Recognition of 5-aminouracil (U) in the central strand of a DNA triplex: Orientation selective binding of different third strand bases

Abstract

A necessary feature of the natural base triads for triplex formation is the requirement of a purine (A or G) in the central position, since only these provide sets of two hydrogen bond donors/acceptors in the major groove of the double helix. Pyrimidine bases devoid of this feature have incompatible complementarity and lead to triplexes with lower stability. This paper demonstrates that 5-aminouracil (U) (I), a pyrimidine nucleobase analogue of T in which 5-methyl is replaced by 5-amino group, with hydrogen bonding sites on both sides, is compatible in the central position of triplex triad X*U·A, where X = A/G/C/T/2-aminopurine (AP), and * and · represent Hoogsteen and Watson-Crick hydrogen bonding patterns respectively. A novel recognition selectivity based on the orientation (parallel/antiparallel) of the third strand purines A, G or AP with A in the parallel motif (A(p)*U·A), and G/AP in the antiparallel motif (G(ap)/AP(ap)*U·A) is observed. Similarly for pyrimidines in the third strand, C is accepted only in a parallel mode (C(p)*U·A). Significantly, T is recognised in both parallel and antiparallel modes (T(p)/T(ap)*U·A), with the antiparallel mode being stable compared to the parallel one. The 'U' triplexes are also more stable than the corresponding control 'T' triplexes. The results expand the lexicon of triplex triads with a recognition motif consisting of pyrimidine in the central strand.