全部 标题 作者
关键词 摘要


Methods for Non-Destructively Separating or Reannealing the Strands of Circular Duplex DNA Chromosomes

DOI: 10.4236/oalib.1103353, PP. 1-31

Subject Areas: Genomics, Molecular Biology, Biochemistry

Keywords: DNA, Z DNA, Helix, Circular, Denature, Plectonemic, Paranemic, Side-by-Side

Full-Text   Cite this paper   Add to My Lib

Abstract

Although it is not widely-known, the strands of circular duplex plasmid and viral chromosomes have been non-destructively separated, and the separated strands have been reconstituted to yield a new duplex structure with all the properties of the native chromosome restored. This suggests a paranemic structure for the DNA, that is, a structure whose strands are not topologically linked by plectonemic (i.e., Watson-Crick) twists. The reason that these phenomena are largely unknown to the general scientific public is that they were either published in obscure journals, or not published at all. Moreover, the methods employed to obtain these results were very difficult, time-consuming and expensive, wherefore they are not likely to be repeated anytime soon. Since these phenomena would be of great interest to the general scientific public, the experiments therefore need to be repeated, but in a way that is easy, fast and inexpensive to perform, so that the results may be readily reproduced in other laboratories. Two such experiments are described herein.

Cite this paper

Biegeleisen, K. (2017). Methods for Non-Destructively Separating or Reannealing the Strands of Circular Duplex DNA Chromosomes. Open Access Library Journal, 4, e3353. doi: http://dx.doi.org/10.4236/oalib.1103353.

