Four-Stranded DNA Structure Stabilized by a Novel G:C:A:T Tetrad

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Abstract
The solution structure of a cyclic oligonucleotide d〈pCGCTCATT〉 has been determined by two-dimensional NMR spectroscopy and restrained molecular dynamics. Under the appropriate experimental conditions, this molecule self-associates, forming a symmetric dimer stabilized by four intermolecular Watson−Crick base pairs. The resulting four-stranded structure consists of two G:C:A:T tetrads, formed by facing the minor groove side of the Watson−Crick base-pairs. Most probably, the association of the base-pairs is stabilized by coordinating a Na+ cation. This is the first time that this novel G:C:A:T tetrad has been found in an oligonucleotide structure. This observation increases considerably the number of sequences that may adopt a four-stranded architecture. Overall, the three-dimensional structure is similar to those observed previously in other quadruplexes formed by minor groove alignment of Watson−Crick base pairs. This resemblance strongly suggests that we may be observing a general motif for DNA−DNA recognition.