Identifying organisms by detecting intronic nucleic acid or...

Details Identifying organisms by detecting intronic nucleic acid or... Identifying organisms by detecting intronic nucleic acid or...

2006-11-27

2010-10-19

Horlick, Kenneth R. (Department: 1637)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S091200, C536S024300, C536S024330

Reexamination Certificate

active

07816080

ABSTRACT:
The present invention provides novel methods for characterizing organisms by identifying the presence, absence, size or sequence polymorphism of intronic regions. The method involves selecting intronic regions from nuclear or organellar gene sequences that are useful for differentiating between and among taxonomic groupings of organisms. Such intronic regions can be analyzed directly or after amplification in a primer extension reaction. The amplification product is then analyzed by, for example, size fractionation, nucleotide sequencing or (RFLP). Intronic regions that contain an open reading frame encoding all or a portion of a protein can be used to generate antibodies to detect the presence or absence of the protein, which indicates the presence or absence of the intronic region. Methods of detecting an organism in a sample by detecting the presence or absence of one or more intronic regions also are provided using nucleic acid based or immunological based approaches. Kits are provided for practicing the methods of the invention.

REFERENCES:
patent: 4458066 (1984-07-01), Caruthers et al.
patent: 4683192 (1987-07-01), Nishiyama
patent: 4683202 (1987-07-01), Mullis
patent: 4800159 (1989-01-01), Mullis et al.
patent: 4889818 (1989-12-01), Gelfand et al.
patent: 4965188 (1990-10-01), Mullis et al.
patent: 5250203 (1993-10-01), Denis et al.
patent: 5545525 (1996-08-01), Montplaisir et al.
patent: 5707802 (1998-01-01), Sandhu et al.
patent: 5763169 (1998-06-01), Sandhu et al.
patent: 5795731 (1998-08-01), Belfort
patent: 5824673 (1998-10-01), Abrams et al.
patent: 5849484 (1998-12-01), Leibowitz et al.
patent: 5849492 (1998-12-01), Rogan
patent: 5874281 (1999-02-01), Dattagupta et al.
patent: 5900406 (1999-05-01), Von Ahsen
patent: 5958693 (1999-09-01), Sandhu et al.
patent: 6007989 (1999-12-01), West et al.
patent: 6156730 (2000-12-01), Little et al.
patent: 0545350 (1992-12-01), None
patent: 2310718 (1997-09-01), None
patent: WO 89/07142 (1989-08-01), None
patent: WO 00/03037 (2000-01-01), None
patent: WO 00/67580 (2000-11-01), None
patent: WO 00/68420 (2000-11-01), None
patent: WO 00/75305 (2000-12-01), None
Fulton et al.,FEMS Microbiology Letters, 157:307-312 (1997).
Garbelotto et al.,Can. J. Bot., 71:565-569 (1993).
Glass et al.,Applied and Environmental Microbiol. 61(4):1323-1330 (1995).
Goldman et al.,Electrophoresis, 3:24-26 (1982).
Gonzalez et al.,Gene, 220:45-53 (1998).
Haase et al.,J. of Clinical Microbiology, 34(8):2049-2050 (1996).
Harlow et al., (1988).In: Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Ch. 9 and Ch. 14.
Hebbar et al.,Nuc. Acids Res., 20(7):1747-1754 (1992).
Heisel et al.,Proc. Natl. Acad. Sci. USA, 91:634-638 (1993).
Henderson et al.,Clin. Chem., 32(9):1637-41 (1986).
Henke et al.,The EMBO J., 14(20):5094-5099 (1995).
Ho et al.,J. Mol. Biol., 292:987-1001 (1999).
Ho et al.,Proc. Natl. Acad. Sci. (USA), 94:8994-8999 (1997).
Holland et al.,Proc. Natl. Acad. Sci(USA), 88:7276-7280 (1991).
Holst-Jensen et al.,Mol. Biol. Evol., 16(1):114-126 (1999).
Honeycutt et al.,Anal. Biochem., 248:303-306 (1997).
Hur et al.,Curr. Genet., 32:399-407 (1997).
Huse et al.,Science, 246:1275-1281 (1989).
Ieven et al.,Clin. Microb. Rev., 10(2):242-256 (1997).
Jacq. et al.,EMBO J. 3:1567-1572 (1984).
Johansen,DNA Sequence—J. DNA Sequencing and Mapping, 2:193-196 (1991).
Jurica et al.,Cell. Mol. Life Sci., 55:1304-1326 (1999).
Knott, (1989)In: The Wheat Rusts—Breeding for Resistance, Springer-Verlang, NY, pp. 1-37.
Kreuzinger et al.,Applied and Environmental Microb., 62(9):3432-3438 (1996).
Lai et al.,Systematic Botany, 22(3):519-528 (1997).
Lazowska et al.,Cell, 22:333-348 (1980).
Li et al.,Curr. Genet., 22:69-74 (1992).
Liu et al.,J. Euk. Microb., 41(1):31-38 (1994).
Liu et al.,Nuc. Acids Res., 23(8):1284-1291 (1995).
Liu et al.,Nuc. Acids Res., 21(10):2415-2421 (1993).
