A combined NMR-molecular dynamics approach has been applied to determine the
solution structure of a truncated analogue of the Bombyx mori telomeric d(TTAGG)
single repeat sequence in Na+ cation-containing aqueous solution. The two-fold
symmetric four-stranded d(TAGG) quadruplex contains two adjacent
G(syn).G(syn).G(anti).G(anti) G-tetrads sandwiched between novel (T.A).A triads
with individual strands having both a parallel and antiparallel neighbour around
the quadruplex. The (T.A).A triad represents the first experimental verification
of a base triad alignment which constitutes a key postulate in the recently
proposed model of triad-DNA. Further, the (T.A).A triad is generated by
positioning an A residue through hydrogen bonding in the minor groove of a
Watson-Crick T.A base pair and includes a T-A platform related to an A-A
platform recently observed in the structure of the P4-P6 domain of the
Tetrahymena self splicing group I ribozyme. The novel architecture of the
truncated Bombyx mori quadruplex structure sets the stage for the design and
potential identification of additional base tetrads and triads that could
participate in pairing alignments of multi-stranded DNA structures during
chromosome association and genetic recombination.
