Biopolym. Cell. 1987; 3(5):227-234.
http://dx.doi.org/10.7124/bc.0001F4
Structure and Function of Biopolymers
B—Z transition in DNA with an arbitrary base-pair sequence
1Mirkin S. M., 1Lyamichev V. I., 2Kumarev V. P., 2Kobzev V. F., 3Nosikov V. V., 1Vologodskii A. V.
  1. Institute of Molecular Genetics, Academy of Sciences of the USSR
    Moscow, USSR
  2. Institute of Cytology and Genetics, Siberian Branch of the Academy of Sciences of the USSR
    Novosibirsk, USSR
  3. All-Union Institute of Genetics
    Moscow, USSR

Abstract

The energetics of formation of the left-handed Z conformation in DNA with an arbitrary base-pair sequence is considered. A statistical-mechanical model of the B–Z transition includes three states for each base pair. The parameters of the model may be determined from comparison of the theory with experiment on the B–Z transition in synthetic inserts incorporated into supercoiled DNA. Four of six parameters of the model were determined before. To determine the rest two parameters a series of oligonucleotides has been synthesized and inserted into plasmid pUC19. The two-dimensional gel electrophoresis technique has been used to determine the superhelix density which induces the B–Z transition in the inserts. As a result a complete set of six energy parameters of the B–Z transition is known. The transition energy for a given base pair is shown to be independent of the neighbouring base pairs.
Full text: (PDF, in Russian)

References

[1] Brahms S, Vergne J, Brahms JG, Di Capua E, Bucher P, Koller T. Natural DNA sequences can form left-handed helices in low salt solution under conditions of topological constraint. J Mol Biol. 1982;162(2):473-93.
[2] Pohl FM, Thomae R, DiCapua E. Antibodies to Z-DNA interact with form V DNA. Nature. 1982;300(5892):545-6.
[3] 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.
[4] Vologodskii AV. Theoretical model of the B-Z transition in DNA with an arbitrary sequence. Mol Biol (Mosk). 1985;19(4):1062-71.
[5] Peck LJ, Wang JC. Energetics of B-to-Z transition in DNA. Proc Natl Acad Sci U S A. 1983;80(20):6206-10. http:. dx.doi.org. 10.1073. pnas.80.20.6206
[6] 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.
[7] Frank-Kamenetskii MD, Vologodskii AV. Thermodynamics of the B-Z transition in superhelical DNA. Nature. 1984 Feb 2-8;307(5950):481-2.
[8] 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.
[9] 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.
[10] 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.
[11] Rich A, Nordheim A, Wang AH. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791-846.
[12] Vologodskii AV, Amirikyan BR, Lyubchenko YL, Frank-Kamenetskii MD. Allowance for heterogeneous stacking in the DNA helix-coil transition theory. J Biomol Struct Dyn. 1984;2(1):131-48.
[13] Wada A, Suyama A. Local stability of DNA and RNA secondary structure and its relation to biological functions. Prog Biophys Mol Biol. 1986;47(2):113-57.
[14] 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.
[15] Lee CH, Mizusawa H, Kakefuda T. Unwinding of double-stranded DNA helix by dehydration. Proc Natl Acad Sci U S A. 1981;78(5):2838-42.
[16] Nordheim A, Rich A. 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;80(7):1821-5.
[17] Yavachev LP, Georgiev OI, Braga EA, Avdonina TA, Bogomolova AE, Zhurkin VB, Nosikov VV, Hadjiolov AA. Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements. Nucleic Acids Res. 1986;14(6):2799-810.
[18] Yanisch-Perron C, Vieira J, Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103-19.
[19] Kumarev V. P., Kolocheva T. I., Motovilova I. P., Potemkin G. A., Sredin Yu. G. Automatic and semiautomatic synthesis of polydeoxynucleotides by diisopropylphosphamidite method. Russian Journal of Bioorganic Chemistry 1986, 12 (8):1132-1134.
[20] Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977;74(2):560-4.
[21] Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979;7(6):1513-23.
[22] 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.
[23] 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.