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Molecular mechanics studies of parallel and antiparallel phosphate‐methylated DNA
Author(s) -
Van Genderen Marcel H. P.,
Koole Leo H.,
Aagaard Olav M.,
Van Lare Coert E. J.,
Buck Henk M.
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.360260902
Subject(s) - antiparallel (mathematics) , chemistry , molecular mechanics , phosphate , duplex (building) , methylation , dna , crystallography , helix (gastropod) , base pair , stereochemistry , molecular dynamics , computational chemistry , biochemistry , physics , ecology , quantum mechanics , snail , magnetic field , biology
Methylation of phosphate groups in oligo‐dT strands leads to a parallel duplex with T · T base pairs. Molecular mechanics calculations on parallel d() 2 show it to be a symmetric right‐handed helix with B‐DNA conformational characteristics. Phosphate methylation stabilizes the duplex by ca. 41 kcal/mol, due to removal of the interstrand phosphate electrostatic repulsions. The chirality introduced with phosphate methylation is important for the molecular geometry, since R P methylation predominantly influences the conformation around the ζ bond (PO 3′ ), while S P methylation mostly changes the α conformation (PO 5′ ). This is also true in antiparallel helices with methylated phosphates, as is shown by molecular mechanics calculations on d(GCGCGC) 2 . These results may be of relevance to protein–DNA interactions, where phosphate charges are also shielded. As the pro‐S P oxygen is most available in a right‐handed helix, we suggest changes around the α bond to occur upon protein complexation, leading to a widening of the major groove in the d(GCGCGC) 2 duplex (from 12 to 13 Å) and reduced minor groove (from 6 to 5 Å).