OJMIP  Vol.4 No.2 , May 2014
Helical Repeats of Left-Handed DNA
Author(s) Youcheng Xu*
DNA is generally assumed as a right-handed double helix and Z-DNA is a special kind of left-handed DNA infrequently found in nature. However, the finding of a zero linking number topoisomer supports a hypothesis that the two strands of DNA are winding ambidextrously, rather than plectonemically. It logically leads to a notion that the left-handed DNA is as common as right-handed DNA and the amount of left-handed DNA in a positively supercoiled plasmid prevails that of the right-handed DNA. In this report, the helical repeat of left-handed DNA, 12 bp per turn, was determined by a new method. How the positively supercoiled DNA was generated in hyperthermophiles and why their DNA can withstand the extreme high temperature are answered from an alternative theory.

Cite this paper
Xu, Y. (2014) Helical Repeats of Left-Handed DNA. Open Journal of Molecular and Integrative Physiology, 4, 20-26. doi: 10.4236/ojmip.2014.42003.
[1]   Wang, A.H.J., et al. (1979) Molecular Structure of a Left-Handed Double Helical DNA Fragment at Atomic Resolution. Nature, 282, 680-686. http://dx.doi.org/10.1038/282680a0

[2]   Xu, Y.C. (2009) Finding of a Zero Linking Number to Poisomer. Biochimica et Biophysica Acta, 1790, 126-133.

[3]   Xu, Y.C. (2011) Replication Demands an Amendment of the Double Helix. In: Seligmann, H., Ed., DNA Replication-Current Advances, InTech, Rijeka, 29-56.

[4]   Keller, W. (1975) Determination of the Number of Superhelical Turns in Simian Virus 40 DNA by Gel Electrophoresis. Proceedings of the National Academy of Sciences of the United States of America, 72, 4876-4880.

[5]   Crick, F.H.C., Wang, J.C. and Bauer, W.R. (1979) Is DNA Really a Double Helix? Journal of Molecular Biology, 129, 499-461. http://dx.doi.org/10.1016/0022-2836(79)90506-0

[6]   Lockshon, D. and Morris, D.R. (1983) Positively Supercoiled Plasmid DNA Is Produced by Treatment of Escherichia Coli with DNA Gyrase Inhibitors. Nucleic Acids Research, 11, 2999-3017.

[7]   Liu, L.F. and Wang. J.C. (1987) Supercoiling of the DNA Template during Transcription. Proceedings of the National Academy of Sciences of the United States of America, 84, 7024-7027.

[8]   Wu, H.Y., Shyy, S., Wang, J.C. and Liu, L.F. (1988) Transcription Generates Positively and Negatively Supercoiled Domains in the Template. Cell, 53, 433-440. http://dx.doi.org/10.1016/0092-8674(88)90163-8

[9]   Tsao, Y.P., Wu, H.Y. and Liu, F. (1989) Transcription-Driven Supercoiling of DNA: Direct Biochemical Evidence from in Vitro Studies. Cell, 56, 111-118. http://dx.doi.org/10.1016/0092-8674(89)90989-6

[10]   Xu, Y.C. and Bremer, H. (1997) Winding of DNA Helix by Divalent Metal Ions. Nucleic Acids Research, 25, 4067-4071. http://dx.doi.org/10.1093/nar/25.20.4067

[11]   Weil, J.H. and Vinograd, J. (1963) The Cyclic Helix and Cyclic Coil Forms of Polyoma Viral DNA. Proceedings of the National Academy of Sciences of the United States of America, 50, 730-738.

[12]   White, J.H. (1969) Self-Linking and the Gauss Integal in Higher Dimensions. American Journal of Mathematics, 41, 693-728. http://dx.doi.org/10.2307/2373348

[13]   Vinograd, J. and Lebowitz, J. (1966) Physical and Topological Properties of Circular DNA. The Journal of General Physiology, 49, 103-125. http://dx.doi.org/10.1085/jgp.49.6.103

[14]   Wang, J.C. (1976) Helical Repeat of DNA in Solution. Proceedings of the National Academy of Sciences of the United States of America, 76, 200-203. http://dx.doi.org/10.1073/pnas.76.1.200

[15]   Charbonnier, F.F., Erauso, G., Barbeyron, T., Prieur, D. and Forterre, P. (1992) Evidence That a Plasmid from a Hyperthermophilic Archaebacterium Is Relaxed at Physiological Temperatures. Journal of Bacteriology, 174, 6103-6108.

