THE BI-LOOP, A NEW GENERAL 4-STRANDED DNA MOTIF

The crystal structure of the cyclic octanucleotide d[pATTCATTC] contai ns two independent molecules that form a novel quadruplex by means of intermolecular Watson-Crick A.T pairs and base stacking, A virtually i dentical quadruplex composed of G.C pairs was found by earlier x-ray a nalysis of the linear heptamer d(GCATGCT), when the DNA was looped in the crystal, The close correspondence between these two structures of markedly dissimilar oligonucleotides suggests that they are both examp les of a previously unrecognized motif. Their nucleotide sequences hav e little in common except for two separated 5'-purine-pyrimidine dinuc leotides forming the quadruplex, and by implication these so-called '' bi-loops'' could occur widely in natural DNA, Such structures provide a mechanism for noncovalent linking of polynucleotides in vivo. Their capacity to associate by base stacking, demonstrated in the crystal st ructure of d(GCATGCT), creates a compact molecular framework made up o f four DNA chains within which strand exchange could take place.