Flanking sequence effects within the pyrimidine triple-helix motif characterized by affinity cleaving

Abstract

Nearest neighbor interactions affect the stabilities of triple-helical complexes. Within a pyrimidine triple-helical motif, the relative stabilities of natural base triplets T·AT, C+GC, and G·TA, as well as triplets, D_3·TA and D_3·CG, containing the nonnatural deoxyribonucleoside 1-(2-deoxy-β-D-ribofuranosyl)-4-(3- benzamido)phenylimidazole (D_3) were characterized by the affinity cleaving method in the context of different flanking triplets (T·AT, T·AT; T·AT, C+GC; C+GC, T·AT; G+GC, C+GC). The T·AT triplet was shown to be insensitive to substitutions in either the 3' or 5' directions, while the relative stabilities of triple helices containing C+GC triplets decreased as the number of adjacent C+GC triplets increased. Triple helices incorporating a G·TA interaction were most stable when this triplet was flanked by two T·AT triplets and were adversely affected when a C+GC triplet was placed in the adjacent 5' direction. Similarly, complexes containing D_3·TA or D_3·CG triplets were most stable when the triplet was flanked by two T·AT triplets but were destabilized when the adjacent 3' neighbor position was occupied with a C+GC triplet. This information regarding sequence composition effects in triple-helix formation establishes a set of guidelines for targeting sequences of double-helical DNA by the pyrimidine triple-helix motif.

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