Replication strand preference for deletions associated with DNA palindromes

Molecular Microbiology

Volumn 28, Issue 4, 1998, Pages 719-727

  Pinder, David J ^a   Blake, Catherine E ^a   Lindsey, Janet C ^a   Leach, David R F ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PALINDROMIC DNA;

ARTICLE; BACTERIOPHAGE LAMBDA; DNA REPLICATION; DNA STRAND; ESCHERICHIA COLI; GENE DELETION; NONHUMAN; ORIENTATION; PLASMID; PRIORITY JOURNAL;

BACTERIOPHAGE LAMBDA; BASE SEQUENCE; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA REPLICATION; DNA, BACTERIAL; ESCHERICHIA COLI; GENETIC VECTORS; MOLECULAR SEQUENCE DATA; SEQUENCE DELETION;

BACTERIA (MICROORGANISMS); BACTERIOPHAGE LAMBDA; ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0031803630     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1998.00831.x     Document Type: Article

References (35)

1. Baumer, A., Zhang, C., Linnane, W., and Nagley, P. (1994) Age-related human mtDNA deletions: A heterogeneous set of deletions arising at a single pair of directly repeated sequences. Am J Hum Genet 54: 618-630.
2. Bi, X., and Liu, L.F. (1994) RecA-independent and recA-dependent intramolecular plasmid recombination. J Mol Biol 235: 414-423.
3. Bichara, M., Schumacher, S., and Fuchs, R.P.P. (1995) Genetic instability within monotonous runs of CpG sequences in Escherichia coll. Genetics 140: 897-907.
4. Bierne, H., and Michel, B. (1994) When replication forks stop. Mol Microbiol 13: 17-23.
5. Bouffler, S., Silver, A., and Cox, R. (1993) The role of DNA repeats and associated secondary structures in genomic instability and neoplasia. BioEssays 15: 409-412.
6. Collick, A., Drew, J., Penberth, J., Bois, P., Luckett, J., Scaerou, F., et al. (1996) Instability of long inverted repeats within mouse transgenes. EMBO 15: 1163-1171.
7. Collins, J. (1981) Instability of palindromic DNA in Escherichia coli. Cold Spring Harbor Symp Quant Biol 45: 409-416.
8. Das Gupta, U., Weston-Hafer, K., and Berg, D.E. (1987) Local DNA sequence control of deletion formation in Escherichia coli plasmid pBR322. Genetics 115: 41-49.
9. Ehrlich, S.D., Bierne, H., d'Alencon, E., Villette, D., Petranovic, M., Noirot, P., and Michel, B. (1993) Mechanisms of illegitimate recombination. Gene 135: 161-166.
10. Franklin, N.C. (1971) Illegitimate recombination. In The Bacteriophage A. Hershey, A.D. (ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 175-194.
11. Glickman, B.W., and Ripley, L.S. (1984) Structural intermediates of deletion mutagenesis: A role for palindromic DNA. Proc Natl Acad Sci USA 81: 512-516.
12. Gordenin, D.A., Lobachev, K.S., Degtyareva, N.P., Malakova, A.L., Perkins, E., and Resnick, M.A. (1993) Inverted DNA repeats: a source of eucaryotic genome instability. Mol Cell Biol 13: 5315-5322.
13. Greenblatt, M.S., Grollman, A.P., and Harris, C.C. (1996) Deletions and insertions in the p53 tumor suppressor gene in human cancers: confirmation of the DNA polymerase slippage/misalignment model. Cancer Res 56: 2130-2136.
14. Hancock, J.M. (1996) Simple sequences and the expanding genome. BioEssays 18: 421-425.
15. Hagan, C.E., and Warren, G.J. (1983) Viability of palindromic DNA is restored by deletions at low but variable frequency in plasmids of Escherichia coli. Gene 24: 317-326.
16. Kulkarni, S. (1990) Deleterious effects of palindromic DNA in the E. coli chromosome. PhD thesis, University of Oregon.
17. Leach, D.R.F. (1994) Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. BioEssays 16: 893-900.
18. Leach, D.R.F., and Stahl, F.W. (1983) Viability of λ phages carrying a perfect palindrome in the absence of recombination nucleases. Nature 305: 448-451.
19. Leach, D.R.F., Lindsey, J.C., and Okely, E.O. (1987) Genome interactions which influence DNA palindrome mediated instability and inviability in Escherichia coli. J Cell Sci Suppl 7: 33-40.
20. Lovett, S.T., and Feschenko, V.V. (1996) Stabilization of diverged tandem repeats by mismatch repair: Evidence for deletion formation via a misaligned replication intermediate. Proc Natl Acad Sci USA 93: 7120-7124.
21. Lovett, S.T., Drapkin, P.T., Sutera, V.A.J., and Gluckman-Peskind, T.J. (1993) A sister-strand exchange mechanism for recA-independent deletion of repeated DNA sequences in Escherichia coli. Genetics 135: 631-642.
22. Matfield, M., Badawi, R., and Brammer, W.J. (1985) Rec-dependent and Rec-independent recombination of plasmid-borne duplications in Escherichia coli. Mol Gen Genet 199: 518-523.
23. Peeters, B.P.H., deBoer, J.H., Bron, S., and Venema, G. (1988) Structural plasmid instability in Bacillus subtilis: Effect of direct and inverted repeats. Mol Gen Genet 212: 450-458.
24. Pinder, D.J., Blake, C.E., and Leach, D.R.F. (1997) DIR: a novel DNA rearrangement associated with inverted repeats. Nucleic Acids Res 25: 523-529.
25. Richards, R.I., and Sutherland, G.R. (1994) Simple repeat DNA is not replicated simply. Nature Genetics 6:114-116.
26. Rosche, W.A., Trinh, T.Q., and Sinden, R.R. (1995) Differential DNA secondary structure-mediated deletion mutation in the leading and lagging-strands. J Bacteriol 177: 4385-4391.
27. Sambrook, J., Frisch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
28. Sanger, F., Nicklen, S., and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467.
29. Sinden, R.R., and Wells, R.D. (1992) DNA structure, mutations and human disease. Curr Opin Biotechnol 3: 612-622.
30. Trinh, T.Q., and Sinden, R.R. (1991) Preferential DNA secondary structure mutagenesis in the lagging-strand of DNA replication in E. coli. Nature 352: 544-547.
31. Warren, G.J., and Green, R.L. (1985) Comparison of physical and genetic properties of palindromic DNA sequences. J Bacteriol 161: 1103-1111.
32. Wallace, D.C., Lott, M.T., Torroni, A., and Shoffner, J.M. (1991) Report of the Committee on Human Mitochondrial DNA. Cytogenet Cell Genet 58: 1103-1123.
33. Wells, R.D. (1996) Molecular basis of genetic instability of triplet repeats. J Biol Chem 271: 2875-2878.
34. Weston-Hafer, C., and Berg, D.E. (1991) Deletions in plasmid pBR322: Replication-slippage involving leading and lagging-strands. Genetics 127: 649-655.
35. Yoshimura, H., Yoshino, T., Hirose, T., Nakamura, Y., Higashi, M., Hase, T., et al. (1986) Biological characteristics of palindromic DNA (II). J Gen Appl Microbiol 32: 393-404.