Analysis of Competitive Ligand Binding to DNA: Using Dyes as Fluorescent Sensors

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Abstract

Determination of interaction parameters of low molecular weight compounds with DNA is difficult in cases where compounds do not exhibit appreciable fluorescence or their spectral changes are difficult to interpret. To solve this problem, an approach involving the use of known fluorescent dyes competitively binding on DNA is proposed. This approach uses a model describing the competitive binding of two extended ligands on a linear DNA matrix. This model allows approximation of experimental data and determination of binding parameters corresponding to two non-fluorescent types of ligands. The first type of ligands exhibits intercalation binding to DNA and competes with ethidium bromide, while the second type binds along a narrow groove and competes with Hoechst 33258 dye.

About the authors

Y. D Nechipurenko

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Research Institute for Brain Development and Peak Performance, RUDN University

Email: nech99@mail.ru
Moscow, Russia; Moscow, Russia

E. A Novikova

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Moscow, Russia

N. M Smirnov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Moscow, Russia

K. K Khorunzheva

Moscow Institute of Physics and Technology (National Research University)

Dolgoprudny, Russia

B. V Paponov

Pavlov First Saint Petersburg State Medical University

Saint Petersburg, Russia

A. F Arutyunyan

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Moscow, Russia

D. N Kaluzhny

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Email: uzhny@mail.ru
Moscow, Russia

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