References

[1]  Wu, R. and Wu, T.T. (1996) A Novel Intact Circular dsDNA Supercoil. Bulletin of Mathematical Biology, 58, 1171-1185.
https://doi.org/10.1007/BF02458388
[2]  Weil, R. and Vinograd, J (1963) The Cyclic Helix and Cyclic Coil Forms of Polyoma viral DNA. Proceedings of the National Academy of Sciences, 50, 730-738.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC221253/pdf/pnas00238-0150.pdf
[3]  Weil, R. (1963) The Denaturation and the Renaturation of the DNA of Polyoma Virus. Proceedings of the National Academy of Sciences, 49, 480-487.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC299883/
https://doi.org/10.1073/pnas.49.4.480
[4]  Strider, W. (1971) Denatured Replicative Form and Complex DNA of ?X174: Isolation, Renaturation, and Sedimentation Properties. PhD Dissertation, Department of Biochemistry, New York University School of Medicine, New York.
[5]  Strider, W. and Warner, R.C. (1971) Denatured Replicative Form and Complex DNA of ?X174: Isolation and Renaturation. Federation Proceedings, 30, 1053.
[6]  Strider, W., Camien, M.N. and Warner, R.C. (1981) Renaturation of Denatured, Covalently Closed Circular DNA. Journal of Biological Chemistry, 256, 7820-7829.
http://www.jbc.org/content/256/15/7820.full.pdf
[7]  Biegeleisen, K. (2016) The Probable Structure of “Form IV” (Alkali-Denatured Circular DNA). Open Access Library Journal, 3, Article ID: e2386.
https://doi.org/10.4236/oalib.1103114
[8]  Biegeleisen, K. (2016) Form IV: The Final Puzzle Piece.
https://notahelix.net
[9]  Stettler, U.H., Weber, H., Koller, T. and Weissmann, C. (1979) Preparation and Characterization of form V DNA, the Duplex DNA Resulting from Association of Complementary, Circular Single-Stranded DNA. Journal of Molecular Biology, 131, 21-40.
https://doi.org/10.1016/0022-2836(79)90299-7
[10]  Rush, M.G. and Warner, R.C. (1970) Alkali Denaturation of Covalently Closed Circular Duplex Deoxyribonucleic Acid. Journal of Biological Chemistry, 245, 2704- 2708.
http://www.jbc.org/content/245/10/2704.full.pdf html
[11]  Biegeleisen, K. (2016) The Double Non-Helix Part 1: The Science and History of Topologically Non-Linked DNA.
https://notahelix.net
[12]  Biegeleisen, K. (2016) The Double Non-Helix Part 2: The Probable Structure of the Protamine-DNA Complex.
https://notahelix.net
[13]  Biegeleisen, K. (2016) Histone Structure. Part 1: Current Concepts.
https://notahelix.net
[14]  Biegeleisen, K. (2016) Histone Structure. Part 2: A Model Which Places the DNA in the N-Terminal Region of the Octamer.
https://notahelix.net
[15]  Biegeleisen, K. (2016) Histone Structure. Part 3: Possible New Structure for Chromosomes.
https://notahelix.net
[16]  Biegeleisen, K. (2016) Form IV: The Final Puzzle Piece. Slides 145-160.
https://notahelix.net
[17]  Biegeleisen, K. (2016) The Double Non-Helix Part 1: The Science and History of Topologically Non-Linked DNA. Slides 302-345.
https://notahelix.net
[18]  Rodley, G.A., Scobie, R.S., Bates, R.H.T. and Lewitt, R.M. (1976) A Possible Conformation for Double-Stranded Polynucleotides. Proceedings of the National Academy of Sciences USA, 73, 2959-2963.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430891/pdf/pnas00039-0021.pdf
https://doi.org/10.1073/pnas.73.9.2959
[19]  Biegeleisen, K. (2016) Form IV: The Final Puzzle Piece. Slides 147-148.
https://notahelix.net
[20]  Wu, T.T. (1969) Secondary Structures of DNA. Proceedings of the National Academy of Sciences USA, 63, 400-405.
http://www.pnas.org/content/63/2/400.full.pdf html
https://doi.org/10.1073/pnas.63.2.400
[21]  Watson, J.D. and Crick, F.H.C. (1953) A Structure for Deoxyribose Nucleic Acid. Nature, 171, 737-738.
http://www.nature.com/nature/dna50/watsoncrick.pdf
[22]  Yakovchuk, P., Protozanova, E. and Frank-Kamenetskii, M. (2006) Base-Stacking and Base-Pairing Contributions into Thermal Stability of the DNA Double Helix. Nucleic Acids Research, 34, 564-574.
https://doi.org/10.1093/nar/gkj454
[23]  Biegeleisen, K. (2016) The Double Non-Helix Part 1: The Science and History of Topologically Non-Linked DNA. Slides 324-328.
https://notahelix.net
[24]  Pouwels, P.H., Knijnenburg, C.M., Van Rotterdam, J., Cohen, J.A. and Jansz, H.S. (1968) Structure of the Replicative form of Bacteriophage fX174. VI. Studies on Alkali-Denatured Double-Stranded fX DNA. Journal of Molecular Biology, 32, 169-182.
https://doi.org/10.1016/0022-2836(68)90002-8
[25]  Chambers, R.W. (1978) Personal Communication. Prof. Chambers, Now Retired, Has Provided Written Consent for These Unpublished Results to Be Publicly Quoted.
[26]  Biegeleisen, K. (2016) The Double Non-Helix Part 1: The Science and History of Topologically Non-Linked DNA. Slides 346-358.
https://notahelix.net
[27]  Bauer, W. and Vinograd, J. (1968) The Interaction of Closed Circular DNA with Intercalative Dyes. I. The Superhelix Density of SV40 DNA in the Presence and Absence of Dye. Journal of Molecular Biology, 33, 141-171.
https://doi.org/10.1016/0022-2836(68)90286-6
[28]  West, L., Henley, A., Hathaway, S., Ownby, C., Adhikari, J. and Abana, C. (2007) Unpublished Study from Lee University Biology Laboratory, Cleveland.
[29]  Delbrück, M. (1954) On the Replication of Desoxyribonucleic Acid (DNA). Proceedings of the National Academy of Sciences, 40, 783-788.
http://www.pnas.org/content/40/9/783.full.pdf
https://doi.org/10.1073/pnas.40.9.783
[30]  Sasisekharan, V., Pattabiraman, N. and Gupta, G. (1976) Double Stranded Polynucleotides: Two Typical Alternative Conformations for Nucleic Acids. Current Science, 45, 779-783.
[31]  Cyriax, B. and G?th, R. (1978) The Conformation of Double-Stranded DNA. Naturwissenschaften, 65, 106-108.
https://doi.org/10.1007/BF00440551
[32]  Pohl, W.F. and Roberts, G.W. (1978) Topological Considerations in the Theory of Replication of DNA. Journal of Mathematical Biology, 6, 383-402.
https://doi.org/10.1007/BF02463003
[33]  Biegeleisen, K. (2002) Topologically Non-Linked Circular Duplex DNA. Bulletin of Mathematical Biology, 64, 589-609.
https://doi.org/10.1006/bulm.2002.0288
[34]  Delmonte, C. and Mann, L.R.B. (2003) Variety in DNA Secondary Structure. Current Science, 85, 1564-1570.
http://www.iisc.ernet.in/currsci/dec102003/1564.pdf
[35]  Biegeleisen, K. (2006) The Probable Structure of the Protamine-DNA Complex. Journal of Theoretical Biology, 241, 533-540.
https://doi.org/10.1016/j.jtbi.2005.12.015
[36]  Xu, Y.C. (2009) Finding of a Zero Linking Number Topoisomer. Biochimica et Biophysica Acta, 1790, 126-133.
https://doi.org/10.1016/j.bbagen.2008.10.012
[37]  Biegeleisen, K. (2016) A New Histone Structure Which Binds DNA at Its Eight Subunit N-Termini. Open Access Library Journal, 3, Article ID: e2386.
https://doi.org/10.4236/oalib.1102386
[38]  Crick, F.H.C., Wang, J.C. and Bauer, W.R. (1979) Is DNA Really a Double Helix? Journal of Molecular Biology, 129, 449-461.
http://profiles.nlm.nih.gov/ps/access/SCBCDD.pdf
https://doi.org/10.1016/0022-2836(79)90506-0

Full-Text


comments powered by Disqus