Issue June 2003

category image Volume 20
No. 6 (p 733-968)
June 2003
ISSN 0739-1102

Ethidium Probing of the Parallel Double- and Four-stranded Structures Formed by the Telomeric DNA Sequences dG(GT)4G and d(GT)5 (p. 789-800)

Oligonucleotides 3´-d(GT)5-(CH2CH2O)3-d(GT)5-3´ (parGT), containing GT repeats present in the telomeric DNA from Saccharomyces cerevisiae, had been demonstrated to form bimolecular structure, GT-quadruplex (qGT) [O. F. Borisova et al. FEBS Letters 306, 140-142 (1992)]. Four d(GT)5 strands of the GT-quadruplex are parallel and form five G-quartets while thymines are bulged out. The four GT repeats when flanked by guanines, 3´-dG(TG)4G-(CH2CH2O)3-dG(GT)4G-3´ (hp-GT), had been shown to form a novel parallel-stranded (ps) double helix with G·G and T·T base pairs (hp-GT ps-DNA) [A. K. Shchyolkina et al. J. Biomol. Struct. Dynam. 18, 493-503 (2001)]. In the present study the intercalator ethidium bromide (Et) was used for probing the two structures. The mode of Et binding and its effect on thermostability of qGT and hp-GT were compared. The quantum yield (q) and the fluorescence lifetime (τ) of Et:qGT (q = 0.15 ± 0.01 and τ = 24 ± 1 ns) and Et:hp-GT (q = 0.10 ± 0.01 and τ = 16.5 ± 1 ns) indicative of intercalation mode of Et binding were determined. Et binding to qGT was found to be cooperative with corresponding coefficient ω = 3.9 ± 0.1 and the binding constant Κ = (6.4 ± 0.1)·104 M-1. The maximum number of Et molecules intercalating into GT-quadruplex is as high as twice the number of inerspaces between G-quartets (eight in our case). The data conform to the model of Et association with GT-quadruplex suggested earlier [O. F. Borisova et al. Mol. Biol. (Russ) 35, 732-739 (2001)]. The anticooperative type of Et binding was observed in case of hp-GT ps-DNA, with the maximum number of bound Et molecules, N = 4 ÷ 5, and the association constant Κ = (1.5 ± 0.1)·105 M-1. Thermodynamic parameters of formation of Et:qGT and EtBr:hp-GT complexes were calculated from UV thermal denaturation profiles.

Irina A. Beschetnova
Dmitry N. Kaluzhny
Mikhail A. Livshits
Anna K. Shchyolkina
Olga F. Borisova*

Engelhardt Institute of Molecular Biology
Russian Academy of Sciences
Vavilova 32
119991 Moscow, Russia
*borisova@eimb.ru

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