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Loop energy in DNA
Author(s) -
Blake R. D.,
Delcourt Scott G.
Publication year - 1987
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360261204
Subject(s) - loop (graph theory) , stacking , chemistry , stiffness , chain (unit) , ideal (ethics) , dna , base pair , function (biology) , resolution (logic) , crystallography , orientation (vector space) , ring (chemistry) , thermodynamics , physics , combinatorics , geometry , mathematics , biochemistry , genetics , biology , quantum mechanics , philosophy , organic chemistry , epistemology , artificial intelligence , computer science
The loop function ƒ( N ), representing the statistical weight of N complementary residues in a closed ring, has been determined by analysis of high‐resolution melting curves of a series of recombinant homopoly(A · T) N inserts in pBR322 DNA, where 150 > N > 50 base pairs (bp). Loops are found more stable and therefore presumably less elastic than expected for an ideal, freely jointed chain. A value of 97 ± 2 bp is obtained for the empirical orientation‐stiffness parameter D in the expression for nonideal chains, ƒ( N ) = ( N + D ) −1.7 . The 10% increase in apparent stiffness over that of an ideal chain closely coincides with the extent of residual stacking in the loop. It is thus concluded that the more favorable loop energy, such as expected of smaller loops, is due to the incipient helical orientation of some residues, predisposing the loop to reclosure. A quantitative loop function is essential for the prediction and assignment of domains in DNA.