Book of Abstracts: Albany 2003
June 17-21 2003
Some New Insights into DNA Triplexes Formed by Non-isomorphous Base Triplets: Concept of Intrinsic ?Residual? Hoogsteen Twist and Sequence Dependent DNA Triplexes
It is well known that DNA can accommodate a third strand along its major groove to form a triplex through sequence specific Hoogsteen/ reverse Hoogsteen hydrogen bonds. Such a triplex formed by the T·AT&C+·GC base triplets is expected to be ?uniform? in much the same way as an ?ideal? DNA duplex due to the isosteric nature of the base triplets, especially in the absence of stereoelectronic effects. On the other hand, DNA triplexes comprising base triplet combinations such as T·AT&G·GC and A·AT&G·GC should necessarily be non-uniform due to their non-isomorphic nature. It is proposed here that the extent of non-isomorphism and its influence on DNA triplex structure can be discerned by recognition of a ?residual? twist angle (Δ°). This is tantamount to a pre-existing helical twist between base pairs of Hoogsteen/reverse Hoogsteen duplex of a DNA triplex even when the applied helical twist (t°) is zero. Non-uniformity in these triplexes may therefore be attributed mainly to mechanistic effects of Δ, besides possible stereoelectronic influence. MD simulations of several nanoseconds on DNA triplexes comprising alternating A·AT&G·GC and T·AT&G·GC triplets taking cognizance of the newly proposed concept of intrinsic ?residual? twist provide several new insights into the structures of DNA triplexes. Some of the prominent outcomes relate to (i) observation of sequence dependent twist angle variations (ii) recognition of an alternating conformation for the third strand in the antiparallel DNA triplex comprising G·GC&T·AT triplets (iii) fluctuating or dynamic nature of G?G Hoogsteen hydrogen bond resulting from large value of Δ, that may be responsible for the unstable nature of parallel triplex formed by G·GC&T·AT triplets and (iv) enhanced stacking interaction in triplexes formed by GA TFOs that may explain their higher stability. Results clearly show that ?residual? twist, intrinsic to non-isomorphous base triplets, causes sequence dependent structural variations in DNA triplexes depending on the magnitude of Δ, in addition to possible stereoelectronic effects.
Superposition of (a) isosteric T·AT&C+·GC and (b)non-isosteric T·AT & G·GC triplets showing the ?residual? twist (Δ°) at t=0°.
Department of Crystallography & Biophysics