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Investigating DNA supercoiling in eukaryotic genomes. [PDF]
Briefings in Functional Genomics, 2017 Supercoiling is a fundamental property of DNA, generated by polymerases and other DNA-binding proteins as a consequence of separating/bending the DNA double helix.
Nick Gilbert
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Science, 2012
Watching Supercoiled DNA The DNA double helix can undergo additional twisting, or supercoiling, that plays a role in transciption and protein binding, in part by bringing distant DNA locations together.
M. T. J. van Loenhout +2 more
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Watching Supercoiled DNA The DNA double helix can undergo additional twisting, or supercoiling, that plays a role in transciption and protein binding, in part by bringing distant DNA locations together.
M. T. J. van Loenhout +2 more
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Biophysical Chemistry, 1988
DNA topoisomerase mutants of Escherichia coli and Saccharomyces cerevisiae were used to study the topological state of intracellular DNA. In E. coli, it is shown that switching off the gene topA encoding DNA topoisomerase I leads to an increase in the degree of negative supercoiling of intracellular DNA and inhibition of the growth of the cells: a d ...
G N, Giaever, L, Snyder, J C, Wang
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DNA topoisomerase mutants of Escherichia coli and Saccharomyces cerevisiae were used to study the topological state of intracellular DNA. In E. coli, it is shown that switching off the gene topA encoding DNA topoisomerase I leads to an increase in the degree of negative supercoiling of intracellular DNA and inhibition of the growth of the cells: a d ...
G N, Giaever, L, Snyder, J C, Wang
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Fluctuations and Supercoiling of DNA
Science, 1994Frequently, DNA in vivo is organized into loops that are partially underwound and consequently form interwound helical supercoils. Methods from polymer statistical mechanics are used to show how the competition between entropy (thermal fluctuations) and elastic energy determines supercoil radius and pitch, in good agreement with recent experiments and ...
J F, Marko, E D, Siggia
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Transcription and DNA supercoiling
Current Opinion in Genetics & Development, 1993Transcription and supercoiling of the DNA template are interrelated. This review summarizes recent progress in the study of how template topology affects transcription, and how transcription affects template topology inside wild-type and DNA topoisomerase mutant cells.
J C, Wang, A S, Lynch
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Statistical mechanics of supercoiled DNA
Physical Review E, 1995The conformation of long supercoiled DNA loops under near physiological conditions has been the subject of a long series of laboratory and Monte Carlo experiments, and impressive agreement between theory and experiment has been achieved [1–2]. A closed unnicked DNA loop has fixed linking number: this constraint leads to a competition between twisting ...
, Marko, , Siggia
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Purification of Supercoiled Plasmid
2003Current technologies for the purification of supercoiled plasmids are limited. The use of cesium chloride gradients in the presence of ethidium bromide is time consuming, labor intensive, requires the use of known mutagens and is not conducive to large scale.
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2005
Abstract In the first chapter, we described the classical double-helical structure of DNA, and the local alterations of that structure that can occur as a consequence of specific nucleotide sequences. We hope you now have a good feel for these concepts, and we will move on to the main subject of this book, the supercoiling of DNA, a ...
Andrew D Bates, Anthony Maxwell
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Abstract In the first chapter, we described the classical double-helical structure of DNA, and the local alterations of that structure that can occur as a consequence of specific nucleotide sequences. We hope you now have a good feel for these concepts, and we will move on to the main subject of this book, the supercoiling of DNA, a ...
Andrew D Bates, Anthony Maxwell
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Supercoiling of f-Actin filaments
Journal of Structural Biology, 1990In the X-ray diffraction pattern from oriented gels of actin-containing filaments sampling of layer lines indicating the development of a well-ordered pseudo-hexagonal lattice within the gels at interfilament spacings as large as 13 nm is observed. This value exceeds by 3 nm the largest estimate of an external diameter of pure f-actin.
V V, Lednev, D, Popp
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Supercoiling transitions of closed DNA
Physical Review E, 1994Conformations of closed DNA molecules are considered within a simple elastic model. The interplay of elastic energies of bending and twisting can lead to supercoiling induced by variations of the linking difference. These shape transformations are studied in the limit of a large length to thickness ratio of the molecule.
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