General Features of Triplex Structures

Abstract

Generally, a triplex consists of a duplex, where the base pairs are formed via Watson-Crick hydrogen bonds, and a third strand, whose bases form hydrogen bonds with one base of each base pair of the duplex. In the earlier studies of polymer or oligomer triplexes, at least one of the strands was homopurine, indicating an important role of hydrogen-bonding capabilities of purine bases in the formation of the structure (Felsenfeld et al., 1957; Rich, 1958a,b; Lipsett, 1963, 1964; Miles, 1964; Sasisekharan and Sigler, 1965; Riley et al., 1966; Morgan and Wells, 1968; Thiele and Guschlbauer, 1968, 1971; Marck and Thiele, 1978; Lee et al., 1979). The underlying basis for triplex formation is that purines have potential hydrogen-bonding donors and acceptors that can form two hydrogen bonds with incoming third bases. By contrast, pyrimidine bases already involved in the duplex can form only one additional hydrogen bond with incoming third bases. The hydrogen bonds of such a type are traditionally called Hoogsteen bonds after their discovery in adenine—thymine cocrystals by Hoogsteen in 1959. To form a more stable structure, the third strand bases bind to the purine bases of the duplex.