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Effect of structural perturbations on helix–coil transitions in covalently closed supercoiled dna
Author(s) -
Majumdar Rabi,
Thakur Ashoke R.
Publication year - 2009
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560280722
Subject(s) - dna supercoil , macromolecule , premelting , superhelix , cooperativity , chemistry , crystallography , helix (gastropod) , base pair , covalent bond , dna , melting point , biology , dna replication , ecology , biochemistry , organic chemistry , snail
The role of base‐pair cooperativity in causing the helix‐coil transition or the “melting” of a linear hydrogen‐bonded macromolecule like DNA is well known. In the present paper, the melting curve for the covalently closed supercoiled DNA is studied, on the basis of statistical mechanics, by assuming the existence of supercoil‐induced cruciforms as significant structural perturbations over the usual regular helical sequence and the bubbles in the premelting region of the macromolecule. In comparison, the nicked circular DNA, like the linear macromolecule, is assumed to consist of the regular helical sequences and the bubbles only. The partition functions are obtained on the basis of the appropriate sequence‐generating functions, so that the number of helical units at a given temperature can be determined. The results are compared with the available experimental data in tetraethylammonium bromide (TEA) solution where the effect of the base‐pair heterogeneity is minimized. The higher melting point and the flatter melting curve for the supercoiled DNA, as obtained from theory, are found to be in close agreement with the corresponding experimental observation.