945679 (1999-08-01), Dorsel et al.
patent: 5948902 (1999-09-01), Honkanen et al.
patent: 5985567 (1999-11-01), Rampal
patent: 6197501 (2001-03-01), Cremer et al.
patent: 6218142 (2001-04-01), Wassenegger et al.
patent: 6221853 (2001-04-01), Salsarulo et al.
patent: 6248535 (2001-06-01), Danenberg et al.
patent: 6335167 (2002-01-01), Pinkel et al.
patent: 6344316 (2002-02-01), Lockhart et al.
patent: 6406849 (2002-06-01), Dorsel et al.
patent: 6579707 (2003-06-01), Fitzgerald et al.
patent: 6992180 (2006-01-01), Engelhardt et al.
patent: 2001/0014446 (2001-08-01), Heroux et al.
patent: 2002/0197621 (2002-12-01), Drmanac
patent: 2003/0190661 (2003-10-01), Gruber et al.
patent: 2006/0160096 (2006-07-01), Cole et al.
patent: 2006/0172317 (2006-08-01), Wang
patent: 2007/0026411 (2007-02-01), Wang
patent: 2008/0272006 (2008-11-01), Gao
patent: WO 94/12518 (1994-06-01), None
patent: WO 9727317 (1997-07-01), None
patent: WO2005/054466 (2005-06-01), None
Bruce et al. (“Reactions at the termini of tRNA with T4 RNA ligase” Nucleic Acids Res. Oct. 1978;5(10):3665-77).
Romaniuk et al. (“Joining of RNA molecules with RNA ligase” Methods Enzymol. 1983;100:52-9).
Bare et al. (Specific substitution into the anticodon loop of yeast tyrosine transfer RNA. Biochemistry. Sep. 23, 1986;25(19):5825-30).
Bruce et al. (“Reactions at the termini of tRNA with T4 RNA ligase” Nucleic Acids Res. Oct. 1978;5(10):3665-77) in view of Engles et al. (U.S. 5,659,025).
Richardson et al. (“Biotin and fluorescent labeling of RNA using T4 RNA ligase” Nucleic Acids Res. Sep. 24, 1983;11(18):6167-84).
Cobianchi et al. (“Enzymes for modifying and labeling DNA and RNA” Methods Enzymol 1987;152:94-110) in view of Romaniuk et al. (“Joining of RNA molecules with RNA ligase” Methods Enzymol. 1983;100:52-9).
Romaniuk et al. (“Joining of RNA molecules with RNA ligase” Methods Enzymol. 1983;100:52-9).
Bare et al. (Specific substitution into the anticodon loop of yeast tyrosine transfer RNA. Biochemistry. Sep. 23, 1986;25(19):5825-30).
A. Gregory Bruce and Olke Uhlenbeck, “Reactions at the termini of tRNA with T4 RNA ligase”, Nucleic Acids Research, vol. 5, No. 10, Oct. 1978, pp. 3665-3677.
Ross W. Richardson, et al., “Biotin and fluorescent labeling RNA using T4 RNA Ligase”, Nucleic Acids Research, vol. 11, No. 18, 1983, pp. 6167-6184.
Thomas E. England, et al., “3′-Terminal Labelling of RNA with T4 RNA Ligase”, Nature vol. 275, Oct. 12, 1978, pp. 560-561.
Kyle Cole, et al., “Direct Labeling of RNA with Multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes”, Nucleic Acids Research, vol. 32, No. 11, pp. 1-9.
Patents Act 1977: Search Report under Section 17(5); Date of Search: Jul. 18, 2006.
Ularich Lehmann and Hans Kreipe.Real-time PCR analysis of DNA and RNA Extracted from Formalin-fixed and Praffin-Embedded Biopsies, Real-Time PCR and Archival Biopsies, A Companion to Methods in Enzymology, Academic Press Inc., NY, NY, US vol. 25, No. 4, Dec. 2001 pp. 409-412, XP00230656.
Richard Cosstick, et al., “Fluorescent labeling of tRNA and oligodeoxynucleotides using T4 RNA ligase”, Nucleic Acids Research, vol. 12, No. 4, 1984, pp. 1791-1810.
Jorge R. Barrio, et al., “Synthesis of Modified Nucleoside 3′, 5′—Bisphosphates and their Incorporation into Oligoribonucleotides with T4 RNA Ligase”, Modified Oligoribonucleotides, vol. 17, No. 11, 1978 pp. 2077-2081.
Wang, H., et al., “Direct and sensitive miRna profiling from low-input total RNA”, vol. 13, Nov. 14, 2006, pp. 1-9, XP002408565.
European Search Report EP 06 25 3554 dated Nov. 28, 2006.
