A triplex-mediated knot between separated potypurine-polypyrimidine tracts in circular DNA blocks transcription by Escherichia coli RNA polymerase

DNA and Cell Biology

Volumn 19, Issue 4, 2000, Pages 235-241

  Ashley, Carolyn ^a   Lee, Jeremy S ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; DOUBLE STRANDED DNA; PURINE DERIVATIVE; PYRIMIDINE DERIVATIVE; RNA POLYMERASE;

ARTICLE; DNA REPLICATION; DNA SUPERCOILING; ESCHERICHIA COLI; GENE OVEREXPRESSION; GENETIC TRANSCRIPTION; HYDROGEN BOND; PLASMID; PRIORITY JOURNAL; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

BASE SEQUENCE; DNA; DNA REPLICATION; DNA, CIRCULAR; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; HYDROGEN-ION CONCENTRATION; PLASMIDS; PURINES; PYRIMIDINES; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI; EUKARYOTA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0034007996     PISSN: 10445498     EISSN: None     Source Type: Journal    
DOI: 10.1089/104454900314500     Document Type: Article

References (44)

1. Agazie, Y.M., Lee, J.S., and Burkholder, G.D. (1994). Characterization of a new monoclonal antibody to triplex DNA and immunofluorescent staining of mammalian chromosomes. J. Biol. Chem. 269, 7019-7023.
2. Aiyar, S.E., Helmann, J.D., and Dehaseth, P.L. (1994). A mismatch bubble in double-stranded DNA suffices to direct precise transcription initiation by Escherichia coli RNA polymerase. J. Biol. Chem. 269, 13179-13184.
3. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (EDS) (1995). Current Protocols in Molecular Biology, ed 4. (John Wiley and Sons, Toronto, Canada).
4. Bacolla A., Ulrich, M.J., Larson, J.E., Ley, T.J., and Wells, R.D. (1995). An intramolecular triplex in the human γ-globin 5′-flanking region is altered by point mutations associated with hereditary persistence of fetal hemoglobin. J. Biol. Chem. 270, 24556-24563.
5. n tracts. Proc. Natl. Acad. Sci. USA 88, 507-511.
6. Birnboim, H.C., Sederoff, R.R., and Paterson, M.C. (1979). Distribution of polypurine-polypyrimidine segments in DNA from diverse organisms. Eur. J. Biochem. 98, 301-307.
7. Boles, T.C., and Hogan, M.E. (1987). DNA structure in the human c-myc gene. Biochemistry 26, 367-376.
8. Bucher, P., and Yagil, G. (1991). Occurrence of oligopurine-oligopyrimidine tracts in eukaryotic and prokaryotic genes. DNA Sequence 1, 157-172.
9. Burkholder, G.D., Latimer L.J.P., and Lee, J.S. (1991). Immunofluorescent localization of triplex DNA in polytene chromosomes of Chironomus and Drosophila. Chromosoma 101, 11-18.
10. Burkholder, G.D., Latimer, L.J.P., and Lee, J.S. (1988). Immunofluorescent staining of mammalian nuclei and chromosomes with a monoclonal antibody to triplex DNA. Chromosoma 97, 185-192.
11. Daube, S.S., and Von Hippel, P.H. (1992). Functional transcription elongation complexes from synthetic RNA-DNA duplexes. Science 258, 1320-1324.
12. Gross, D.S., and Garrard, W.T. (1988). Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159-197.
13. Guarente, L. (1988). UACs and enhancers: Common mechanism of transcriptional activation in yeast and mammals. Cell 52, 303-305.
14. Hampel, K.J., Ashley, C., and Lee, J.S. (1994). Kilobase-range communication between polypurine-polypyrimidine tracts in linear plasmids mediated by triplex formation: A braided knot between two linear duplexes. Biochemistry 33, 5674-5681.
15. Hampel, K.J., Burkholder, G.D., and Lee, J.S. (1993). Plasmid dimerization mediated by triplex formation between polypurine-polypyrimidine repeats. Biochemistry, 32, 1072-1077.
16. Hampel, K.J., Crosson, P., and Lee, J.S. (1991). Polyamines favour triplex formation at neutral pH. Biochemistry 30, 4455-4459.
17. Hinkle, D.C., Ring, J., and Chamberlin, M.J. (1972). Studies of the binding of Escherichia coli RNA polymerase to DNA III: Tight binding of RNA polymerase holoenzyme to single-stranded breaks in T7 DNA. J. Mol. Biol. 70, 197-207.
