Tagging DNA mismatches by selective 2'-amine acylation

Chemistry and Biology

Volumn 7, Issue 6, 2000, Pages 405-410

  John, Deborah M ^a   Weeks, Kevin M ^a  

^a University of North Carolina at Chapel Hill   (United States)

Author keywords

2' amino 2' deoxyribonucleotide; Mismatch proofreading; Mutation detection; Single nucleotide polymorphism (SNP)

Indexed keywords

ACYLATION; BASE PAIRING; GENE TAGGING; NUCLEOTIDE SUBSTITUTION; OLIGONUCLEOTIDE PROBE; POINT MUTATION; SUCCINIMIDYL ESTER;

EID: 0034086396     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(00)00121-6     Document Type: Article

References (30)

1. Schafer A.J., Hawkins J.R. DNA variation and the future of human genetics. Nat. Biotechnol. 16:1998;33-39.
2. Evans W.E., Relling M.V. Pharmacogenomics: translating functional genomics into rational therapeutics. Science. 286:1999;487-491.
3. Stoneking M., Hedgecock D., Higuchi R.G., Vigilant L., Erlich H.A. Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am. J. Hum. Genet. 48:1991;370-382.
4. Howell W.M., Jobs M., Gyllensten U., Brookes A.J. Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat. Biotechnol. 17:1999;87-88.
5. Tyagi S., Kramer F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:1996;303-308.
6. Newton C.R., Markham A.F.et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17:1989;2503-2516.
7. Lishanski A., Ostrander E.A., Rine J. Mutation detection by mismatch binding protein, MutS, in amplified DNA: application to the cystic fibrosis gene. Proc. Natl. Acad. Sci. USA. 91:1994;2674-2678.
8. Okano K., Kambara H. DNA probe assay based on exonuclease III digestion of probes hybridized on target DNA. Anal. Biochem. 228:1995;101-108.
9. Del Tito B.J. Jr., Bailey A.L.et al. Automated fluorescent analysis procedure for enzymatic mutation detection. Clin. Chem. 44:1998;731-739.
10. Cotton R.G., Rodrigues N.R., Campbell R.D. Reactivity of cytosine and thymine in single-base-pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations. Proc. Natl. Acad. Sci. USA. 85:1988;4397-4401.
11. Jackson B.A., Barton J.K. Recognition of DNA base mismatches by a rhodium intercalator. J. Am. Chem. Soc. 119:1997;12986-12987.
12. Ellis T.P., Humphrey K.E., Smith M.J., Cotton R.G. Chemical cleavage of mismatch: a new look at an established method. Hum. Mutat. 11:1998;345-353.
13. Marshall A., Hodgson J. DNA chips: an array of possibilities. Nat. Biotechnol. 16:1998;27-31.
14. Wang D.G., Lander E.S.et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 280:1998;1077-1082.
15. Johnston D.H., Glasgow K.C., Thorp H.H. Electrochemical measurement of the solvent accessibility of nucleobases using electron transfer between DNA and metal complexes. J. Am. Chem. Soc. 117:1995;8933-8938.
16. Caruana D.J., Heller A. Enzyme-amplified amperometric detection of hybridization and of a single base pair mutation in an 18-base oligonucleotide on a 7-μm-diameter microelectrode. J. Am. Chem. Soc. 121:1999;769-774.
17. Kelley S.O., Boon E.M., Barton J.K., Jackson N.M., Hill M.G. Single-base mismatch detection based on charge transduction through DNA. Nucleic Acids Res. 27:1999;4830-4837.
18. Peyret N., Seneviratne P.A., Allawi H.T., SantaLucia J. Jr. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A-A, C-C, G-G, and T-T mismatches. Biochemistry. 38:1999;3468-3477.
19. SantaLucia J. Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA. 95:1998;1460-1465.
20. Nguyen H.K., Auffray P., Asseline U., Dupret D., Thuong N.T. Modification of DNA duplexes to smooth their thermal stability independently of their base content for DNA sequencing by hybridization. Nucleic Acids Res. 25:1997;3059-3065.
21. Imazawa M., Eckstein F. Facile synthesis of 2′-amino-2′-deoxyribofuranosyl purines. J. Org. Chem. 44:1979;2039-2041.
22. Aurup H., Tuschl T., Benseler F., Ludwig J., Eckstein F. Oligonucleotide duplexes containing 2′-amino-2′-deoxycytidines: thermal stability and chemical reactivity. Nucleic Acids Res. 22:1994;20-24.
23. Cohen S.B., Cech T.R. Dynamics of thermal motions within a large catalytic RNA investigated by cross-linking with thiol-disulfide interchange. J. Am. Chem. Soc. 119:1997;6259-6268.
24. Chamberlin S.I., Weeks K.M. Mapping local nucleotide flexibility by selective acylation of 2′-amine substituted RNA. J. Am. Chem. Soc. 122:2000;216-224.
25. Patel D.J., Kozlowski S.A., Ikuta S., Itakura K. Dynamics of DNA duplexes containing internal G-T, G-A, A-C, and T-C pairs: hydrogen exchange at and adjacent to mismatch sites. Fed. Proc. 43:1984;2663-2670.
26. Guest C.R., Hochstrasser R.A., Sowers L.C., Millar D.P. Dynamics of mismatched base pairs in DNA. Biochemistry. 30:1991;3271-3279.
27. Bertina R.M., Reitsma P.H.et al. Mutation in blood coagulation factor V associated with resistance to activated protein C. Nature. 369:1994;64-67.
28. Hunter W.N., Brown T., Anand N.N., Kennard O. Structure of an adenine-cytosine base pair in DNA and its implications for mismatch repair. Nature. 320:1986;552-555.
29. Boulard Y., Cognet J.A., Gabarro-Arpa J., Le Bret M., Carbonnaux C., Fazakerley G.V. Solution structure of an oncogenic DNA duplex, the K-ras gene and the sequence containing a central C-A or A-G mismatch as a function of pH: nuclear magnetic resonance and molecular dynamics studies. J. Mol. Biol. 246:1995;194-208.
30. Gralla J., Crothers D.M. Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches. J. Mol. Biol. 78:1973;301-319.