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Molecular mechanics studies of parallel and antiparallel phosphate-methylated DNA

✍ Scribed by Marcel H. P. Van Genderen; Leo H. Koole; Olav M. Aagaard; Coert E. J. Van Lare; Henk M. Buck

Publisher: Wiley (John Wiley & Sons)
Year: 1987
Tongue: English
Weight: 704 KB
Volume: 26
Category: Article
ISSN: 0006-3525
DOI: 10.1002/bip.360260902

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✦ Synopsis

Synopsis

Methylation of phosphate groups in oligo-dT strands leads to a parallel duplex with T . T base pairs. Molecular mechanics calculations on parallel d ( l T M T T ) , 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 Rp methylation predominantly influences the conformation around the { bond (P-Ox), while Sp methylation mostly changes the a conformation (P-0,). This is also true in antiparallel helices with methylated phosphates, as is shown by molecular mechanics calculations on d(GCGCGC),. These results may be of relevance to protein-DNA interactions, where phosphate charges are also shielded. As the pro-Sp oxygen is most available in a right-handed helix, we suggest changes around the a bond to occur upon protein complexation, leading to a widening of the major groove in the d(GCGCGC), duplex (from 12 to 13 A) and reduced minor groove (from 6 to 5 A).

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