A new trick for an old dog: Tray binding to a homopurine-homopyrimidine run attenuates DNA replication

Journal of Molecular Biology

Volumn 313, Issue 2, 2001, Pages 271-282

  Krasilnikova, Maria M ^a   Smirnova, Ekaterina V ^a   Krasilnikov, Andrei S ^a   Mirkin, Sergei M ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

DNA replication; Escherichia coli; Homopurine homopyrimidine repeat; Termination; TraY protein

Indexed keywords

CANIS FAMILIARIS; ESCHERICHIA COLI;

CHLORAMPHENICOL; DIMETHYL SULFATE; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; SULFATE; TRAY PROTEIN, E COLI;

AFFINITY CHROMATOGRAPHY; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BACTERIUM CONJUGATION; BIOLOGICAL MODEL; BIOSYNTHESIS; CHEMISTRY; DNA FOOTPRINTING; DNA REPLICATION; DOG; DRUG EFFECT; ESCHERICHIA COLI; GEL MOBILITY SHIFT ASSAY; GENETICS; METABOLISM; MOLECULAR GENETICS; MOLECULAR WEIGHT; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PLASMID;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CHLORAMPHENICOL; CHROMATOGRAPHY, AFFINITY; CONJUGATION, GENETIC; DNA FOOTPRINTING; DNA REPLICATION; DNA-BINDING PROTEINS; DOGS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PLASMIDS; REPETITIVE SEQUENCES, NUCLEIC ACID; SULFURIC ACID ESTERS;

EID: 0035914472     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5059     Document Type: Article

References (63)

