Conformational Flexibility of Deoxyoligonucleotide d(GGTATACC)(2) in Water

AT-rich deoxyoligonucleotide provides a binding site possibly at the minor groove for some anti-tumor drugs by hydrophobic or Van der Waals interactions. In this paper, it is demonstrated by study of d (GGTATACC)(2) that the DNA-drug interaction may be dependent on the structural flexibility at the minor groove. The solution structure of d (GGTATACC)(2) in water is described by distance-restrained molecular dynamics calculation and it is suggested that d (GGTATACC)(2) in solution maintains the double helix of B-type with trans conformations of base to sugar and C2'-endo conformation for the deoxyribose ring. It is found that the end moieties GGT and ACC are relatively rigid while T(5) residue is flexible, which may account for the activity of the minor groove.