Conformational diversity versus nucleic acid triplex stability, a combinatorial study

The stability of a triple helix formed between a DNA duplex and an incoming oligonucleotide strand strongly depends on the solvent conditions and on i ntrinsic chemical and conformational factors. Attempts to increase triple h elix stability in the past included chemical modification of the backbone, sugar ring, and bases in the third strand. However, the predictive power of such modifications is still rather poor. We therefore developed a method t hat allows for rapid screening of conformationally diverse third strand oli gonucleotides for triplex stability in the parallel pairing motif to a give n DNA double helix sequence. Combinatorial libraries of oligonucleotides of the requisite (fixed) base composition and length that vary in their sugar unit (ribose or deoxyribose) at each position were generated. After affini ty chromatography against their corresponding immobilized DNA target duplex , utilizing a temperature gradient as the selection criterion, the oligonuc leotides forming the most stable triple helices were selected and character ized by physicochemical methods. Thus, a series of oligonucleotides were id entified that allowed us to define basic rules for triple helix stability i n this conformationally diverse system. It was found that ribocytidines in the third strand increase triplex stability relative to deoxyribocytidines independently of the neighboring bases and position along the strand. Howev er, remarkable sequence-dependent differences in stability were found for ( deoxy)thymidines and uridines.