1984
DOI: 10.1002/bip.360230503
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DNA–topoisomer analysis on the basis of the helical wormlike chain

Abstract: In a recent paper,' we evaluated the ring-closure probability with the end orientations specified, or the corresponding Jacobson-Stockmayer ( J ) factor,2 defined as the ratio of equilibrium constants for cyclization and bimolecular association, for a twisted wormlike chain, that is, a special case of the helical wormlike chain.3--5For short contour lengths, evaluation has been made through (topological-) linking-number-dependent ring-closure probabilities. Also, the equation for the J factor has been applied … Show more

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Cited by 19 publications
(11 citation statements)
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“…n = 0.5. We obtain for this n { ( Wr) 2 } = (0.8±0.3) 10-3 , whereas on the basis of data from (20,21) one can arrive at the figure of 1.0·10-3 • Thus, for very small as well as for large n our present calculations agree with available theoretical data.…”
Section: Frank-kamenetskii Eta/supporting
confidence: 84%
See 2 more Smart Citations
“…n = 0.5. We obtain for this n { ( Wr) 2 } = (0.8±0.3) 10-3 , whereas on the basis of data from (20,21) one can arrive at the figure of 1.0·10-3 • Thus, for very small as well as for large n our present calculations agree with available theoretical data.…”
Section: Frank-kamenetskii Eta/supporting
confidence: 84%
“…Let us compare our data with the results of Shimada and Yamakawa (20,21). Since their analysis presupposes that n = L!2a is small, such a comparison is sensible only …”
Section: Resultsmentioning
confidence: 80%
See 1 more Smart Citation
“…At the other extreme, when the length of DNA separating the sites decreases, the stiffness of the DNA should hold the sites (and the proteins bound to the sites) apart and hinder loop formation. Maximal loop formation ought to occur at some intermediate loop size, much like the maximum that is seen in DNA ring closure or cyclization as a function of DNA length (5,13,14).…”
mentioning
confidence: 98%
“…Traditional concepts hold that chromatin remodeling factors are important for this process (6), but there is a chicken-and-egg situation inherent in this scenario: how do remodeling factors access the DNA and "relax" its association with the nucleosome if the DNA is wrapped so tightly that the remodeling factors themselves cannot gain access? Because short promoter sequences are believed to be relatively stiff (12,14), it seems unlikely that transcriptional complexes, by themselves, impart sufficient energy to overcome the intrinsic rigidity of the DNA sequence, unwrapping it from the associated nucleosome. However, introduction of a dsDNA nick could serve to relax the DNA, while base oxidation products, such as 8-oxoguanine or its repair intermediate, an abasic site, introduce considerable tortional flexibility (1,11).…”
mentioning
confidence: 99%