Electrophoretic behavior of d(GGAAAAAAGG)n, d(CCAAAAAACC)n, and (CCAAAAAAGG)n, and implications for a DNA bending model

Abstract

Double stranded multimers (C2A6C2)n, (C2A6G2)n and (G2A6G2)n were prepared from chemically synthesized oligonucleotides to study the influence of sequences flanking the An tract on the curvature of DNA. All these duplexes, including polypurine.polypyrimidine one, exhibit strong retardation in polyacrylamide gel which is indicative of pronounced DNA curvature. It has been proposed previously that among the bends at the boundary with the oligo(A) tract two types should be distinguished: 5'-bends and 3'-bends (Koo et al., 1986) This distinction was deduced from different relative mobilities of two specially designed sequences having phased 5'-bends and 3'-bends, respectively. Our data indicate that the substitutions of nucleotides at both 5' and 3' boundaries of A6 tract result in comparable changes in relative mobility. Therefore, for B-B' bends it is important to take into account not only whether they are at the 5' or 3' end of an oligo(dA) tract, but also the particular sequences at the boundaries of this tract.