1. Schroth G. P., Ho P. S. Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA. Nucl. Acids Res. 23:1995;1977-1983
2. Cox R., Mirkin S. M. Characteristic enrichment of DNA repeats in different genomes. Proc. Natl Acad. Sci. USA. 94:1997;5237-5242
3. Modrich P. Mismatch repair, genetic stability, and cancer. Science. 266:1994;1959-1960
4. Kunkel T. A. Slippery DNA and diseases. Nature. 365:1993;207-208
5. Wells R. D., Warren S. T. Genetic Instabilities and Hereditary Neurological Disorders. 1998;Academic Press, San Diego
6. McMurray C. T. Mechanisms of DNA expansion. Chromosoma. 104:1995;2-13
7. Wells R. D. Molecular basis of genetic instability of triplet repeats. J. Biol. Chem. 271:1996;2875-2878
8. Siyanova E. Y., Mirkin S. M. Expansion of trinucleotide repeats. Mol. Biol (Moscow). 35:2001;168-182
9. Sherman L. A., Gefter M. L. Studies of the mechanism of enzymatic DNA elongation of by Escherichia coli DNA polymerase II. J. Mol. Biol. 103:1976;61-76
10. Chalberg M. D., Englund P. T. The effect of template secondary structure on vaccinia DNA polymerase. J. Biol. Chem. 254:1979;7820-7826
11. Huang C. C., Hearst J. E. Pauses at positions of secondary structure during in vitro replication of single-stranded fd bacteriophage DNA by T4 DNA polymerase. Anal. Biochem. 103:1980;127-139
12. Kaguni L. S., Clayton D. A. Template-directed pausing in in vitro DNA synthesis by DNA polymerase α from Drosophila melanogaster embryos. Proc. Natl Acad. Sci. USA. 79:1982;983-987
13. Weaver D. T., DePamphilis M. L. Specific sequences in native DNA that arrest synthesis by DNA polymerase alpha. J. Biol. Chem. 257:1982;2075-2086
14. Abbotts J., SenGupta D. N., Zon G., Wilson S. H. Studies on the mechanisms of Escherichia coli DNA polymerase I large fragment. Effect of template sequence and substrate variation on termination of synthesis. J. Biol. Chem. 263:1988;15094-15103
15. ntracts arrest single stranded DNA replication in vitro. Nucl. Acids Res. 17:1989;883-900
16. ntracts. Proc. Natl Acad. Sci. USA. 88:1991;507-511
17. Dayn A., Samadashwily G. M., Mirkin S. M. Intramolecular DNA triplexes: unusual sequence requirements and influence on DNA polymerization. Proc. Natl Acad. Sci. USA. 89:1992;11406-11410
18. Samadashwily G. M., Dayn A., Mirkin S. M. Suicidal nucleotide sequences for DNA polymerization. EMBO J. 12:1993;4975-4983
19. Woodford K. J., Howell R. M., Usdin K. A novel K(+)-dependent DNA synthesis arrest site in a commonly occuring sequence motif in eukaryotes. J. Biol. Chem. 269:1994;27029-27035
20. Usdin K., Woodford K. J. CGG repeats associated with DNA instability and chromosome fragility from structures that block DNA synthesis in vitro. Nucl. Acids Res. 23:1995;4202-4209
21. Kang S., Ohshima K., Shimizu M., Amirhaeri S., Wells R. D. Pausing of DNA synthesis in vitro at specific loci in CTG and CGG triplet repeats from human hereditary disease genes. J. Biol. Chem. 270:1995;27014-27021
22. Ohshima K., Wells R. D. Hairpin formation during DNA synthesis primer realignment in vitro in triplet repeat sequences from human hereditary disease genes. J. Biol. Chem. 272:1997;16798-16806
23. Samadashwily G. M., Raca G., Mirkin S. M. Trinucleotide repeats affect DNA replication in vivo. Nature Genet. 17:1997;298-304
24. Samadashwily G. M., Mirkin S. M. Trapping DNA polymerases using triplex-forming oligodeoxyribonucleotides. Gene. 149:1994;127-136
25. Kopel V., Pozner A., Baran N., Manor H. Unwinding of the third strand of a DNA triple helix, a novel activity of the SV40 large T-antigen helicase. Nucl. Acids Res. 24:1996;330-335
26. Baran N., Pucshansky L., Marco Y., Benjamin S., Manor H. The SV40 large T-antigen helicase can unwind four stranded DNA structures linked by G-quartets. Nucl. Acids Res. 25:1997;297-303
27. nJ. Biol. Chem. 274:1999;12797-12802
28. ntrinucleotide repeat sequence. J. Biol. Chem. 276:2001;16439-16446
29. 27Nucl. Acids Res. 16:1988;8077-8094
30. Brinton B. T., Caddle M. S., Heintz N. H. Position and orientation-dependent effects of a eukaryotic Z-triplex DNA motif on episomal DNA replication in COS-7 cells. J. Biol. Chem. 266:1991;5153-5161
31. ntracts. Gene. 140:1994;233-237
32. Krasilnikova M. M., Samadashwily G. M., Krasilnikov A. S., Mirkin S. M. Transcription through a simple DNA repeat blocks replication elongation. EMBO J. 17:1998;5095-5102
