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Nucleic Acids Research, 2000, Vol. 28, No. 5 1162-1169
© 2000 Oxford University Press

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

Vipul S. Rana and Krishna N. Ganesh*

Division of Organic Chemistry (Synthesis), National Chemical Laboratory, Pune 411 008, India

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 (Ap*U#·A), and G/AP in the antiparallel motif (Gap/APap*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 (Tp/Tap*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.

* To whom correspondence should be addressed. Tel/Fax: +91 20 589 3153; Email: kng@ems.ncl.res.in


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