Helical Repeats of Left-Handed DNA

DOI: 10.4236/ojmip.2014.42003   PDF   HTML     6,852 Downloads   8,543 Views   Citations

Abstract

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.

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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.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[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.
http://dx.doi.org/10.1073/pnas.72.12.4876
[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.
http://dx.doi.org/10.1093/nar/11.10.2999
[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.
http://dx.doi.org/10.1073/pnas.84.20.7024
[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.
http://dx.doi.org/10.1073/pnas.50.4.730
[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.
http://dx.doi.org/10.1016/j.bpc.2010.02.016
[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.
http://dx.doi.org/10.1073/pnas.200221397
[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.
http://dx.doi.org/10.1093/nar/gks1003
[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.
http://dx.doi.org/10.1126/science.1086823
[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.
http://dx.doi.org/10.1073/pnas.87.15.5788
[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.
http://dx.doi.org/10.1128/JB.186.14.4829-4833.2004
[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.
http://dx.doi.org/10.1073/pnas.72.11.4275
[29] Duguet, M. (1993) The Helical Repeat of DNA at High Temperature. Nucleic Acids Research, 21, 463-468.
http://dx.doi.org/10.1093/nar/21.3.463
[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.
http://dx.doi.org/10.1006/jmbi.2001.5031

  
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