A COMPARISON OF DNA OLIGOMER DUPLEXES CONTAINING FORMACETAL AND PHOSPHODIESTER LINKERS USING MOLECULAR-DYNAMICS AND QUANTUM-MECHANICS

The replacement of the phosphodiester linker in a DNA duplex by a form acetal linker has been investigated by computational techniques. Confo rmational energy as a function of torsional angle was initially evalua ted for formacetal and dimethyl phosphate anion using the 6-31G basis set. In these calculations, one COCO or COPO torsional angle was cons trained at 60-degrees, and the second was rotated in 30-degrees increm ents from 0-degrees to 180-degrees. Accurate force field parameters we re developed from these potential surfaces. Molecular dynamics simulat ions, incorporating the force field parameters and NMR-derived restrai nts, were then conducted for a dodecamer duplex, dCGCGTT(OCH2O)TTGCGC/ dGCGCAAAACGCG, with explicit water and counterions. Several simulation s incorporating a range of restraints were conducted for 40-86 ps at 3 00 K. The results were compared to results from simulations of the unm odified DNA duplex of the same sequence. The molecular dynamics simula tions satisfactorily reproduced experimental data obtained from NMR st udies, provided a restraint was used for the C5'C4'-C3'-O3' dihedral a ngle of the deoxyribose moieties to maintain a B-family sugar conforma tion. A well-formed helix is observed with normal base stacking and no apparent structural disruptions in the region of the formacetal linke r. COCO dihedral values are similar to those seen for COPCO in a B-for m duplex. The detrimental effect of the formacetal linker on the T(m) of the duplex (-3-degrees-C) is attributed primarily to the rotation o f one COCO torsional angle into the -90-degrees to -100-degrees range seen in the simulations and common to B-form nucleic acids. The energy cost of this rotation from an optimum gauche conformation is on the o rder of 1.0-1.5 kcal/mol higher than a similar rotation for a COPO tor sion and is due to a much stronger stereoelectronic effect for COCO. C onsequently, this conformational energy difference can explain the obs erved decrease in T(m) caused by incorporation of formacetal linkers.