Kinetics and mechanism of K+ and Na +-induced folding of models of human telomeric DNA into G-quadruplex structures

Abstract

Cation-induced folding into quadruplex structures for three model human telomeric oligonucleotides, d[AGGG(TTAGGG)3], d[TTGGG(TTAGGG)3A] and d[TTGGG(TTAGGG)3], was characterized by equilibrium titrations with KCl and NaCl and by multiwavelength stopped flow kinetics. Cation binding was cooperative with Hill coefficients of 1.5-2.2 in K + and 2.4-2.9+ in Na+ with half-saturation concentrations of 0.5-1 mM for K+ and 4-13 mM for Na+ > depending on the oligonucleotide sequence. Oligonucleotide folding in 50 mM KCl at 25°C consisted of single exponential processes with relaxation times τ of 20-60 ms depending on the sequence. In contrast, folding in100 mM NaCl consisted of three exponentials with τ-values of 40-85 ms, 250-950 ms and 1.5-10.5 s. The folding rate constants approached limiting values with increasing cation concentration; in addition, the rates of folding decreased with increasing temperature over the range 15-45°C. Taken together, these results suggest that folding of G-rich oligonucleotides into quadruplex structures proceeds via kinetically significant intermediates. These intermediates may consist of antiparallel hairpins in rapid equilibrium with less ordered structures. The hairpins may subsequently form nascent G-quartets stabilized by H-bonding and cation binding followed by relatively slow strand rearrangements to form the final completely folded topologies. Fewer kinetic intermediates were evident with K+ than Na+ suggesting a simpler folding pathway in K+ solutions. © 2008 The Author(s).