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PMID: 2995917 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Altered DNA conformations detected by mung bean nuclease occur in promoter and terminator regions of supercoiled pBR322 DNA.

Nucleic acids research ·Vol. 13 ·No. 17 ·1985-09-11 ·Pages 6137-54

Sheflin LG, Kowalski D

Abstract

Mung bean nuclease was used to probe for recognizable DNA unwinding and unpairing in the plasmid pBR322. In negatively supercoiled DNA, but not relaxed DNA, cleavages occurred preferentially in non-coding regions of the genome. The types of nucleotide sequences cleaved and which non-coding regions were cleaved depended upon environmental conditions. At 37 degrees C, cleavages occurred in an 84 bp A+T-rich sequence in the terminator region of the ampicillin-resistance gene. Recognition is likely based on a novel DNA conformation which occurs in the longest, most dA+dT-rich region of pBR322. In the presence of 1 mM Mg2+, cleavages occurred in inverted repeated sequences in the promoter regions of the RNA primer for DNA replication and ampicillin- and tetracycline-resistance genes as well as the terminator of RNA-1. Potential loops of hairpin (cruciform) structures were cleaved. At 27 degrees C, cleavages occurred near a promoter activated by cAMP receptor protein in vitro and in the 3' non-coding region of the tetracycline-resistance gene. Thus, in supercoiled pBR322 DNA, recognizable DNA unwinding and unpairing occurs preferentially in regulatory regions for transcription and DNA replication.

