Cation binding to unusual DNA structures: NMR spectroscopy and gel electrophoresis studies

Cation binding environments and the effect of cation binding on duplex, homoduplex and G-quadruplex DNA were investigated by 1H, 23Na NMR and quantitative gel electrophoresis. The guanine-rich strands of telomeric, DNA usually contain thymine but sometimes adenine. G-quartet formation involves the association of four guanine bases through Hoogsteen base pairing in a square planer array.; To determine the roles of the flanking residues at the ends of G-quartets, the effect of different cations on quadruplex formation by the oligonucleotides d(AAGGGGA) and d(TTGGGGT) were studied and the results were compared. Under all experimental cation concentrations, d(AAGGGGA) stabilized the quadruplexes and homoduplexes more than those formed by d(TTGGGGT). In the case of foldback quadruplexes, the effects of different cations on quadruplex formation by the oligonucleotides d(TG4T4G4T) were studied and results were compared with d(G4T4G4). The oligonucleotide displayed structural polymorphism in low, Na+ concentration. The quadruplex formed by d(TG4T4G 4T) in the presence of K+ was more stabilized than in the presence of Na+. The 23Na NMR line shape was bi-Lorentzian suggesting rapid exchange of the specifically bound Na + from the quadruplex core.; Trinucleotide repeats are involved in several human neurodegenarative, diseases such as Fragile X Syndrome. The effect of cations on trinucleotide repeat oligomers as (CGC)n/(CGG)n were studied using gel-electrophoresis and UV melting. We initiated experiments to determine and to characterize factors modulating the equilibria among the self-structures and heteroduplexes. We have discovered very sharp dependence of homoduplex stabilization on monovalent cation concentration and pH. The homoduplex-heteroduplex equilibrium favored the heteroduplex formation in different K+ concentrations and for very short (7--11 mer) oligonucleotides.