Biopolym. Cell. 1986; 2(6):283-292.
Reviews
DNA: supercoiling and alternative structures
1Lazurkin Yu. S.
  1. Institute of Molecular Genetics, Academy of Sciences of the USSR
    Moscow, USSR

Abstract

The effect of superhelicity of DNA on its structure and properties is reviewed. The superhelicity is shown to induce in the DNA double helix three alternative structures: cruciform, the Z form and the H form (a novel structure formed in homopurine-homopyrimidine tracts). Convincing evidence of these structures in vitro is obtained in recent years by the method of two-dimensional gel electrophoresis. Their occurrence in vivo is closely related to specific proteins which stabilize them. These proteins are believed to play an important role in regulation of the gene activity.

References

[1] Gragerob AI, Mirkin SM. Influence of DNA superhelicity on the major genetic processes in prokaryotes. Mol Biol (Mosk). 1980;14(1):8-34.
[2] Kmiec EB, Worcel A. The positive transcription factor of the 5S RNA gene induces a 5S DNA-specific gyration in Xenopus oocyte extracts. Cell. 1985;41(3):945-53.
[3] Frank-Kamenetskii MD, Vologda AV. Topological aspects of the physics of polymers: theory and its biophysical applications. Uspekhi fizicheskikh nauk, 1981; 134 (4):641-73.
[4] Vedenov AA, Dykhne AM, Frank-Kamenetskii MD. The helix-coil transition in DNA. Uspekhi fizicheskikh nauk, 1971; 105 (3):479-519.
[5] Vologodskii AV, Lukashin AV, Anshelevich VV, Frank-Kamenetskii MD. Fluctuations in superhelical DNA. Nucleic Acids Res. 1979;6(3):967-82.
[6] Hsieh TS, Wang JC. Thermodynamic properties of superhelical DNAs. Biochemistry. 1975;14(3):527-35.
[7] Anshelevich VV, Vologodskii AV, Lukashin AV, Frank-Kamenetskii MD. Statistical-mechanical treatment of violations of the double helix in supercoiled DNA. Biopolymers. 1979;18(11):2733-44.
[8] Vologodskii AV, Frank-Kamenetskii MD. Theoretical study of cruciform states in superhelical DNAs. FEBS Lett. 1982;143(2):257-60.
[9] Lilley DM. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc Natl Acad Sci U S A. 1980;77(11):6468-72.
[10] Panayotatos N, Wells RD. Cruciform structures in supercoiled DNA. Nature. 1981;289(5797):466-70.
[11] Wang JC, Peck LJ, Becherer K. DNA supercoiling and its effects on DNA structure and function. Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:85-91.
[12] Lyamichev VI, Panyutin IG, Frank-Kamenetskii MD. Evidence of cruciform structures in superhelical DNA provided by two-dimensional gel electrophoresis. FEBS Lett. 1983;153(2):298-302.
[13] Panyutin I, Klishko V, Lyamichev V. Kinetics of cruciform formation and stability of cruciform structure in superhelical DNA. J Biomol Struct Dyn. 1984;1(6):1311-24
[14] Panyutin I, Lyamichev V, Mirkin S. A structural transition in d(AT)n.d(AT)n inserts within superhelical DNA. J Biomol Struct Dyn. 1985;2(6):1221-34.
[15] Greaves DR, Patient RK, Lilley DM. Facile cruciform formation by an (A-T)34 sequence from a Xenopus globin gene. J Mol Biol. 1985;185(3):461-78.
[16] Haniford DB, Pulleyblank DE. Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo. Nucleic Acids Res. 1985;13(12):4343-63.
[17] Vologodskii AV, Frank-Kamenetskii MD. The relaxation time for a cruciform structure in superhelical DNA. FEBS Lett. 1983;160(1-2):173-6.
[18] Nordheim A, Lafer EM, Peck LJ, Wang JC, Stollar BD, Rich A. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell. 1982;31(2 Pt 1):309-18.
[19] Rich A, Nordheim A, Wang AH. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791-846.