18. Hoffman-Liebermann, B., Liebermann, D., Troutt, A., Kedes, L.H., and Cohen, S.N. (1986). Human homologues of TU transposon sequences: Polypurine/polypyrimidine sequence elements that can alter DNA conformation in vitro and in vivo. Mol. Cell. Biol. 6, 3632-3642.
19. Htun, H., and Dalhberg, J.E. (1988). Single strands, triple strands, and kinks in H-DNA. Science 241, 1791-1796.
20. Htun, H., and Dalhberg, J.E. (1989). Topology and formation of triple-stranded H-DNA. Science 243, 1571-1576.
21. n tracts arrest single stranded DNA replication in vitro. Nucleic Acids Res. 17, 883-900.
22. Larsen, A., and Weintraub, H. (1982). An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell 29, 609-622.
23. Lee, J.S., Ashley, C., Hampel, K.J., Bradley, R., and Scraba, D.G. (1995a). A stable interaction between separated pyrimidine-purine tracts in circular DNA. J. Mol. Biol. 252, 283-288.
24. Lee, J.S., Ashley, C., Hampel, K.J., Bradley, R., and Scraba, D.G. (1995b). Triplex mediated knotting in circular DNA: T-loops. Biol. Struct. Dyn. 2, 121-128.
25. Lee, J.S., Woodsworth, M.L., Latimer, L.J.P., and Morgan, A.R. (1984). Poly(pyrimidine)-poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH. Nucleic Acids Res. 12, 6603-6614.
26. Lyamichev, V.I., Mirkin, S.M., and Frank-Kamenetskii, M.D. (1986). Structures of homopurine-homopyrimidine tract in superhelical DNA. J. Biomol. Struct. Dyn. 4, 667-669.
27. Mangel, W.F., and Chamberlin, M.J. (1974). Studies of ribonucleic acid chain initiation by Escherichia coli ribonucleic acid polymerase bound to T7 deoxyribonucleic acid: Assay for the rate and extent of ribonucleic acid chain initiation. J. Biol. Chem. 249, 3007-3013.
28. n sequences. J. Mol. Evol. 27, 96-101.
29. Mirkin, S.M., Lyamichev, V.I., Drushlyak, K.N., Dobrynin, V.N., Filippov, S.A., and Frank-Kamenetskii, M.D. (1987). DNA H form requires a homopurine-homopyrimidine mirror repeat. Nature 330, 495-497.
30. Mollegaard, N.E., Buchardt, O., Egholm, M., and Nielsen, P.E. (1994). Peptide nucleic acid-DNA strand displacement loops as artificial transcription promoters. Proc. Natl. Acad. Sci. USA, 91, 3892-3895.
31. Morgan, A.R., Lee, J.S., Pulleyblank, D.E., Murray, N.L., and Evans, D.H. (1979). Ethidium fluorescence assays I: Physicochemical studies. Nucleic Acids Res. 7:547-569.
32. Ozoline, O.N., and Tsyganov, M.A. (1995). Structure of open promoter complexes with Escherichia coli RNA polymerase as revealed by the DNase I footprinting technique: Compilation analysis. Nucleic Acids Res. 23, 4533-4541.
33. Palecek, E. (1991). Local supercoil-stabilized DNA structures. Crit. Rev. Biochem. Mol. Biol. 26, 151-226.
34. Parvin, J.D., and Sharp, P.A. (1993). DNA topology, and a minimal set of basal factors for transcription by RNA polymerase II. Cell 73, 533-540.
35. Samadashwily, G.M., Dayn, A., and Mirkin, S.M. (1993). Suicidal nucleotide sequences for DNA polymerization. EMBO J. 12, 4975-4983.
36. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor Laboratory, New York).
37. Schleif, R. (1992). DNA looping. Annu. Rev. Biochem. 61, 199-223.
38. Soyfer, V.N., and Potaman, V.N. (1996). Triple-Helical Nucleic Acids. (Springer-Verlag, New York).
39. Spencer, C.A., and Groudine, M. (1990). Transcription elongation and eukaryotic gene regulation. Oncogene 5, 777-785.
40. Thomas, T., and Thomas, T.J. (1993). Selectivity of polyamines in triplex stabilization. Biochemistry 32, 14068-14074.
41. n sequences in human and rodent genomes. J. Biomol. Struct. Dyn, 9, 387-397.
42. Ulrich, M.J., Gray, W.J., and Ley, T.J. (1992). An intramolecular DNA triplex is disrupted by point mutations associated with hereditary persistence of fetal hemoglobin. J. Biol. Chem. 267, 18649-18658.
43. Vogt, V. (1969). Breaks in DNA stimulate transcription by core RNA polymerase. Nature 223, 854-855.
44. Wang, J.C., and Lynch, A.S. (1993). Transcription and DNA supercoiling. Curr. Opin. Genet. Dev. 3, 764-768.