STRAND ORIENTATION IN THE DNA QUADRUPLEX FORMED FROM THE OXYTRICHA TELOMERE REPEAT OLIGONUCLEOTIDE D(G4T4G4) IN SOLUTION

The structure formed from the DNA oligonucleotide d(G4T4G4)(Oxy-1.5), which contains the Oxytricha telomere repeat T4G4, has been investigated by two-dimensional H-1 and P-31 NMR spectroscopy. Sequence-specific assignments have been obtained for the H-1 and P-31 resonances, using a combination of methods including comparisons to the inosine- and uracil-containing derivatives d(G4T4G3I) and d(G4UT3G4). The oligonucleotide forms a symmetrical bimolecular G-quadruplex with four G-quartets and thymine loops at opposite ends of the G-quartets. Guanines are alternately syn and anti along each ''strand'' and all of the thymines are anti. The thymines loop diagonally across the G-quartet, resulting in a structure in which adjacent strands are alternately parallel and antiparallel and the glycosidic torsion angles are syn-syn-anti-anti around each G-quartet. There are three different types of grooves, a wide, a narrow, and two medium grooves. A diagonally looped quadruplex is formed in the presence of both Na+ and K+ counterions. The model structure of Oxy-1.5 is compared to the recently published crystal structure of Oxy-1.5 (Kang et al., 1992), which contains many of the same features as those found in solution but differs in that the thymines loop across an edge of the G-quartet.