MeSH Terms
Base Sequence DNA Restriction Enzymes DNA, Superhelical/genetics Endonucleases/metabolism Escherichia coli/genetics Genes, Regulator Kinetics Nucleic Acid Conformation Plants/enzymology Plasmids Promoter Regions, Genetic Single-Strand Specific DNA and RNA Endonucleases Substrate Specificity Terminator Regions, Genetic
Chemicals
DNA, Superhelical Endonucleases DNA Restriction Enzymes Single-Strand Specific DNA and RNA Endonucleases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Sheflin L G
Kowalski D
References (64)
64 references, click to expand
  1. A dye-buoyant-density method for the detection and isolation of closed circular duplex DNA: the closed circular DNA in HeLa cells.
    Proc Natl Acad Sci U S A. 1967 May;57(5):1514-21 PMID: 5231757
  2. Evolutionary selection for perfect hairpin structures in viral DNAs.
    Nature. 1982 Aug 5;298(5874):582-5 PMID: 7099254
  3. Thermodynamic properties of superhelical DNAs.
    Biochemistry. 1975 Feb 11;14(3):527-35 PMID: 1111569
  4. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions.
    Nature. 1982 Sep 23;299(5881):312-6 PMID: 6287292
  5. An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin.
    Cell. 1982 Jun;29(2):609-22 PMID: 6288265
  6. Analysis of chromatin structure and DNA sequence organization: use of the 1,10-phenanthroline-cuprous complex.
    Nucleic Acids Res. 1982 Oct 11;10(19):5835-52 PMID: 6292854
  7. Control of ColE1 DNA replication: the rop gene product negatively affects transcription from the replication primer promoter.
    Proc Natl Acad Sci U S A. 1982 Oct;79(20):6313-7 PMID: 6183660
  8. The RNA primer promoter, as defined in vitro, is essential for pMB1 plasmid replication in vivo.
    J Mol Biol. 1982 Sep;160(1):123-6 PMID: 6816942
  9. Perfect palindromic lac operator DNA sequence exists as a stable cruciform structure in supercoiled DNA in vitro but not in vivo.
    Proc Natl Acad Sci U S A. 1983 Apr;80(7):1797-801 PMID: 6340109
  10. Effects of salts, temperature, and stem length on supercoil-induced formation of cruciforms.
    J Biol Chem. 1983 Jun 25;258(12):7661-8 PMID: 6863259
  11. Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions.
    Cell. 1983 Jul;33(3):817-29 PMID: 6871994
  12. Revised sequence of the tetracycline-resistance gene of pBR322.
    Gene. 1983 May-Jun;22(2-3):277-80 PMID: 6307828
  13. Slow cruciform transitions in palindromic DNA.
    Proc Natl Acad Sci U S A. 1983 Sep;80(18):5545-9 PMID: 6577442
  14. Eukaryotic genes--are they under torsional stress?
    Nature. 1983 Sep 22-28;305(5932):276-7 PMID: 6621682
  15. Superhelicity induces hypersensitivity of a human polypyrimidine . polypurine DNA sequence in the human alpha 2-alpha 1 globin intergenic region to S1 nuclease digestion--high resolution mapping of the clustered cleavage sites.
    Nucleic Acids Res. 1983 Nov 25;11(22):7899-910 PMID: 6316277
  16. DNA conformation at the 5' end of the chicken adult beta-globin gene.
    Cell. 1983 Dec;35(2 Pt 1):467-77 PMID: 6317190
  17. Conformation of promoter DNA: fine mapping of S1-hypersensitive sites.
    Cell. 1983 Dec;35(3 Pt 2):837-48 PMID: 6197185
  18. Patterns of DNA structural polymorphism and their evolutionary implications.
    Cell. 1984 Jan;36(1):121-9 PMID: 6319004
  19. S1 nuclease recognizes DNA conformational junctions between left-handed helical (dT-dG n. dC-dA)n and contiguous right-handed sequences.
    J Biol Chem. 1984 Feb 10;259(3):1963-7 PMID: 6319416
  20. A chicken repetitive DNA sequence that is highly sensitive to single-strand specific endonucleases.
    Nucleic Acids Res. 1983 Dec 10;11(23):8495-508 PMID: 6231528
  21. Chromatin assembly in Xenopus oocytes: in vivo studies.
    Cell. 1984 May;37(1):21-32 PMID: 6202419
  22. Cruciform transitions in DNA.
    J Biol Chem. 1984 May 25;259(10):6593-600 PMID: 6373762
  23. Mung bean nuclease cleaves Plasmodium genomic DNA at sites before and after genes.
    Science. 1984 Aug 10;225(4662):625-8 PMID: 6330899
  24. Effect of supercoiling on the abortive initiation kinetics of the RNA-I promoter of ColE1 plasmid DNA.
    J Biol Chem. 1984 Sep 25;259(18):11184-7 PMID: 6206065
  25. Protein-DNA recognition.
    Annu Rev Biochem. 1984;53:293-321 PMID: 6236744
  26. Changes in site specificity of single-strand-specific endonucleases on supercoiled PM2 DNA with temperature and ionic environment.
    Nucleic Acids Res. 1984 Sep 25;12(18):7071-86 PMID: 6091053
  27. Mung bean nuclease cleavage of a dA + dT-rich sequence or an inverted repeat sequence in supercoiled PM2 DNA depends on ionic environment.
    Nucleic Acids Res. 1984 Sep 25;12(18):7087-104 PMID: 6091054
  28. Effect of superhelicity on the transcription from the tet promoter of pBR322. Abortive initiation and unwinding experiments.
    Nucleic Acids Res. 1984 Oct 25;12(20):7741-52 PMID: 6387626
  29. Biology of bacterial deoxyribonucleic acid topoisomerases.
    Microbiol Rev. 1984 Dec;48(4):273-89 PMID: 6097803
  30. The kinetic properties of cruciform extrusion are determined by DNA base-sequence.
    Nucleic Acids Res. 1985 Mar 11;13(5):1443-65 PMID: 4000940
