SOLUTION STRUCTURES OF UNIMOLECULAR QUADRUPLEXES FORMED BY OLIGONUCLEOTIDES CONTAINING OXYTRICHA TELOMERE REPEATS

Background: Oligonucleotides containing the guanine-rich telomeric sequence of Oxytricha chromosomes (dT(4)G(4)) have previously been shown to form DNA quadruplexes comprising guanine quartets stabilized by cations. Two different structures have been reported for both d(G(4)T(4)G(4)) (Oxy1.5) and d(G(4)T(4)G(4)T(4)G(4)T(4)G(4)) (Oxy3.5). Results: Here we present the solution structure of a uracil- and inosine-containing derivative of Oxy3.5, d(G(4)TUTUG(4)T(4)G(4)UUTTG(3)I) (Oxy3.5-U(4)I28), determined using two-dimensional H-1 and P-31 NMR techniques. This oligonucleotide forms a unimolecular quadruplex that is very similar to the dimeric Oxy1.5 solution structure, in that it contains a loop spanning the diagonal of an end quarter. The groove widths, strand polarities, and positions of the syn bases along the G(4) tracts and within the quarters are all as reported for Oxy1.5. The first and third pyrimidine tracts form parallel loops spanning a wide groove and a narrow groove respectively. Conclusions: Both Oxy3.5 and Oxy3.5-U(4)I28 form unimolecular quadruplexes in solution with a diagonal central T-4 loop. These results conflict with those reported for d(G(4)TUTUG(4)TTUUG(4)UUTTG(4)) in solution, in which the central loop spans a wide groove.