Structural polymorphism of telomere DNA: interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy.

The solution secondary structures and nucleotide conformations in the telomeric DNA of Oxytricha nova have been determined by Raman spectroscopy. Structural polymorphism is demonstrated for both single-stranded [d(T4G4)4] and double-stranded [d(G4T4G4).d(C4A4C4)] telomere models. In the case of d(T4G4)4, which is a prototype for the single-stranded telomeric tail, an interquadruplex equilibrium involving parallel and antiparallel strand configurations is shown to be governed by the solution concentrations of both Na+ and K+. In both the parallel and antiparallel quadruplexes of d(T4G4)4, the local geometry of the phosphodiester backbone is similar to that of canonical B DNA, and associations between bases of the guanine quartet involve Hoogsteen hydrogen bonding. However, the deoxyguanosine (dG) sugar conformations are significantly different in the two quadruplexes. In the extended parallel form, dG residues assume only the C2'-endo/anti conformation with respect to deoxyribose pucker and glycosyl orientation. In the foldback antiparallel form, dG residues are distributed equally between C2'-endo/anti and C2'-endo/syn conformations. In the case of d(G4T4G4).d(C4A4C4), which serves as a model for the double-stranded B DNA regions of Oxytricha telomeres, we show that disproportionation of the B form duplex to yield stable parallel quadruplexes of the guanine-rich strand occurs reversibly at high solution concentrations of either Na+ or K+. The present study reveals that both interquadruplex and duplex-quadruplex conversions of Oxytricha telomeric DNA are under the control of an alkali cation switch.(ABSTRACT TRUNCATED AT 250 WORDS)