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Relevant bibliographies by topics / Writhe transition in circular DNA

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Journal articles

Academic literature on the topic 'Writhe transition in circular DNA'

Author: Grafiati

Published: 22 February 2023

Last updated: 23 February 2023

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Journal articles on the topic "Writhe transition in circular DNA"

1

Gebe, John A., and J. Michael Schurr. "Thermodynamics of the first transition in writhe of a small circular DNA by Monte Carlo simulation." Biopolymers 38, no. 4 (1998): 493–503. http://dx.doi.org/10.1002/(sici)1097-0282(199604)38:4<493::aid-bip5>3.0.co;2-o.

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2

MILLER, DAVID, and CRAIG BENHAM. "FIXED-WRITHE ISOTOPIES AND THE TOPOLOGICAL CONSERVATION LAW FOR CLOSED, CIRCULAR DNA." Journal of Knot Theory and Its Ramifications 05, no. 06 (1996): 859–66. http://dx.doi.org/10.1142/s0218216596000461.

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3

Li, Xiuyan, Yangtao Fan, Qingqing Gao, Hu Chen, and Yanhui Liu. "Identification of effects of YOYO-1 intercalation on the topological states of circular DNA." Modern Physics Letters B 32, no. 20 (2018): 1850231. http://dx.doi.org/10.1142/s0217984918502317.

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YOYO-1 intercalation leads to the reduction of twist rigidity, unwinding of DNA, elongation of DNA contour length and YOYO-1 concentration-dependent persistence length, until now few works identified their roles in determining the topological states of circular DNA. Based on the convolution of the writhe distribution of circular DNA obtained by using Monte Carlo simulation and the twist distribution, effects of YOYO-1 intercalation on the linking number distribution of circular DNA are predicted and identified. YOYO-1 intercalation leads to larger fluctuation, but not to the obvious enlargement of the writhe distribution, so that the variance of the linking number distribution mainly depends on the variance of the twist distribution. The unwinding angle contributes to the drifting of the linking number distribution away from the original equilibrium value of zero and has no effects on the variance of the linking number distribution, converse to the roles of the reduced twist rigidity in the linking number distribution. Furthermore, the method used in the work can be generalized to detect the effects of other intercalators on the topological states of circular DNA.

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4

Tobias, Irwin. "The Twist, Writhe, and Linking Number Distributions in Closed Circular DNA." Journal of Biomolecular Structure and Dynamics 3, no. 2 (1985): 315–25. http://dx.doi.org/10.1080/07391102.1985.10508419.

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5

Bauer, William R., Hisako Ohtsubo, Eiichi Ohtsubo, and Craig J. Benham. "Energetics of Coupled Twist and Writhe Changes in Closed Circular pSM1 DNA." Journal of Molecular Biology 253, no. 3 (1995): 438–52. http://dx.doi.org/10.1006/jmbi.1995.0565.

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6

Zhang, Wenke, Stephanie Allen, Clive J. Roberts, and Panos Soultanas. "The Bacillus subtilis Primosomal Protein DnaD Untwists Supercoiled DNA." Journal of Bacteriology 188, no. 15 (2006): 5487–93. http://dx.doi.org/10.1128/jb.00339-06.

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ABSTRACT The essential Bacillus subtilis DnaD and DnaB proteins have been implicated in the initiation of DNA replication. Recently, DNA remodeling activities associated with both proteins were discovered that could provide a link between global or local nucleoid remodeling and initiation of replication. DnaD forms scaffolds and opens up supercoiled plasmids without nicking to form open circular complexes, while DnaB acts as a lateral compaction protein. Here we show that DnaD-mediated opening of supercoiled plasmids is accompanied by significant untwisting of DNA. The net result is the conversion of writhe (Wr) into negative twist (Tw), thus maintaining the linking number (Lk) constant. These changes in supercoiling will reduce the considerable energy required to open up closed circular plectonemic DNA and may be significant in the priming of DNA replication. By comparison, DnaB does not affect significantly the supercoiling of plasmids. Binding of the DnaD C-terminal domain (Cd) to DNA is not sufficient to convert Wr into negative Tw, implying that the formation of scaffolds is essential for duplex untwisting. Overall, our data suggest that the topological effects of the two proteins on supercoiled DNA are different; DnaD opens up, untwists and converts plectonemic DNA to a more paranemic form, whereas DnaB does not affect supercoiling significantly and condenses DNA only via its lateral compaction activity. The significance of these findings in the initiation of DNA replication is discussed.

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7

Morozov, Vladimir F., Eugene Sh Mamasakhlisov, Arsen V. Grigoryan, Artem V. Badasyan, Shura Hayryan, and Chin-Kun Hu. "Helix–coil transition in closed circular DNA." Physica A: Statistical Mechanics and its Applications 348 (March 2005): 327–38. http://dx.doi.org/10.1016/j.physa.2004.09.037.

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8

Sato, Y., T. Hamada, K. Kubo, T. Kishida, Mazda, and K. Yoshikawa. "2P122 Conformational Transition of DNA : Difference between Linier DNA and Circular DNA." Seibutsu Butsuri 44, supplement (2004): S140. http://dx.doi.org/10.2142/biophys.44.s140_2.

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9

Wu, Chenyi, and Andrew Travers. "Modelling and DNA topology of compact 2-start and 1-start chromatin fibres." Nucleic Acids Research 47, no. 18 (2019): 9902–24. http://dx.doi.org/10.1093/nar/gkz495.

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Abstract We have investigated the structure of the most compact 30-nm chromatin fibres by modelling those with 2-start or 1-start crossed-linker organisations. Using an iterative procedure we obtained possible structural solutions for fibres of the highest possible compaction permitted by physical constraints, including the helical repeat of linker DNA. We find that this procedure predicts a quantized nucleosome repeat length (NRL) and that only fibres with longer NRLs (≥197 bp) can more likely adopt the 1-start organisation. The transition from 2-start to 1-start fibres is consistent with reported differing binding modes of the linker histone. We also calculate that in 1-start fibres the DNA constrains more torsion (as writhe) than 2-start fibres with the same NRL and that the maximum constraint obtained is in accord with previous experimental results. We posit that the coiling of the fibre is driven by overtwisting of linker DNA which, in the most compact forms - for example, in echinoderm sperm and avian erythrocytes - could adopt a helical repeat of ∼10 bp/turn. We argue that in vivo the total twist of linker DNA could be modulated by interaction with other abundant chromatin-associated proteins and by epigenetic modifications of the C-terminal tail of linker histones.

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10

Tomanee, Panarat, and James T. Hsu. "Transition Between Supercoiled and Open Circular Plasmid DNA During Alcohol Precipitation." Journal of Liquid Chromatography & Related Technologies 27, no. 10 (2004): 1483–90. http://dx.doi.org/10.1081/jlc-120034086.

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