Loffler et al.,QIAGEN News, 4:16-17 (1996).
MacDonald et al.,Plant Disease, 74:655-659 (1990).
MacLean et al.,Adv. Plant Path., 10:207-244 (1993).
Makimura et al.,J. Med. Microb., 40:358-364 (1994).
Manulis et al.,Phytopath., 84:98-101 (1994).
Marshall,Electrophoresis, 4:269-272 (1983).
McCullough et al.,J. of Clin. Microbiology, 37(2):417-421 (1998).
Mei et al.,Nuc. Acids Res. 24(24):5051-5053 (1996).
Mercure et al.,Nuc. Acids Res., 21(25):6020-6027 (1993).
Mercure et al.,Nuc. Acids Res., 25(2):431-437 (1997).
Michel et al.,Annu. Rev. Biochem., 64:435-461 (1995).
Miller et al.,Phytopath., 78:1516 (1998).
Mueller et al.,Histochem. Cell Biol., 108:431-437 (1997).
Müller et al.,J. Clin. Microb., 36(6):1625-1629(1998).
Neuveglise et al.,Molecular Ecology, 6:373-381 (1997).
Narang et al.,Meth. Enzymol., 68:90(1979).
Oellerich,J. Clin. Chem. Clin. Biochem., 18:197-208 (1980).
Paquin et al.,Curr. Genet., 31:380-395(1997).
Perlman et al., (1990).In: Intervening Sequences in Evolution and Development, E.M. Stone and R.J. Schwartz, eds., Oxford Univ. Press, New York, p. 112-161.
Qlu et al.,Nature, 394:671-674 (1998).
Reddy et al.,Mol. Cell Probes, 7:121-126 (1993).
Rigby et al.,J. Mol. Biol., 113:237 (1977).
Rogers et al.,Nuc. Acids Res., 22(23):4983-4988 (1994).
Rubenstein,Biochem. Biophys. Res. Comm., 47(4):846-851 (1972).
Saldahna et al.Biochem., 38:9069-9083 (1999).
Sambrook et al., (1989).In: Nucleic Acid Electrophoresis, D. Teitz, ed., Springer Verlag, New York, 11.21-11.44; 14.22-14.29.
Schafer et al.Curr. Genet., 35:602-608 (1999).
Sellem et al.,Mol. Evol. Biol., 14:518-526 (1997).
Smith et al.,Genome Res., 6:454-462 (1996).
Suh et al.,J. Mol. Evol., 48:493-500 (1999).
Swaminathan et al., (1993)In: Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C., pp. 26-50.
Tan,J. Mol. Evol., 44:637-645 (1997).
Tang et al.,Clin. Chem., 43:2021-2038 (1997).
Tanner et al.,J. Mol. Biol., 252:583-595 (1995).
Tegelstrom,Electrophoresis, 7:226-229 (1986).
Testa et al.,Proc. Natl. Acad. Sci., USA, 96:2734-2739 (1999).
Urdea et al.,Nucleic Acids Symp. Ser., 24:197-200 (1991).
Van Belkum et al.,Clin. Infect. Dis., 18:1017-1019 (1994).
Verweij et al.,J. Clin. Pathol.., 48:474-476 (1995).
Walker et al.,Nucleic Acids Res., 20(7):1691-1696 (1992).
Wang et al.,Medical Mycology, 36(3):153-164 (1998).
Wank et al.Mol. Cell, 4:239-250 (1999).
Waring et al.,Gene, 28:277-291 (1984).
Wisdom,Clin. Chem., 22(8):1243-1255 (1976).
Yamakami et al.,J. Clin. Microbiol., 34(10):2464-2468 (1996).
Zambino et al.,Proc. Finnish Forest Res. Instit., 712:297-198 (1998).
Allen et al.,BioTechniques, 7:736-744 (1989).
Ausubel et al., (1994)In: Current Protocols in Molecular Biology, John Wiley & Sons, Inc., New York, pp. 13.11.1-13.11.4.
Ausubel et al., (1997)In: Short Protocols in Molecular Biology, 3rdEd., John Wiley & Sons, Inc., New York, pp. 15-32.
Barany et al.,PCR Meth. Applic., 1:15-16 (1991).
Beaucage et al.,Tetrahedron Letters, 22:1859-1962 (1981).
Belcour et al.,Curr. Genet., 31:308-317 (1997).
Belfort et al.,Nuc. Acid Res., 25:3379-3388 (1997).
Berres et al.,Mycologia, 87:821-840 (1995).
Boerwinkle et al.,Proc. Natl. Acad. Sci., USA, 86:212-216 (1989).
Boucher et al.,Gene, 180:189-196 (1996).
Bretagne et al.,J. Clin. Microbiol., 33(5):1164-1168 (1995).
Brown,In: Evolution of Genes and Proteins, Masatoshi et al., eds., Sinauer Associates, Inc., Mass., pp. 63-88 (1983).
Brown et al.,J. Mol. Evol., 18:225-239 (1982).
Brown et al.,Meth. Enzymol., 68:109 (1979).
Castellino et al.Biochem., 7(6):2207-2217 (1968).
Cech,Annu. Rev. Biochem., 59:543-568 (1990).
Caruthers,Science, 230:281-285 (1985).
Dalgaard et al.,Nuc. Acids Res., 35:4626-4638 (1997).
Dandliker et al.,J. Exp. Med., 122:1029-1048 (1965).
Denhardt,Biochem. Biophys. Res. Commun., 23:641-646 (1966).
Descenzo et al.,Phytopath., 84:534-540 (1994).
Doetsch, et al.,Mol. Biol. Evol., 15(1):76-86 (1998).
Donnelly et al.,Microbiology, 145:1871-1882 (1999).
Du Jardin, et al.,Curr. Genet., 25:158-163 (1994).
Ehrict et al.,Eur. J. Biochem., 243:358-364 (1997).
Einsele et al.,J. Clin. Microbiol., 35(6):1353-1360 (1997).
Everett et al.,J. of Bacteriology, pp. 4734-4740 (1999).
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