33. Ohshima K., Montermini L., Wells R. D., Pandolfo M. Inhibitory effects of expanded GAA·TTC triplet repeats from intron I of the Freidreich’s ataxia gene on transcription and replication in vivo. J. Biol. Chem. 273:1998;14588-14595
34. nsequences. J. Mol. Evol. 27:1988;96-101
35. Mirkin S. M., Frank-Kamenetskii M. D. H-DNA and related structures. Annu. Rev. Biophys. Biomol. Struct. 23:1994;541-576
36. Mirkin S. M. Structure and biology of H DNA. Malvy C., Harel-Bellan A., Pritchard L. L. Triple Helix Forming Oligonucleotides. 1999;193-222 Kluwer Academic Publishers, Boston
37. Perucho M. et al. Defects in replication fidelity of simple repeated sequences reveal a new mutator mechanism for oncogenesis. Cold Spring Harbor Symp. Quant. Biol. 59:1994;339-348
38. Friedman K. L., Brewer B. J. Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. Methods Enzymol. 262:1995;613-627
39. Brewer B. J., Fangman W. L. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell. 51:1987;463-471
40. Clewell D. B. Nature of Col E1 plasmid replication in Escherichia coli in the presence of chloramphenicol. J. Bacteriol. 110:1972;667-676
41. Kim M. G., Camerini-Otero R. D. An alteration in the structure of the minor groove of duplex DNA induced by the formation of the intermolecular d(GA):d(GA)·d(TC)n triplex. Mol. Cells. 7:1997;641-647
42. Wolfson J. S., Hooper D. C., Swartz M. N., Swartz M. D., McHugh G. L. Novobiocin-induced elimination of F′lac and mini-F plasmids from Escherichia coli. J. Bacteriol. 156:1983;1165-1170
43. Lahue E. E., Matson S. W. Purified Escherichia coli F-factor TraY protein binds oriT. J. Bacteriol. 172:1990;1385-1391
44. Nelson W. C., Morton B. S., Lahue E. E., Matson S. W. Characterization of the Escherichia coli F factor traY gene product and its binding sites. J. Bacteriol. 175:1993;2221-2228
45. Luo Y., Deonier R. C. Mutational and physical analysis of F plasmid traY protein binding to oriT. Mol. Microbiol. 11:1994;459-469
46. Nelson W. C., Matson S. W. The F plasmid traY gene product binds DNA as a monomer or a dimer: structural and functional implications. Mol. Microbiol. 20:1996;1179-1187
47. Schildbach J. F., Robinson C. R., Sauer R. T. Biophysical characterization of the TraY protein of Escherichia coli F factor. J. Biol. Chem. 273:1998;1329-1333
48. Lanka E., Wilkins B. M. DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64:1995;141-169
49. Howard M. T., Nelson W. C., Matson S. W. Stepwise assembly of a relaxosome at the F plasmid origin of transfer. J. Biol. Chem. 270:1995;28381-28386
50. Raumann B. E., Brown B. M., Sauer R. Y. Major groove DNA recognition by β-sheets: the ribbon-helix-helix family of gene regulatory proteins. Curr. Opin. Struct. Biol. 4:1994;36-43
51. Raumann B. E., Rould M. A., Pabo C. O., Sauer R. T. DNA recognition by β-sheets in the Arc repressor-operator crystal structure. Nature. 367:1994;754-757
52. Lum P. L., Schildbach J. F. Specific DNA recognition by F factor TraY involves β-sheet residues. J. Biol. Chem. 274:1999;19644-19648
53. Wilkins R. C., Lis J. T. Dynamics of potentiation and activation: GAGA factor and its role in heat shock gene regulation. Nucl. Acids Res. 25:1997;3963-3968
54. Parniewski P., Kwinkowski M., Wilk A., Klysik J. Dam methyltransferase sites located within the loop region of the oligopurine-oligopyrimidine sequences capable of forming H-DNA are undermethylated in vivo. Nucl. Acids Res. 18:1990;605-611
55. Klysik J. Both an altered DNA structure and cellular proteins are involved in protecting a triplex forming an oligopurine-rich sequence from Dam methylation in E. coli. Biochem. Genet. 34:1996;165-178
56. 37insert in superhelical plasmids. J. Biol. Chem. 267:1992;5495-5501
57. ninserts. Nucl. Acids Res. 17:1989;9417-9423
58. Aman E., Ochs B., Abel K.-J. Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in Escherichia coli. Gene. 69:1988;301-315
59. Miller J. H. A Short Course in Bacterial Genetics. 1992;Cold Spring Harbor Laboratory Press, Cold Spring Harbor
60. Boiteux S., O’Connor T. R., Laval J. Formamidopyrimidine-DNA glycolsylase of E. coli. EMBO J. 6:1987;3177-3183
61. Kerrigan L. A., Kadonaga J. T. DNA protein interactions. Ausubel F. M. et al. Current Protocols in Molecular Biology. 1989;12.10.1-12.10.8 Green Publishing Associates and Wiley-Interscience, New York
62. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor
63. Krasilnikov A. S., Podtelezhnikov A., Vologodskii A., Mirkin S. M. Large-scale effects of transcriptional DNA supercoiling in vivo. J. Mol. Biol. 292:1999;1149-1160