Home LiteratureArticle Details
PMID: 3012460 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Highly selective chemical modification of cruciform loops by diethyl pyrocarbonate.

Nucleic acids research ·Vol. 14 ·No. 10 ·1986-05-27 ·Pages 3995-4007

Furlong JC, Lilley DM

Abstract

Diethyl pyrocarbonate reacts with the single-stranded loops of cruciform structures with great selectivity. Adenine bases are carbethoxylated, as a result of which the backbone may be cleaved with piperidine, and the level of chemical modification at each base may be determined. We have studied the ColE1 and (A-T)34 cruciforms of pColIR315 and pXG540. In each case we observe maximal modification at the most central adenosine of the loop, and an overall pattern of modification corresponding to a total loop size of about six bases. The results may be interpreted in terms of a model in which the loop has a defined tertiary structure. No modification was detected at either cruciform four-way junction, suggesting that this region is fully base-paired.

MeSH Terms
Base Sequence DNA/analysis DNA Restriction Enzymes/metabolism DNA, Bacterial/analysis DNA, Single-Stranded/analysis DNA, Superhelical/analysis Deoxyribonuclease BamHI Deoxyribonuclease EcoRI Diethyl Pyrocarbonate Electrophoresis, Agar Gel Escherichia coli/genetics Formates Nucleic Acid Conformation
Chemicals
DNA, Bacterial DNA, Single-Stranded DNA, Superhelical Formates DNA DNA Restriction Enzymes Deoxyribonuclease BamHI Deoxyribonuclease EcoRI Diethyl Pyrocarbonate
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Furlong J C
Lilley D M
References (33)
33 references, click to expand
  1. The twisted circular form of polyoma viral DNA.
    Proc Natl Acad Sci U S A. 1965 May;53(5):1104-11 PMID: 4287964
  2. Recognition of the structural distortions at the junctions between B and Z segments in negatively supercoiled DNA by osmium tetroxide.
    J Biomol Struct Dyn. 1985 Dec;3(3):467-78 PMID: 3917032
  3. Reaction of diethyl pyrocarbonate with nucleic acid components. Bases and nucleosides derived from guanine, cytosine, and uracil.
    J Am Chem Soc. 1973 Apr 18;95(8):2677-82 PMID: 4694530
  4. Liver-microsome-mediated formation of alkylating agents from vinyl bromide and vinyl chloride.
    Biochem Biophys Res Commun. 1975 Nov 17;67(2):596-603 PMID: 1201042
  5. Polynucleotide kinase exchange reaction: quantitave assay for restriction endonuclease-generated 5'-phosphoroyl termini in DNA.
    J Biol Chem. 1977 May 25;252(10):3176-84 PMID: 16886
  6. DNA gyrase and DNA supercoiling.
    Cold Spring Harb Symp Quant Biol. 1979;43 Pt 1:35-40 PMID: 225107
  7. Molecular structure of a left-handed double helical DNA fragment at atomic resolution.
    Nature. 1979 Dec 13;282(5740):680-6 PMID: 514347
  8. Sequencing end-labeled DNA with base-specific chemical cleavages.
    Methods Enzymol. 1980;65(1):499-560 PMID: 6246368
  9. 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
  10. Cruciform structures in supercoiled DNA.
    Nature. 1981 Feb 5;289(5797):466-70 PMID: 7464915
  11. 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
  12. Sequence-dependent variation in the conformation of DNA.
    J Mol Biol. 1981 Jul 15;149(4):745-60 PMID: 6273590
  13. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure.
    J Mol Biol. 1981 Jul 15;149(4):761-86 PMID: 6273591
  14. 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
  15. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions.
    Nature. 1982 Sep 23;299(5881):312-6 PMID: 6287292
  16. Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling.
    Proc Natl Acad Sci U S A. 1982 Aug;79(15):4560-4 PMID: 6956879
  17. Structural perturbation in supercoiled DNA: hypersensitivity to modification by a single-strand-selective chemical reagent conferred by inverted repeat sequences.
    Nucleic Acids Res. 1983 May 25;11(10):3097-112 PMID: 6304622
  18. Chiral probes for the handedness of DNA helices: enantiomers of tris(4,7-diphenylphenanthroline)ruthenium(II).
    Proc Natl Acad Sci U S A. 1984 Apr;81(7):1961-5 PMID: 6585785
  19. DNA structural variations in the E. coli tyrT promoter.
    Cell. 1984 Jun;37(2):491-502 PMID: 6327070
  20. The supercoil-stabilised cruciform of ColE1 is hyper-reactive to osmium tetroxide.
    EMBO J. 1984 May;3(5):1187-92 PMID: 6329743
  21. Possible structures of homopurine-homopyrimidine S1-hypersensitive sites.
    Nucleic Acids Res. 1984 Nov 12;12(21):8059-72 PMID: 6095187
  22. Unusual frequencies of certain alternating purine-pyrimidine runs in natural DNA sequences: relation to Z-DNA.
    FEBS Lett. 1985 Jun 3;185(1):197-202 PMID: 3996596
  23. The kinetic properties of cruciform extrusion are determined by DNA base-sequence.
    Nucleic Acids Res. 1985 Mar 11;13(5):1443-65 PMID: 4000940
  24. A structural basis for S1 nuclease sensitivity of double-stranded DNA.
    Cell. 1985 Aug;42(1):271-80 PMID: 2990727
  25. Site-specific cleavage of left-handed DNA in pBR322 by lambda-tris(diphenylphenanthroline)cobalt(III).
    Proc Natl Acad Sci U S A. 1985 Oct;82(19):6460-4 PMID: 3863105
  26. Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution.
    Cell. 1985 Oct;42(3):713-24 PMID: 4053183
  27. (AT)n is an interspersed repeat in the Xenopus genome.
    EMBO J. 1985 Oct;4(10):2617-26 PMID: 4054102
  28. Facile cruciform formation by an (A-T)34 sequence from a Xenopus globin gene.
    J Mol Biol. 1985 Oct 5;185(3):461-78 PMID: 2997451
  29. Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA.
    Proc Natl Acad Sci U S A. 1985 Dec;82(23):8009-13 PMID: 3865212
  30. Poly(dG)-poly(dC) sequences, under torsional stress, induce an altered DNA conformation upon neighboring DNA sequences.
    Cell. 1985 Nov;43(1):199-206 PMID: 4075394
  31. Hairpin formation in synthetic oligonucleotides.
    Biochimie. 1985 Jul-Aug;67(7-8):685-95 PMID: 4084598
  32. The structure of cruciforms in supercoiled DNA: probing the single-stranded character of nucleotide bases with bisulphite.
    EMBO J. 1986 Jan;5(1):191-6 PMID: 3007115
  33. Reaction of diethyl pyrocarbonate with nucleic acid components. Adenosine.
    Biochemistry. 1971 Aug 31;10(18):3335-42 PMID: 5118618
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/14.10.3995
Published
1986-05-27
Pages
3995-4007
Language
English
Region
England
NLM ID
0411011
PMCID
PMC339841
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/14.10.3995 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