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

A necessary feature of the natural base triads for tripler 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 tripler triad X*U-# A, where X = A/G/C/T/2-aminopurine (AP), and k 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 Vie 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 (Cp*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 tripler triads with a recognition motif consisting of pyrimidine in the central strand.