DNA-Directed mutations. Leading and lagging strand specificity

Annals of the New York Academy of Sciences

Volumn 870, Issue , 1999, Pages 173-189

  Sinden, Richard R ^a   Hashem, Vera I ^a   Rosche, William A ^b  

^a TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

^b BOSTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REPETITIVE DNA;

CONFERENCE PAPER; DNA CONFORMATION; DNA REPLICATION; DNA TEMPLATE; ESCHERICHIA COLI; FRAMESHIFT MUTATION; PROTEIN SECONDARY STRUCTURE; SITE DIRECTED MUTAGENESIS; SPONTANEOUS MUTATION; TRIPLE HELIX;

ESCHERICHIA COLI;

EID: 0032774402     PISSN: 00778923     EISSN: None     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.1999.tb08878.x     Document Type: Conference Paper

References (66)

1. DRAKE, J.W. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88: 7160-7164.
2. DRAKE, J.W., B. CHARLESWORTH, D. CHARLESWORTH & J.F. Crow. 1998. Rates of spontaneous mutation. Genetics 148: 1667-1686.
3. RIPLEY, L.S. 1990. Frameshift mutation: Determinants of specificity Annu. Rev. Genet. 24: 189-213.
4. KUNKEL, T.A. 1992. DNA Replication Fidelity. J. Biol. Chem. 267: 18251-18254.
5. KUNKEL, T.A. 1990. Misalignment-mediated DNA synthesis errors. Biochemistry 29:8003-8011.
6. ECHOLS, H. & M.F. GOODMAN. 1991. Fidelity mechanisms in DNA replication. Ann. Rev. Biochem. 60: 477-511.
7. UMAR, A. & T.A. KUNKEL. 1996. DNA-replication fidelity, mismatch repair and genome instability in cancer cells. Eur. J. Biochem. 238: 297-307.
8. SINDEN, R.R. 1994. DNA Structure and Function. Academic Press. San Diego.
9. VAN BELKUM, A., S. SCHERER, L. VAN ALPHEN & H. VERBAUGH. 1998. Short sequence DNA repeats in prokaryotic genomes. Microbiol. Mol. Biol. Rev. 62:, 275-293.
10. LUPSKI, J.R. & G.M. WEINSTOCK. 1992. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J. Bacteriol. 174: 4525-4529.
11. FIELD, D. & C. WILLS. 1996. Long, polymorphic microsatellites in simple organisms. Proc. Roy. Soc. of Lond. Ser. B. Biol. Sci. 263: 209-215.
12. ZHANG, J.R., J.M. HARDHAM, A.G. BARBOUR & S.J. NORRIS. 1997. Antigenic variation in Lyme disease borreliae by promiscuous recombination of VMP-like sequence cassettes. Cell 89: 275-285.
13. MOORE, G.P., A.R. MOORE & L.I. GROSSMAN. 1984. The frequency of matching sequences in DNA Theor. Biol. 108: 111-122.
14. BECKMANN, J.S. & J. WEBER. 1992. Survey of human and rat microsatellites. Genomics 12: 627-631.
15. HWU, H.R., J.W. ROBERTS, E.H. DAVIDSON & R.J. BRITTEN. 1986. Insertion and/or deletion of many repeated DNA sequences in human and higher ape evolution. Proc. Natl. Acad. Sci. USA 83, 3875-3879.
16. WEINER, A.M., P.L. DEININGER & A. EFSTRATIADIS. 1986. Nonviral retoposons: Genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55: 631-661.
17. BRITTEN, R.J., W.F. BARON, D.B. STOUT & E.H. DAVIDSON. 1988. Sources and evolution of human alu repeated sequences Proc. Natl. Acad. Sci. USA 85: 4770-4774.
18. DANIELS, G.R. & P.L. DEININGER. Integration site preferences of the Alu family and similar repetitive DNA sequences. Nucleic Acids Res. 13: 8939-8954.
19. KARIYA, Y., K. KATO, Y. HAYASHIZAKI, S. HIMENO, S. TARUI & K. MATSUBARA. 1987. Revision of consensus sequence of human Alu repeats - a review. Gene 53: 1-10.
20. PEARSON, C.E. & R.R. SINDEN. 1998. Slipped strand DNA, dynamic mutations, and human disease. In Genetic Instabilities and Hereditary Neurological Diseases. R.D. Wells & S.T. Warren, Eds.: 585-621. Academic Press. New York.
21. KANG, S., A. JAWORSKI, K. OHSHIMA & R.D. WELLS. 1995. Expansion and deletion of CTG triplet repeats from human disease genes are determined by the direction of replication in E. coli. Nature Genet. 10: 213-218.
