Fluorescent detection and isolation of DNA variants using stabilized recA-coated oligonucleotides

Genome Research

Volumn 14, Issue 1, 2004, Pages 116-125

  Rice, Michael C ^a   Heckman, Brandy M ^a   Liu, Yi ^b   Kmiec, Eric B ^a  

^a UNIVERSITY OF DELAWARE   (United States)

^b NaPro Genomics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; RECA PROTEIN;

ARTICLE; CATALYSIS; CHEMICAL MODIFICATION; CONTROLLED STUDY; DISSOCIATION; DNA HYBRIDIZATION; DNA ISOLATION; DNA PURIFICATION; DNA STRAND; FLUORESCENCE ANALYSIS; GENE TARGETING; GENETIC PROCEDURES; GENETIC VARIABILITY; HAPLOTYPE; MOLECULAR STABILITY; OLIGONUCLEOTIDE PROBE; PHARMACOGENOMICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA REPAIR; DNA, BACTERIAL; DNA, CIRCULAR; FLUORESCENT DYES; NANOTECHNOLOGY; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACIDS; OLIGONUCLEOTIDES; POLYMORPHISM, SINGLE NUCLEOTIDE; REC A RECOMBINASES; SEQUENCE ANALYSIS, DNA; STAINING AND LABELING; TEMPERATURE; VARIATION (GENETICS);

EID: 0347765999     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1386204     Document Type: Article

References (24)

1. Brachman, E.E. and Kmiec, E.B. 2002. The 'biased' evolution of targeted gene repair. Curr. Opin. Mol. Ther. 4: 171-176.
2. Burkardt, H.J. 2000. Standardization and quality control of PCR analyses. Clin. Chem. Lab Med. 38: 87-91.
3. Cunningham, R.P., Shibata, T., DasGupta, C., and Radding, C.M. 1979. Single strands induce recA protein to unwind duplex DNA for homologous pairing. Nature 281: 191-195.
4. Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J., and Lander, E.S. 2001. High-resolution haplotype structure in the human genome. Nat. Genet. 29: 229-232.
5. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. 2002. The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
6. Gamper, H.B., Nulf, C.J., Corey, D.R., and Kmiec, E.B. 2003. The synaptic complex of RecA protein participates in hybridization and inverse strand exchange reactions. Biochemistry 42: 2643-2655.
7. Jayasena, V.K. and Johnston, B.H. 1993. Complement-stabilized D-loop. RecA-catalyzed stable pairing of linear DNA molecules at internal sites. J. Mol. Biol. 230: 1015-1024.
8. Kirk, B.W., Feinsod, M., Favis, R., Kliman, R.M., and Barany, F. 2002. Single nucleotide polymorphism seeking long term association with complex disease. Nucleic Acids Res. 30: 3295-3311.
9. Liu, L., Rice, M.C., and Kmiec, E.B. 2001. In vivo gene repair of point and frameshift mutations directed by chimeric RNA/DNA oligonucleotides and modified single-stranded oligonucleotides. Nucleic Acids Res. 29: 4238-4250.
10. Liu, L., Cheng, S., van Brabant, A.J., and Kmiec, E.B. 2002. Rad51p and Rad54p, but not Rad52p, elevate gene repair in Saccharomyces cerevisiae directed by modified single-stranded oligonucleotide vectors. Nucleic Acids Res. 31: 2742-2750.
11. Lizardi, P.M., Huang, X., Zhu, Z., Bray-Ward, P., Thomas, D.C., and Ward, D.C. 1998. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19: 225-232.
12. Lyamichev, V., Mast, A.L., Hall, J.G., Prudent, J.R., Kaiser, M.W., Takova, T., Kwiatkowski, R.W., Sander, T.J., de Arruda, M., Arco, D.A., et al. 1999. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17: 292-296.
13. Millar, B.C., Xu, J., and Moore, J.E. 2002. Risk assessment models and contamination management: Implications for broad-range ribosomal DNA PCR as a diagnostic tool in medical bacteriology. J. Clin. Microbiol. 40: 1575-1580.
14. Morel, P., Stasiak, A., Ehrlich, S.D., and Cassuto, E. 1994. Effect of length and location of heterologous sequences on RecA-mediated strand exchange. J. Biol. Chem. 269: 19830-19835.
15. Parekh-Olmedo, H., Drury, M., and Kmiec, E.B. 2002. Targeted nucleotide exchange in Saccharomyces cerevisiae directed by short oligonucleotides containing locked nucleic acids. Chem. Biol. 9: 1073-1084.
16. Riley, J.H., Allan, C.J., Lai, E., and Roses, A. 2000. The use of single nucleotide polymorphisms in the isolation of common disease genes. Pharmacogenomics 1: 39-47.
17. Ryan, D., Nuccie, B., and Arvan, D. 1999. Non-PCR-dependent detection of the factor V Leiden mutation from genomic DNA using a homogeneous invader microtiter plate assay. Mol. Diagn. 4: 135-144.
18. Sena, E.P. and Zarling, D.A. 1993. Targeting in linear DNA duplexes with two complementary probe strands for hybrid stability. Nat. Genet. 3: 365-372.
19. Shi, M.M. 2002. Technologies for individual genotyping: Detection of genetic polymorphisms in drug targets and disease genes. Am. J. Pharmacogenomics 2: 197-205.
20. Shibata, T., Cunningham, R.P., DasGupta, C., and Radding, C.M. 1979. Homologous pairing in genetic recombination: Complexes of recA protein and DNA. Proc. Natl. Acad. Sci. 76: 5100-5104.
21. Smigielski, F.M., Sirotkin, K., Ward, M., and Sherry, S.T. 2000. dbSNP: A database of single nucleotide polymorphisms. Nucleic Acids Res. 28: 352-355.
22. Wiegand, R.C., Beattie, K.L., Holloman, W.K., and Radding, C.M. 1977. Uptake of homologous single-stranded fragments by superhelical DNA. III. The product and its enzymic conversion to a recombinant molecule. J. Mol. Biol. 116: 805-824.
23. Zeng, H., Allen, E., Lehman, C.W., Sargent, R.G., Pati, S., and Zarling, D.A. 2002. Discovery of gene families and alternatively spliced variants by RecA-mediated cloning. Genomics 80: 543-551.
24. Zhong, X.B., Lizardi, P.M., Huang, X.H., Bray-Ward, P.L., and Ward, D.C 2001. Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification. Proc. Natl. Acad. Sci. 98: 3940-3945.