[20] Singleton CK, Klysik J, Stirdivant SM, Wells RD. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature. 1982;299(5881):312-6.
[21] Haniford DB, Pulleyblank DE. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions. Nature. 1983;302(5909):632-4.
[22] Frank-Kamenetskii MD, Vologodskii AV. Thermodynamics of the B-Z transition in superhelical DNA. Nature. 1984 Feb 2-8;307(5950):481-2.
[23] Singleton CK, Klysik J, Wells RD. Conformational flexibility of junctions between contiguous B- and Z-DNAs in supercoiled plasmids. Proc Natl Acad Sci U S A. 1983;80(9):2447-51.
[24] Wang AH, Gessner RV, van der Marel GA, van Boom JH, Rich A. Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence. Proc Natl Acad Sci U S A. 1985;82(11):3611-5.
[25] Ellison MJ, Kelleher RJ 3rd, Wang AH, Habener JF, Rich A. Sequence-dependent energetics of the B-Z transition in supercoiled DNA containing nonalternating purine-pyrimidine sequences. Proc Natl Acad Sci U S A. 1985;82(24):8320-4.
[26] Vologodskii AV. Theoretical model of the B-Z transition in DNA with an arbitrary sequence. Mol Biol (Mosk). 1985;19(4):1062-71.
[27] Cantor CR, Efstratiadis A. Possible structures of homopurine-homopyrimidine S1-hypersensitive sites. Nucleic Acids Res. 1984;12(21):8059-72.
[28] Nickol JM, Felsenfeld G. DNA conformation at the 5' end of the chicken adult beta-globin gene. Cell. 1983;35(2 Pt 1):467-77.
[29] Pulleyblank DE, Haniford DB, Morgan AR. A structural basis for S1 nuclease sensitivity of double-stranded DNA. Cell. 1985;42(1):271-80.
[30] Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD. A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn. 1985;3(2):327-38.
[31] Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD. Structures of homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn. 1986;3(4):667-9.
[32] Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD. A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. Biopolym Cell. 1986; 2(3):115-24
[33] Lee JS, Johnson DA, Morgan AR. Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded. Nucleic Acids Res. 1979;6(9):3073-91.
[34] Lyamichev V, Panyutin I, Mirkin S. The absence of cruciform structures from pAO3 plasmid DNA in vivo. J Biomol Struct Dyn. 1984;2(2):291-301.
[35] Mirkin SM, Duzhyy DYe, Panyutin IG, Lyamichev VI. Detection cruciform structures in supercoiled plasmid DNA in vivo. Physico-chemical properties of biopolymers in solution and cells: Proc. of reports Int. symp. Pushchino, 1985; P. 89.
[36] Haniford DB, Pulleyblank DE. The in-vivo occurrence of Z DNA. J Biomol Struct Dyn. 1983;1(3):593-609.
[37] Kmiec EB, Holloman WK. Synapsis promoted by Ustilago rec1 protein. Cell. 1984;36(3):593-8.
[38] Azorin F, Rich A. Isolation of Z-DNA binding proteins from SV40 minichromosomes: evidence for binding to the viral control region. Cell. 1985;41(2):365-74.
[39] Emerson BM, Lewis CD, Felsenfeld G.Interaction of specific nuclear factors with the nuclease-hypersensitive region of the chicken adult beta-globin gene: nature of the binding domain. Cell. 1985;41(1):21-30.
[40] Luchnik AN, Bakayev VV, Zbarsky IB, Georgiev GP. Elastic torsional strain in DNA within a fraction of SV40 minichromosomes: relation to transcriptionally active chromatin. EMBO J. 1982;1(11):1353-8.
[41] Ryoji M, Worcel A. Chromatin assembly in Xenopus oocytes: in vivo studies. Cell. 1984;37(1):21-32.
[42] Glikin GC, Ruberti I, Worcel A. Chromatin assembly in Xenopus oocytes: in vitro studies. Cell. 1984;37(1):33-41.