22. n triplet repeats from human hereditary diseases Proc. Natl. Acad. Sci. USA 92: 11019-11023.
23. ROSCHE, W.A., A. JAWORSKI, S. KANG, S.F. KRAMER, J.E. LARSON, D.P. GIEDROC, R.D. WELLS & R.R. SINDEN. 1996. Single-stranded DNA binding protein enhances the stability of CTG triplet repeats in Escherichia coli. J. Bacteriol. 178: 5042-5044.
24. SCHROTH, G.P., P.J. CHOU & P.S. HO. 1992. Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA forming sequences in human genes. J. Biol. Chem. 267: 11846-11855.
25. SCHROTH, G.P. & P.S. HO. 1995. Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA. Nucleic Acids Res. 23: 1977-1983.
26. The International Polycystic Kidney Disease Consortium. 1995. Polycystic kidney disease: The complete structure of the PKD1 gene and its protein. Cell 81: 289-298.
27. AKGUN, E., J. ZAHN, S. BAUMES, G. BROWN, F. LIANG, P.J. ROMANIENKO, S. LEWIS & M. JASIN. 1997. Palindrome resolution and recombination in the mammalian germ line. Mol. Cell. Biol. 17: 5559-5570.
28. GLUCKSMANN, M.A., P. MARKIEWICZ, C. MALONE & L.B. ROTHMAN-DENES. 1992. Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition Cell 70: 491-500.
29. JIN, R., M.E. FERNANDEZ-BEROS, & R.P. NOVICK. 1997. Why is the initiation nick site of an AT-rich rolling circle plasmid at the tip of a GC-rich cruciform? EMBO J. 16: 4456-4466.
30. COOPER, D.N. & M. KRAWCZAK. 1993. Human Gene Mutation. Bios Scientific Publishers. Oxford, UK.
31. CHEN, S.J., Z. CHEN, L. D'AURIOL, M. LE CONIAT, D. GRAUSZ & R. BERGER. 1989. Phl+bcr-acute leukemias: Implication of Alu sequences in a chromosomal translocation occurring in the new cluster region within the bcr gene. Oncogene 4: 195-202.
32. SCHICHMAN, S.A., M.A. CALIGIURI, M.P. STROUT, S.L. CARTER, Y. GU, E. CANAANI, C.D. BLOOMFIELD & C.M. CROCE. 1994. ALL-1 tandem duplication in acute myeloid leukemia with a normal karyotype involves homologous recombination between Alu elements. Cancer Res. 54: 4277-4280.
33. LEHRMAN, M.A., W.J. SCHNEIDER, T.C. SUDHOF, M.S. BROWN, J.L. GOLDSTEIN, & D.W. RUSSELL. 1985. Mutation in LDL receptor: Alu-alu recombination deletes exons encoding transmembrane and cytoplasmic domains. Science 227: 140-146.
34. HOBBS, H.H., M.S. BROWN, J.L. GOLDSTEIN & D.W. RUSSELL. 1986. Deletion of exon encoding cysteine-rich repeat of low density lipoprotein receptor alters its binding specificity in a subject with familial hypercholesterolemia. J. Biol. Chem. 261: 13114-13120.
35. NICHOLLS, R.D., N. FISCHEL-GHODSIAN & D.R. HIGGS. 1987. Recombination at the human alphaglobin gene cluster: Sequence features and topological constraints. Cell 49: 369-378.
36. WOODS-SAMUELS, P., H.H. KAZAZIAN & S.E. ANTONARAKIS. 1991. Nonhomologous recombination in the human genome: Deletions in the human factor VIII gene. Genomics 10: 94-101.
37. ROUYER, F., M.C. SIMMLER, D.C. PAGE & J. WEISSENBACH. 1987. A sex chromosome rearrangement in a human XX male caused by alu- alu recombination. Cell 51: 417-425.
38. STREISINGER, G., Y. OKADA, J. EMRICH, J. NEWTON, A. TSUGITA, E. TERZAGHI & M. INOUYE. 1966. Frameshift mutations and the genetic code. Cold Spring Harbor Symp. Quant. Biol. 31: 77-84.
39. LILLEY, D.M. 1981. In vive consequences of plasmid topology. Nature 292: 380-382.
40. BETZ, J.L. & J.R. SADLER. 1981. Variants of a cloned synthetic lactose operator. I. A palindromic dimer lactose operator derived from one strand of the cloned 40-base pair operator. Gene 13: 1-12.
41. SINDEN, R.R., G. ZHENG, R.G. BRANKAMP & K.N. ALLEN. 1991. On the deletion of inverted repeated DNA in Escherichia coli: Effects of length, thermal stability, and cruciform formation in vivo. Genetics 129: 991-1005.
