Predictability of mutant sequences. Relationships between mutational mechanisms and mutant specificity

Annals of the New York Academy of Sciences

Volumn 870, Issue , 1999, Pages 159-172

  Ripley, Lynn S ^a  

^a RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; CONFERENCE PAPER; DNA SEQUENCE; EVOLUTION; FRAMESHIFT MUTATION; MUTAGENESIS; SPONTANEOUS MUTATION;

EID: 0032796616     PISSN: 00778923     EISSN: None     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.1999.tb08877.x     Document Type: Conference Paper

References (36)

1. KARLIN, S. & J. MRAZEK. 1997. Compositional differences within and between eukaryotic genomes. Proc. Natl. Acad. Sci. USA 94: 10227-10232.
2. DRAKE, J.W. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88: 7160-7164.
3. RIPLEY, L.S., A. CLARK & J.G. DE BOER. 1986. Spectrum of spontaneous frameshift mutations. Sequences of bacteriophage T4 rII gene frameshifts. J. Mol. Biol. 191: 601-613.
4. WANG, F.J. & L.S. RIPLEY. 1998. The spectrum of acridine resistant mutants of bacteriophage T4 reveals cryptic effects of the tsL141 DNA polymerase allele on spontaneous mutagenesis. Genetics 148: 1655-1665.
5. RIPLEY, L.S. 1997. Optimum Mutation Rates in Evolution & Disease: A Debate. (Day 1, message 7 of 10) in HMS Beagle: The BioMedNet Magazine. (http://biomednet.com/hmsbeagle/14/cutedge/dayl.htm), Issue 13, July 25.
6. DEMARINI, D.M., M.L. SHELTON, A. ABU-SHAKRA, A. SZAKMARY & J.G. LEVINE. 1998. Spontaneous frameshift mutations at the hisD3052 allele of Salmonella typhimurium in four DNA repair backgrounds. Genetics 149: 17-36.
7. RIPLEY, L.S. 1974. Transversion mutagenesis in bacteriophage T4. Mol. Gen. Genet. 141: 23-40.
8. GILLESPIE, J.H. 1991. The Causes of Molecular Evolution. Oxford University Press. New York, NY.
9. OHTA, T. & J.H. GILLESPIE. 1996. Development of neutral and nearly neutral theories. Theor. Popul. Biol. 49: 128-142.
10. ROSCHE, W.A., L.S. RIPLEY & R.R. SINDEN. 1998. Primer-template misalignments during leading strand DNA synthesis account for the most frequent spontaneous mutations in a quasipalindromic region in Escherichia coli. J. Mol. Biol. In press.
11. SINGER, B.S. 1984. A hotspot for transition mutations in the rIIB gene of bacteriophage T4. I. The extent of the hotspot. Mol. Gen. Genet. 193: 104-109.
12. STREISINGER, G. & J.E. OWEN. 1985. Mechanisms of spontaneous and induced frameshift mutation in bacteriophage T4. Genetics 109: 633-659.
13. RIPLEY, L.S. 1990. Frameshift mutation: Determinants of specificity. Ann. Rev. Genet. 24: 189-213.
14. Ripley, L.S. 1994. Deletion and duplication sequences induced in CHO cells by teniposide (VM-26), a topoisomerase II targeting drug, can be explained by the processing of DNA nicks produced by the drug-topoisomerase interaction. Mutation Res. 312: 67-78.
15. RIPLEY, L.S., J.S. DUHINS, J.G. DE BOER, D.M. DEMARINI, A.M. BOGERD & K.N. KREUZER. 1988. Hotspot sites for acridine-induced frameshift mutations in bacteriophage T4 correspond to sites of action of the T4 type II topoisomerase. J. Mol. Biol. 200: 665-680.
16. MASUREKAR, M., K.N. KREUZER & L.S. RIPLEY. 1991. The specificity of topoisomerasc-mediated DNA cleavage defines acridine-induced frameshift specificity within a hotspot in bacteriophage T4. Genetics 127: 453-462.
17. BROWN, M.D., L.S. RIPLEY & D.H. HALL. 1993. A proflavin-induced frameshift hotspot in the thymidylate synthase gene of bacteriophage T4. Mutation Res. 286: 189-197.