[16]   Vetcher, A.A., McEwen, A.E., Abujarour, R., Hanke, A. and Levene, S.D. (2010) Gel Mobilities of Linking Number Topoisomers and Their Dependence on DNA Helical Repeat and Elasticity. Biophysical Chemistry, 148, 104-111.

[17]   Qu, X., Trent, J.O., Fokt, I., Priebe, W. and Chaires, J.B. (2000) Allosteric, Chiral-Selective Drug Binding to DNA. Proceedings of the National Academy of Sciences of the United States of America, 97, 12032-12037.

[18]   Sumners, D.W. (1987) The Role of Knot Theory in DNA Research. In: McCrory, C. and Shifrin, T., Eds., Geometry and Topology, Marcel Dekker, Inc., New York, 297-318.

[19]   Popper, K. (1963) Conjectures and Refutations. Routledge & Kegan Paul, London, 9.

[20]   Moradi, M., Babin, V., Roland, C. and Sagus, C. (2013) Reaction Path Ensemble of the B-Z-DNA Transition: A Comprehensive Atomistic Study. Nucleic Acids Research, 41, 33-43.

[21]   Du, X.J., Wojtowicz, D., Bowers, A.A., Levens, D., Benham, C.J. and Przytycka, T.M. (2013) The Genome-Wide Distribution of Non-B DNA Motifs Is Shaped by Operon Structure and Suggests the Transcriptional Importance of Non-B DNA Structures in Escherichia coli. Nucleic Acids Research, 41, 5965-5977. http://dx.doi.org/10.1093/nar/gkt308

[22]   Kashefi, K. and Lovley, D.R. (2003) Extending the Upper Temperature Limit for Life. Science, 301, 934.

[23]   Stein, D.B. and Searcy, G.D. (1978) Physiologically Important Stabilization of DNA by a Prokaryotic Histone-Like Protein. Science, 202, 219-221. http://dx.doi.org/10.1126/science.694528

[24]   Sandman, K., Krzycki, J.A., Dobinski, B., Lurz, R. and Reeve, J.N. (1990) HMf, a DNA-Binding Protein Isolated from the Hyperthermophilic Archaeon Methanothermus fervidus, Is Most Closely Related to Histones. Proceedings of the National Academy of Sciences of the United States of America, 87, 5788-5791.

[25]   Forterre, P. and Elie, C. (1993) Chromosome Structure, DNA Topoisomerases and DNA Polymerases in Archaebacteria. In: Kates, M., Kushnes, D. and Matheson, A., Eds., The Biochemistry of Archaea, Vol. 26, Elsevier Science Publisher, Amsterdam, 325-361. http://dx.doi.org/10.1016/S0167-7306(08)60260-4

[26]   Kikuchi, K. (1990) Reverse Gyrase and Other Archaebacterial Topoisomerases. In: Cozzarelli, N.R. and Wang, J.C., Eds., DNA Topology and Its Biological Effects, Cold Spring Harbor Laboratory Press, New York, 285-298.

[27]   Atomi, H.R., Matsumi, R. and Imanaka, T. (2004) Reverse Gyrase Is not a Prerequisite for Hyperthermophilic Life. Journal of Bacteriology, 186, 4829-4833.

[28]   Depew, D.E. and Wang, J.C. (1975) Conformational Fluctuations of DNA Helix. Proceedings of the National Academy of Sciences of the United States of America, 72, 4275-4279.

[29]   Duguet, M. (1993) The Helical Repeat of DNA at High Temperature. Nucleic Acids Research, 21, 463-468.

[30]   Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning. Cold Spring Harbor Laboratory Press, New York.

[31]   Cherny, D.I. and Jovin, T.M. (2001) Electron and Scanning Force Microscopy Studies of Alteration in Supercoiled DNA Tertiary Structure. Journal of Molecular Biology, 313, 295-307.