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Molecular dynamics of structural transitions and intercalation in DNA
Author(s) -
Prabhakaran M.,
Harvey Stephen C.
Publication year - 1988
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.360270805
Subject(s) - intercalation (chemistry) , chemistry , molecular dynamics , dna , crystallography , kinetic energy , energy minimization , helix (gastropod) , chemical physics , computational chemistry , physics , biochemistry , inorganic chemistry , ecology , snail , biology , quantum mechanics
The large‐scale flexibility of DNA and the intercalation of actinomycin D have been studied by computer simulation using molecular dynamics. The stretching and unwinding of B and Z forms of DNA and intercalation in B‐DNA were examined through molecular dynamics simulations, and the energetics of transitions were calculated by the conformational energy minimization method. The principal results of this research are as follows: (1) A dynamic conformational pathway is presented for longitudinal stretching and unwinding of the double helix to open an intercalation site. (2) Large‐scale transitions are possible in both B and Z forms of DNA through a conformationally allowed kinetic pathway. (3) The stretching and untwisting of a 5′(CG)3′ step is energetically more favorable than for a GC step in B‐DNA. (4) The formation of an adjacent second cavity in B‐DNA requires larger energy than the formation of the first cavity, affirming the neighbor‐exclusion principle of intercalation. (5) Docking an intercalated actinomycin D in the stretched structure is shown to be geometrically and energetically feasible.