Nucleic Acids Research Advance Access originally published online on June 21, 2008
Nucleic Acids Research 2008 36(12):4191-4203; doi:10.1093/nar/gkn379
Nucleic Acids Research, 2008, Vol. 36, No. 12 4191-4203
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures
James Graham Brown Cancer Center, University of Louisville, 529 S. Jackson Street, Louisville, KY 40202 and Department of Biochemistry & Molecular Biology, University of Louisville, Louisville, KY 40292, USA
*To whom correspondence should be addressed. Tel: +1 502 852 1172; Fax: +1 502 852 1153; Email: j.chaires{at}louisville.edu
Received April 22, 2008. Revised May 28, 2008. Accepted May 29, 2008.
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 
of 20–60 ms depending on the sequence. In contrast, folding in100 mM NaCl consisted of three exponentials with -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.
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