title: 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# x A, where X = A/G/C/T/2-aminopurine (AP), and * and x 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# x A), and G/AP in the antiparallel motif (G(ap)/AP(ap)*U# x A) is observed. Similarly for pyrimidines in the third strand, C is accepted only in a parallel mode (C(p)*U(#) x A). Significantly, T is recognised in both parallel and antiparallel modes (T(p)/T(ap)*U(#) x 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.
authors.affiliation: Division of Organic Chemistry (Synthesis), National Chemical Laboratory, Pune 411 008, India.
authors.forename: V S
authors.initials: VS
authors.lastname: Rana
authors.forename: K N
authors.initials: KN
authors.lastname: Ganesh
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000235:genetics*; D006801:Humans; D009841:Oligonucleotides; D014498:Uracil / Q000031:analogs & derivatives*
chemical_list: D009841:Oligonucleotides; D014498:Uracil; D004247:DNA; C011166:5-aminouracil