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

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.