Magnesium Ion-dependent Triple-helix Structure Formed by Homopurine-homopyrimidine Sequences in Supercoiled Plasmid DNA

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1988 Jun 1

PMID 3375241

Citations 100

Authors

Y Kohwi

T Kohwi-Shigematsu

Affiliations

Soon will be listed here.

Abstract

DNA can be chemically cleaved at the site of chloroacetaldehyde-modified residues by the chemicals used for Maxam-Gilbert sequencing reactions. Use of this technique facilitates fine structural analysis of unpaired DNA bases in DNA with non-B-DNA structure. This method was used to study the non-B-DNA structure adopted by the poly-(dG).poly(dC) sequence under torsional stress at various ionic conditions. In the presence of 2 mM Mg2+, the 5' half of the deoxycytosine tract is very reactive to chloroacetaldehyde, while the 3' half is virtually unreactive. In the poly(dG) tract, chloroacetaldehyde reaction is restricted to the center guanine residues. In the absence of Mg2+, however, it is the 5' half of the deoxyguanine tract that is reactive to chloroacetaldehyde, while the 3' half is unreactive. And chloroacetaldehyde reaction is restricted to the center cytosine residues in the poly(dC) stretch. These results strongly suggest that the poly(dG).poly(dC) sequence is folded into halves from the center of the sequence to form a tetra-stranded-like structure. Such a structure contains either a triplex consisting of poly(dG).poly(dG).poly(dC) strands in the presence of Mg2+ or a triplex consisting of poly(dC).poly(dG).poly(dC) strands in the absence of Mg2+. The fourth strand, not involved in triplex formation, is closely associated with the triplex and is positioned in such a way that DNA bases are exposed and freely accessible to the chloroacetaldehyde reaction.

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References

Morgan A, Wells R . Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J Mol Biol. 1968; 37(1):63-80. DOI: 10.1016/0022-2836(68)90073-9. View

Lyamichev V, Mirkin S, Frank-Kamenetskii M . A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn. 1985; 3(2):327-38. DOI: 10.1080/07391102.1985.10508420. View

Maxam A, Gilbert W . A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977; 74(2):560-4. PMC: 392330. DOI: 10.1073/pnas.74.2.560. View

Kimura K, Nakanishi M, Yamamoto T, Tsuboi M . A correlation between the secondary structure of DNA and the reactivity of adenine residues with chloroacetaldehyde. J Biochem. 1977; 81(6):1699-703. DOI: 10.1093/oxfordjournals.jbchem.a131629. View

Sattsangi P, LEONARD N, Frihart C . 1,N2-ethenoguanine and N2,3-ethenoguanine. Synthesis and comparison of the electronic spectral properties of these linear and angular triheterocycles related to the Y bases. J Org Chem. 1977; 42(20):3292-6. DOI: 10.1021/jo00440a020. View

Marck C, Thiele D, Schneider C, GUSCHLBAUER W . Protonated polynucleotides structures - 22.CD study of the acid-base titration of poly(dG).poly(dC). Nucleic Acids Res. 1978; 5(6):1979-96. PMC: 342139. DOI: 10.1093/nar/5.6.1979. View

Kohwi-Shigematsu T, Enomoto T, YAMADA M, Nakanishi M, Tsuboi M . Exposure of DNA bases induced by the interaction of DNA and calf thymus DNA helix-destabilizing protein. Proc Natl Acad Sci U S A. 1978; 75(10):4689-93. PMC: 336185. DOI: 10.1073/pnas.75.10.4689. View

Lee J, Johnson D, Morgan A . Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded. Nucleic Acids Res. 1979; 6(9):3073-91. PMC: 327918. DOI: 10.1093/nar/6.9.3073. View

Hentschel C . Homocopolymer sequences in the spacer of a sea urchin histone gene repeat are sensitive to S1 nuclease. Nature. 1982; 295(5851):714-6. DOI: 10.1038/295714a0. View

10.

Goding C, Russell W . S1 sensitive sites in adenovirus DNA. Nucleic Acids Res. 1983; 11(1):21-36. PMC: 325688. DOI: 10.1093/nar/11.1.21. View

11.

Mace H, Pelham H, Travers A . Association of an S1 nuclease-sensitive structure with short direct repeats 5' of Drosophila heat shock genes. Nature. 1983; 304(5926):555-7. DOI: 10.1038/304555a0. View

12.

Kohwi-Shigematsu T, Gelinas R, Weintraub H . Detection of an altered DNA conformation at specific sites in chromatin and supercoiled DNA. Proc Natl Acad Sci U S A. 1983; 80(14):4389-93. PMC: 384043. DOI: 10.1073/pnas.80.14.4389. View

13.

Shen C . 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; 11(22):7899-910. PMC: 326548. DOI: 10.1093/nar/11.22.7899. View

14.

Nickol J, Felsenfeld G . DNA conformation at the 5' end of the chicken adult beta-globin gene. Cell. 1983; 35(2 Pt 1):467-77. DOI: 10.1016/0092-8674(83)90180-0. View

15.

Schon E, Evans T, Welsh J, Efstratiadis A . Conformation of promoter DNA: fine mapping of S1-hypersensitive sites. Cell. 1983; 35(3 Pt 2):837-48. DOI: 10.1016/0092-8674(83)90116-2. View

16.

Pulleyblank D, Haniford D, Morgan A . A structural basis for S1 nuclease sensitivity of double-stranded DNA. Cell. 1985; 42(1):271-80. DOI: 10.1016/s0092-8674(85)80122-7. View

17.

Kohwi-Shigematsu T, Kohwi Y . Poly(dG)-poly(dC) sequences, under torsional stress, induce an altered DNA conformation upon neighboring DNA sequences. Cell. 1985; 43(1):199-206. DOI: 10.1016/0092-8674(85)90024-8. View

18.

Siegfried E, Thomas G, Bond U, Elgin S . Characterization of a supercoil-dependent S1 sensitive site 5' to the Drosophila melanogaster hsp 26 gene. Nucleic Acids Res. 1986; 14(23):9425-44. PMC: 311968. DOI: 10.1093/nar/14.23.9425. View

19.

BOLES T, Hogan M . DNA structure equilibria in the human c-myc gene. Biochemistry. 1987; 26(2):367-76. DOI: 10.1021/bi00376a006. View

20.

Kohwi-Shigematsu T, Manes T, Kohwi Y . Unusual conformational effect exerted by Z-DNA upon its neighboring sequences. Proc Natl Acad Sci U S A. 1987; 84(8):2223-7. PMC: 304621. DOI: 10.1073/pnas.84.8.2223. View