Kyle Cole, et al., “Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes”, Nucleic Research, vol. 32, No. 11 Oxford University Press 2004; pp. 1-9.
Volker Lohman, et al.; “Mutations in Hepatitis C virus RNAs Conferring Cell Culture Adaptation”, Journal of Virology, Vo. 75, No. 3, Feb. 2001, pp. 1437-1449.
Ross W. Richardson, et al., “Biotin and fluorescent labeling of RNA using T4 RNA ligase”, Nucleic Acids Research, vol. 11, No. 18, 1983, pp. 6167-6184.
Thomas E. England, et al., Enzymatic Oligoribonucleotide Synthesis with T4 RNA Ligase, American Chemical Society and reprinted by permission of the copyright owner, Reprinted from Biochemistry, 1978 pp. 2070-2076.
Finke et al., “An improved strategy and a useful housekeeping gene for RNA analysis from formalin-fixed, paraffin-embedded tissues by PCR,” Biotechniques, Mar. 1993, vol. 14, No. 3, pp. 448-453.
Sundberg, Steven A. et al., “Microchip-based systems for target validation and HTS”, Drug Discovery Today, 2000, S92-S103, vol. 5, No. 12 (Suppl).
Kurata, Shinya et al., “Quick two-step RNA ligation empolying periodate oxidation”, Nucleic Acids Research, 2003, 6 pages, vol. 31, No. 22, e145.
Babak, T., et al. Probing microRNAs with microarrays: Tissue specificity and functional interference. RNA. 2004, vol. 10, pp. 1813-1819.
Cole, K., et al. Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes. Nucleic Acids Research. 2004, vol. 32, No. 11, pp. e86.
Dostie, J., et al. Numerous microRNPs in neuronal cells containing novel microRNAs. RNA. 2003, vol. 9, pp. 180-186.
Griffiths-Jones, S. The microRNA registry. Nucleic Acids Research. 2004, vol. 32, pp. D109-D111.
Kim, J., et al., Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. PNAS. 2004, vol. 101, No. 1, pp. 360-365.
Kurata, S., et al. Quick two-step RNA ligation employing periodate oxidation. Nucleic Acids Research. 2003, vol. 31, No. 22, pp. e145.
Lagos-Quintana, M., et al. New microRNAs from mouse and human. RNA. 2003, vol. 9, pp. 175-179.
Liang, R., et al. An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Research. 2005, vol. 33, No. 2, pp. e17. Epub Jan. 31, 2005.
Liu, C., et al. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. PNAS. 2004, vol. 101, No. 26, pp. 9740-9744.
McLaughlin, L.W., et al. Donor activation in the T4 RNA ligase reaction. Biochemistry. 1985, vol. 24, pp. 267-273.
Michael, M., et al. Reduced accumulation of specific microRNAs in colorectal neoplasia. Molecular Cancer Research. 2003, vol. 1, pp. 882-891.
Middleton, T., et al. Synthesis and purification of oligoribonucleotides using T4 RNA ligase and reverse-phase chromatography. Analytical Biochemistry. 1985, vol. 144, pp. 110-117.
Nelson, P., et al. Microarray-based, high-throughput gene expression profiling of microRNAs. Nature Methods. 2004, vol. 1, No. 2, pp. 155-161.
Ohtsuka, E., et al. Comparison of substrate base sequences for RNA ligase reactions in the synthesis of a tetradecanucleotide corresponding to bases 21-34 ofE. colitRNAfMet 1. Nucleic Acids Research. 1980, vol. 8, No. 17, pp. 3909-3916.
Tessier, D., et al. Ligation of single-stranded oligodeoxyribonucleotides by T4 RNA ligase. Analytical Biochemistry. 1986, vol. 158, pp. 171-178.
Thomson, J.M., et al. A custom microarray platform for analysis of microRNA gene expression. Nature Methods. 200

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

RNA labeling method does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with RNA labeling method, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and RNA labeling method will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-4110526

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