18. KAISER, V.L. & L.S. RIPLEY. 1995. DNA nick processing by exonuclease and polymerase activities of T4 DNA polymerase accounts for acridine-induced mutation specificities in T4. Proc. Natl. Acad. Sci. USA 92: 2234-2238.
19. CAPRANICO, G. S. TINELLI, F. ZUNINO, K.W. KOHN & Y. POMMIER. 1993. Effects of base mutations on topoisomerase II DNA cleavage stimulated by mAMSA in short DNA oligomers. Biochemistry 32: 145-152.
20. FERGUSON, L.R., P.M. TURNER, D.W. HART & K.R. TINDALL. 1998. Amsacrine-induced mutations in AS52 cells. Environ. Mol. Mutagen 32: 47-55.
21. DEMARINI, D.M., C.L. DOERR, M.K. MEYER, K.H. BROCK, J. HOZIER & M.M. MOORE. 1987. Mutagenicity of m-AMSA and o-AMSA in mammalian cells due to clastogenic mechanism: Possible role of topoisomerase. Mutagenesis 2: 349-355.
22. HAN, Y.H., M.J. AUSTIN, Y. POMMIER & L.F. POVIRK. 1993. Small deletion and insertion mutations induced by the topoisomerase II inhibitor teniposide in CHO cells and comparison with sites of drug-stimulated DNA cleavage in vitro. J. Mol. Biol. 229: 52-66.
23. FELIX, C.A., B.J. LANGE, M.R. HOSLER, J. FERTALA & M.A. BJORNSTI. 1995. Chromosome band IIq23 translocation breakpoints are DNA topoisomerase II cleavage sites. Cancer Res. 55: 4287-4292.
24. FELIX, C.A. 1998. Secondary leukemias induced by topoisomerase-targeted drugs. Biochim. Biophys. Acta 1400: 233-255.
25. RIPLEY, L.S. & N.B. SHOEMAKER. 1983. A major role for bacteriophage T4 DNA polymerase in frameshift mutagenesis. Genetics 103: 353-366.
26. RIPLEY, L.S., B.W. GLICKMAN & N.B. SHOEMAKER. 1983. Mutator versus antimutator activity of a T4 DNA polymerase mutant distinguishes two different frameshifting mechanisms. Mol. Gen. Genet. 189: 113-117.
27. RIPLEY, L.S. 1982. Model for the participation of quasi-palindromic DNA sequences in frameshift mutation. Proc. Natl. Acad. Sci. USA 79: 4128-4132.
28. PAPANICOLAOU, C. & L.S. RIPLEY. 1989. Polymerase-specific differences in the DNA intermediates of frameshift mutagenesis. In vitro synthesis errors of Escherichia coli DNA polymerase I and its large fragment derivative. J. Mol. Biol. 207: 335-353.
29. PAPANICOLAOU, C. & L.S. RIPLEY. 1991. An in vitro approach to identifying specificity determinants of mutagenesis mediated by DNA misalignments. J. Mol. Biol. 221: 805-821.
30. DE BOER, J. G. & L.S. RIPLEY. 1984. Demonstration of the production of frameshift and base-substitution mutations by quasipalindromic DNA sequences. Proc. Natl. Acad. Sci. USA 82: 3616-3620.
31. KLEIN, J. 1987. Origin of major histocompatibility complex polymorphism: The trans-species hypothesis. Hum. Immunol. 19: 155-162.
32. HUGHES, A. L., M.K. HUGHES, C.Y. HOWELL & M. NEI. 1994. Natural selection at the class II major histocompatibility complex. Philos. Trans. R. Soc. Lond. B Biol. Sci. 346: 359-366.
33. HUGHES, A.L. & M. NEI. 1988. Nucleotide substitutions at major histocompatibility complex class II loci: Evidence for overdominant selection. Proc. Natl. Acad. Sci. USA 86: 958-962.
34. SHE, J.X., S. BOEHME, T.W. WANG, F. BONHOMME & E.K. WAKELAND. 1990. The generation of MHC class II gene polymorphism in the genes Mus. Biol. J. Linnean Soc. 41: 141-161.
35. RIPLEY, L.S. 1991. Concerted mutagenesis: Its potential impact on interpretation of evolutionary relationships. In Molecular Evolution of the Major Histocompatibility Complex. Klein, J. and D. Klein, Eds.: 63-94. Springer-Verlag, Berlin.
36. BERGSTOM, T.F., A. JOSEFSSON, H.A. ERLICH & U. GYLLENSTEN. 1998. Recent origin of HLA-DRB 1 alleles and implications for human evolution. Nat. Genet. 18: 237-242.