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)(3)A] 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 degrees C consisted of single exponential processes with relaxation times tau of 20-60 ms depending on the sequence. In contrast, folding in100 mM NaCl consisted of three exponentials with tau-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 degrees 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.
James Graham Brown Cancer Center, University of Louisville, 529 S. Jackson Street, Louisville, KY 40202, USA.
Robert D
RD
Gray
Jonathan B
JB
Chaires
D002412:Cations / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011188:Potassium / Q000737:chemistry*; D011189:Potassium Chloride / Q000494:pharmacology; D012964:Sodium / Q000737:chemistry*; D012965:Sodium Chloride / Q000494:pharmacology; D016615:Telomere / Q000737:chemistry*; D013696:Temperature
D002412:Cations; D009838:Oligodeoxyribonucleotides; D012965:Sodium Chloride; D011189:Potassium Chloride; D004247:DNA; D012964:Sodium; D011188:Potassium