Vs. Rana et Kn. Ganesh, Recognition of 5-aminouracil (U-#) in the central strand of a DNA triplex:orientation selective binding of different third strand bases, NUCL ACID R, 28(5), 2000, pp. 1162-1169
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 dem
onstrates that 5-aminouracil (U-#) (I), a pyrimidine nucleobase analogue of
T in which 5-methyl is replaced by 5-amino group, with hydrogen bonding si
tes 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 recogniti
on selectivity based on the orientation (parallel/antiparallel) of the thir
d 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 antiparall
el 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 cor
responding control 'T' triplexes. The results expand the lexicon of tripler
triads with a recognition motif consisting of pyrimidine in the central st
rand.