  31. The absence of cruciform structures from pAO3 plasmid DNA in vivo.
    J Biomol Struct Dyn. 1984 Oct;2(2):291-301 PMID: 6401131
  32. Dye titrations of covalently closed supercoiled DNA analyzed by agarose gel electrophoresis.
    Biochem Biophys Res Commun. 1976 Mar 22;69(2):446-54 PMID: 178312
  33. Mung bean nuclease I. Physical, chemical, and catalytic properties.
    Biochemistry. 1976 Oct 5;15(20):4457-63 PMID: 9973
  34. A new method for sequencing DNA.
    Proc Natl Acad Sci U S A. 1977 Feb;74(2):560-4 PMID: 265521
  35. Action of single-strand specific nucleases on model DNA heteroduplexes of defined size and sequence.
    Biochemistry. 1977 May 31;16(11):2374-9 PMID: 301043
  36. An endonuclease activity of venom phosphodiesterase specific for single-stranded and superhelical DNA.
    J Biol Chem. 1977 Dec 10;252(23):8652-9 PMID: 200616
  37. Supercoiling in closed circular DNA: dependence upon ion type and concentration.
    Biochemistry. 1978 Feb 21;17(4):594-601 PMID: 623732
  38. Gene-sized pieces produced by digestion of linear duplex DNA with mung bean nuclease.
    Biochemistry. 1978 Aug 8;17(16):3236-43 PMID: 687580
  39. Comparison of theoretical denaturation maps of phiX174 and SV40 with their gene maps.
    Nucleic Acids Res. 1979 Mar;6(3):1073-9 PMID: 220591
  40. The structure of a transcriptional unit on colicin E1 plasmid.
    Eur J Biochem. 1979 Jul;97(2):435-43 PMID: 380993
  41. Complete nucleotide sequence of the Escherichia coli plasmid pBR322.
    Cold Spring Harb Symp Quant Biol. 1979;43 Pt 1:77-90 PMID: 383387
  42. Comparison of partial denaturation maps with the known sequence of simian virus 40 and phi X174 replicative form DNA.
    J Mol Biol. 1979 Jun 25;131(2):331-40 PMID: 226718
  43. Differential sensitivity of gene expression in vitro to inhibitors of DNA gyrase.
    Proc Natl Acad Sci U S A. 1979 Jul;76(7):3304-8 PMID: 226966
  44. Regulatory sequences involved in the promotion and termination of RNA transcription.
    Annu Rev Genet. 1979;13:319-53 PMID: 94251
  45. Purification and properties of venom phosphodiesterase.
    Methods Enzymol. 1980;65(1):276-84 PMID: 6246352
  46. Supercoils in prokaryotic DNA restrained in vivo.
    Proc Natl Acad Sci U S A. 1980 Mar;77(3):1331-5 PMID: 6246488
  47. Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H.
    Proc Natl Acad Sci U S A. 1980 May;77(5):2450-4 PMID: 6156450
  48. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells.
    Cell. 1980 Oct;21(3):773-83 PMID: 6254668
  49. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules.
    Proc Natl Acad Sci U S A. 1980 Nov;77(11):6468-72 PMID: 6256738
  50. DNA structure and gene regulation.
    Prog Nucleic Acid Res Mol Biol. 1980;24:167-267 PMID: 7005967
  51. Cruciform structures in supercoiled DNA.
    Nature. 1981 Feb 5;289(5797):466-70 PMID: 7464915
  52. Hairpin-loop formation by inverted repeats in supercoiled DNA is a local and transmissible property.
    Nucleic Acids Res. 1981 Mar 25;9(6):1271-89 PMID: 6262723
  53. Organization of transcriptional signals in plasmids pBR322 and pACYC184.
    Proc Natl Acad Sci U S A. 1981 Jan;78(1):167-71 PMID: 7017708
  54. DNA topoisomerases.
    Annu Rev Biochem. 1981;50:879-910 PMID: 6267993
  55. A promoter of pBR322 activated by cAMP receptor protein.
    Nucleic Acids Res. 1981 Jul 24;9(14):3365-77 PMID: 6269081
  56. A rapid boiling method for the preparation of bacterial plasmids.
    Anal Biochem. 1981 Jun;114(1):193-7 PMID: 6269464
  57. Theoretical analysis of competitive conformational transitions in torsionally stressed DNA.
    J Mol Biol. 1981 Jul 25;150(1):43-68 PMID: 7299820
  58. A study of the reversibility of helix-coil transition in DNA.
    Nucleic Acids Res. 1981 Aug 25;9(16):4043-59 PMID: 7301577
  59. Micrococcal nuclease as a probe of DNA sequence organization and chromatin structure.
    Cell. 1981 Nov;27(1 Pt 2):57-64 PMID: 6799212
  60. Homocopolymer sequences in the spacer of a sea urchin histone gene repeat are sensitive to S1 nuclease.
    Nature. 1982 Feb 25;295(5851):714-6 PMID: 6276782
  61. Apple II software for M13 shotgun DNA sequencing.
    Nucleic Acids Res. 1982 Jan 11;10(1):39-49 PMID: 6278410
  62. Action of mung bean nuclease on supercoiled PM2 DNA.
    J Biol Chem. 1982 Jul 10;257(13):7820-5 PMID: 6282855
  63. Precise location of two promoters for the beta-lactamase gene of pBR322. S1 mapping of ribonucleic acid isolated from Escherichia coli or synthesized in vitro.
    J Biol Chem. 1982 Aug 10;257(15):9205-10 PMID: 6178738
  64. Cleavage of circular, superhelical simian virus 40 DNA to a linear duplex by S1 nuclease.
    J Virol. 1973 Dec;12(6):1303-13 PMID: 4357509
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/13.17.6137
Published
1985-09-11
Pages
6137-54
Language
English
Region
England
NLM ID
0411011
PMCID
PMC321943
Subset
IM
Grants
NIGMS NIH HHS · GM30614 · United States
External Links
PubMed source DOI: 10.1093/nar/13.17.6137 PMC Full Text View journal details
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