42. WILLIAMS, W.L. & U.R. MULLER. 1987. Effects of palindrome size and sequence on genetic stability in the bacteriophage phi X174 genome. J. Mol. Biol. 196: 743-755.
43. SINGER, B.S. & J. WESTLYE. 1988. Deletion formation in Bacteriophage T4. J. Mol. Biol. 202: 233-243.
44. BALBINDER, E., C. MAC VEAN & R.E. WILLIAMS. 1989. Overlapping direct repeats stimulate deletions in specifically designed derivatives of plasmid pBR325 in Escherichia coli. Mutat. Res. 214: 233-252.
45. WESTON-HAFER, K. & D.E. BERG. 1989. Palindromy and the location of deletion endpoints in Escherichia coli. Genetics 121: 651-658.
46. SINDEN, R.R. & R.D. WELLS. 1992. DNA structure, mutations, and human genetic disease. Curr. Opin. Biotechol. 3: 612-622.
47. DRAKE, J.W., B.W. GLICKMAN & L.S. RIPLEY. 1983. Updating the theory of mutation. Am. Scientist 71: 621-630.
48. GLICKMAN, B.W. & L.S. RIPLEY. 1984. Structural intermediates of deletion mutagenesis: A role for palindromic DNA. Proc. Natl. Acad. Sci. USA 81: 512-516.
49. RIPLEY, L.S. & B.W. GLICKMAN. 1983. Unique self-complementarily of palindromic sequences provides DNA structural intermediates for mutation. Cold Spring Harbor Symp. Quant. Biol. 47: 851-861.
50. DASGUPTA, U., K. WESTON-HAFER & D.E. BERG. 1987. Local DNA sequence control of deletion formation in Escherichia coli plasmid pBR322. Genetics 115: 41-49.
51. PIERCE, J.C., D. KONG & W. MASKER. 1991. The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7. Nucleic Acids Res. 14: 3901-3905.
52. TRINH, T.Q. & R.R. SINDEN. 1993. The influence of primary and secondary DNA structure in deletion and duplication between direct repeats in Escherichia coli. Genetics 134: 409-422.
53. ROSCHE, W.A., T.Q. TRINH & R.R. SINDEN. 1995. Differential DNA secondary structure mediated deletion mutagenesis in the leading and lagging strands. J. Bacteriol. 177: 4385-4391.
54. TRINH, T.Q. & R.R. SINDEN. 1991. Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature 352: 544-547.
55. SCOTT, J.R. 1984. Regulation of plasmid replication. Microbiol. Rev. 48: 1-23.
56. KAZIC, T. & D.E. BERG. 1990. Context effects in the formation of deletions in Escherichia coli. Genetics 126: 17-24.
57. RIPLEY, L.S. 1982. Model for the participation of quasi-palindromic DNA sequences in frameshift mutation. Proc. Natl. Acad. Sci. USA 79: 4128-4132.
58. ROSCHE, W.A., T.Q. TRINH & R.R. SINDEN. 1997. Leading strand specific spontaneous mutation corrects a quasi-palindrome by an intermolecular strand switch mechanism. J. Mol. Biol. 269: 176-187.
59. 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. 284: 633-646.
60. BOHR, V.A., C.A. SMITH, D.A. OKUMOTO & P.C. HANAWALT. 1985. DNA repair in an active gene: Removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall. Cell 40: 359-369.
61. MELLON, I. & P.C. HANAWALT. 1989. Induction of the Eseherichia coli lactose operon selectively increases repair of its transcribed DNA strand. Nature 342: 95-98.
62. MELLON, I., G. SPIVAK & P.C. HANAWALT. 1988. Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell 51: 241-249.
63. BREWER, B.J. 1988. When polymerases collide: Replication and the transcriptional organization of the E. coli chromosome. Cell 53: 679-686.
64. VEAUTE, X. & R.P. FUCHS. 1993. Greater susceptibility to mutations in lagging strand of DNA replication in Escherichia coli than in leading strand. Science 261: 598-600.
65. BASIC-ZANINOVIC, T., F. PALOMHO, M. BIGNAMI & E. DOGLIOTTI. 1992. Fidelity of replication of the leading and lagging DNA strands opposite N-methyl-N-nitrosourea-induced DNA damage in human cells. Nucleic Acids Res. 20: 6543-6548.
66. ROBERTS, J.D., D. NGUYEN, & T.A. KUNKEL. 1993. Frameshift fidelity during replication of double-stranded DNA in HeLa cell extracts. Biochemistry 32: 4083-4090.