Home LiteratureArticle Details
PMID: 6095187 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Possible structures of homopurine-homopyrimidine S1-hypersensitive sites.

Nucleic acids research ·Vol. 12 ·No. 21 ·1984-11-12 ·Pages 8059-72

Cantor CR, Efstratiadis A

Abstract

S1 nuclease hypersensitive sites in the 5' flanking regions of eukaryotic genes, present in small artificial supercoiled DNA circles, reside in homopurine-homopyrimidine stretches. The hierarchical behavior which these sites exhibit is consistent with the notion that they act as sinks of torsional free energy. By employing DMS as a single-strand-specific reagent, we show that these sites (despite their S1 sensitivity) are regions of duplex DNA. A simple thermodynamic treatment indicates that the high torsional stress in the small DNA circles is almost certain to be relieved by the formation of alternate DNA structures. The same treatment places some constraints on the types and sizes of the regions with alternate conformation. While no definitive structural conclusions can be drawn, left-handed helices seem most consistent with the extent and the pattern of sensitivity to S1 nuclease.

MeSH Terms
Base Sequence DNA DNA, Superhelical Electrophoresis, Polyacrylamide Gel Endonucleases/metabolism Nucleic Acid Conformation Purines Pyrimidines Single-Strand Specific DNA and RNA Endonucleases Substrate Specificity Thermodynamics
Chemicals
DNA, Superhelical Purines Pyrimidines DNA Endonucleases Single-Strand Specific DNA and RNA Endonucleases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Cantor C R
Efstratiadis A
References (35)
35 references, click to expand
  1. Biochemical method for mapping mutational alterations in DNA with S1 nuclease: the location of deletions and temperature-sensitive mutations in simian virus 40.
    Proc Natl Acad Sci U S A. 1975 Mar;72(3):989-93 PMID: 165498
  2. Conformational fluctuations of DNA helix.
    Proc Natl Acad Sci U S A. 1975 Nov;72(11):4275-9 PMID: 172901
  3. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers.
    Proc Natl Acad Sci U S A. 1975 Nov;72(11):4280-4 PMID: 1060106
  4. 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
  5. Sequencing end-labeled DNA with base-specific chemical cleavages.
    Methods Enzymol. 1980;65(1):499-560 PMID: 6246368
  6. Visualization of an unwound DNA duplex.
    Nature. 1980 Oct 9;287(5782):561-3 PMID: 7191477
  7. Conformational flexibility of DNA: polymorphism and handedness.
    Proc Natl Acad Sci U S A. 1980 Nov;77(11):6486-90 PMID: 6935663
  8. Cruciform structures in supercoiled DNA.
    Nature. 1981 Feb 5;289(5797):466-70 PMID: 7464915
  9. Theoretical analysis of competitive conformational transitions in torsionally stressed DNA.
    J Mol Biol. 1981 Jul 25;150(1):43-68 PMID: 7299820
  10. Stable cruciform formation at inverted repeat sequences in supercoiled DNA.
    Biopolymers. 1982 Mar;21(3):679-96 PMID: 7066478
  11. Cruciform structures in palindromic DNA are favored by DNA supercoiling.
    J Mol Biol. 1982 Apr 5;156(2):229-43 PMID: 6283098
  12. Energetic and structural inter-relationship between DNA supercoiling and the right- to left-handed Z helix transitions in recombinant plasmids.
    J Biol Chem. 1982 Sep 10;257(17):10159-65 PMID: 6286642
  13. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions.
    Nature. 1982 Sep 23;299(5881):312-6 PMID: 6287292
  14. 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
  15. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions.
    Nature. 1983 Apr 14;302(5909):632-4 PMID: 6835398
  16. The sequence (dC-dA)n X (dG-dT)n forms left-handed Z-DNA in negatively supercoiled plasmids.
    Proc Natl Acad Sci U S A. 1983 Apr;80(7):1821-5 PMID: 6572943
  17. A dominant role for DNA secondary structure in forming hypersensitive structures in chromatin.
    Cell. 1983 Apr;32(4):1191-203 PMID: 6301683
  18. Mapping of single-stranded regions in duplex DNA at the sequence level: single-strand-specific cytosine methylation in RNA polymerase-promoter complexes.
    Proc Natl Acad Sci U S A. 1983 May;80(9):2544-8 PMID: 6573669
  19. Dynamic, sequence-dependent DNA structure as exemplified by cruciform extrusion from inverted repeats in negatively supercoiled DNA.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:101-12 PMID: 6305553
  20. DNA formed by reassociation of complementary single-stranded circles from natural DNA is shown to contain left- and right-handed double helices.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:119-24 PMID: 6574835
  21. Statistical mechanical analysis of competing conformational transitions in superhelical DNA.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:219-27 PMID: 6574842
  22. Left-handed DNA duplexes.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:45-52 PMID: 6574854
  23. DNA secondary structures: helices, wrinkles, and junctions.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:53-65 PMID: 6574857
  24. DNA supercoiling and its effects on DNA structure and function.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:85-91 PMID: 6345067
  25. Supercoiling and left-handed Z-DNA.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:93-100 PMID: 6574859
  26. Heteronomous DNA.
    Nucleic Acids Res. 1983 Jun 25;11(12):4141-55 PMID: 6866768
  27. Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions.
    Cell. 1983 Jul;33(3):817-29 PMID: 6871994
  28. Detection of an altered DNA conformation at specific sites in chromatin and supercoiled DNA.
    Proc Natl Acad Sci U S A. 1983 Jul;80(14):4389-93 PMID: 6308620
  29. Energetics of B-to-Z transition in DNA.
    Proc Natl Acad Sci U S A. 1983 Oct;80(20):6206-10 PMID: 6578505
  30. Energetics of DNA twisting. II. Topoisomer analysis.
    J Mol Biol. 1983 Nov 15;170(4):983-1007 PMID: 6644817
  31. Conformation of promoter DNA: fine mapping of S1-hypersensitive sites.
    Cell. 1983 Dec;35(3 Pt 2):837-48 PMID: 6197185
  32. Thermodynamics of the B-Z transition in superhelical DNA.
    Nature. 1984 Feb 2-8;307(5950):481-2 PMID: 6694740
  33. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling.
    J Mol Biol. 1984 Feb 15;173(1):75-91 PMID: 6321743
  34. DNA structural variations in the E. coli tyrT promoter.
    Cell. 1984 Jun;37(2):491-502 PMID: 6327070
  35. Poly(pyrimidine) . poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH.
    Nucleic Acids Res. 1984 Aug 24;12(16):6603-14 PMID: 6473110
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/12.21.8059
Published
1984-11-12
Pages
8059-72
Language
English
Region
England
NLM ID
0411011
PMCID
PMC320275
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/12.21.8059 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2