d(G3T4G3) forms an asymmetric diagonally looped dimeric quadruplex with guanosine 5′-syn-syn-anti and 5′-syn-anti-anti N-glycosidic conformations

Abstract

The structure formed by the DNA oligonucleotide d(G3T4G3) has been studied by one- and two-dimensional 1H NMR spectroscopy. In NaCl solution, d(G3T4G3), like d(G4T4G4) (Oxy-1.5), forms a dimeric quadruplex with the thymines in loops across the diagonal of the end quartets. Unlike Oxy-1.5, the dimer is not symmetric, and both monomer strands are observed in NMR spectra. Three quartets are formed from the GGG tracts. Glycosidic conformations of the guanines are 5′-syn-syn-anti-(loop)-syn-anti-anti in one strand and 5′-syn-anti-anti-(loop)-syn-syn-anti in the other strand. Thus, the stacking of the quartets (tail-to-tail, head-to-tail) is unlike all previously described fold-back (tail-to-tail, head-to-head) and parallel-stranded (head-to-tail, head-to-tail) quadruplexes.