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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Competition Between Different Ligand-DNA Complexes Produces S-shaped Binding Curves

S-shaped binding curves often characterize interactions of ligands with nucleic acid molecules as analyzed by different physicochemical and biophysical techniques. S-shaped experimental binding curves are usually interpreted as indicative of the positive cooperative interactions between the bound ligand molecules.

This paper demonstrates that S-shaped binding curves may be obtained as a result of the "mixed mode" of DNA binding by the same ligand molecule. Mixed mode of the ligand-DNA binding can occur, for example, owing to (i) isomerization or dimerization of the ligands in solution or on the DNA lattice, (ii) ligand ability to intercalate into DNA and to bind within the minor groove in different orientations.

DNA-ligand complexes are characterized by the length of the ligand binding site on the DNA lattice (so-called "multiple-contact" model). We show here that, if one and the same ligand can give rise to two or more complexes with different lengths of the ligand binding sites, then (i) the dependence of the concentration of the complex with the shorter binding site on the total concentration of ligand should be S-shaped; (ii) the dependence of the concentration of the complex with the longer binding site on the total concentration of DNA should be S-shaped, even without positive cooperativity (1,2).

Our theoretical model is confirmed by comparison of the calculated and experimental CD binding curves for bis-netropsin binding to poly(dA-dT)ápoly(dA-dT). Bis-netropsin forms two types of DNA complex owing to its ability to interact with DNA as monomer and trimer (3,4). The experimental S-shaped bis-netropsin-DNA binding curve is shown to be in good correlation with the one calculated on the basis of our theoretical model. The present work provides a new angle to the analysis of ligand-DNA binding curves.

Supported by RFBR grants # 01-04-48657, # 00-15-97834 and INTAS grant # 97-0522.

References and Footnotes
  1. Yu.D. Nechipurenko, A.L. Mikheikin and S.A. Streltsov, Biofizika (Engl. Transl.) 45, 1011-1015 (2000).
  2. Yu.D. Nechipurenko, A.L. Mikheikin, S.A. Streltsov, A.S. Zasedatelev and I.R. Nabiev, J. Biomol Struct.& Dynam., in press (2001).
  3. A.S. Zasedatelev, V.B. Borodulin, S.L.Grokhovsky, A.M. Nikitin, D.V. Salmanova,A.L. Zhuze, G.V. Gursky and R.H. Shafer, FEBS Letters 375, 304-306 (1995)
  4. V.B. Borodulin, A.L. Mikheikin, S.L. Grokhovsky, A.M. Nikitin, D.V. Salmanova, A.L. Zhuze, G.V. Gursky, R.H. Shafer and A.S. Zasedatelev, Mol. Biol. (Moscow) Engl. Transl. 30, 661-665 (1996)

A.L. Mikheikin, Yu.D. Nechipurenko, A.S. Zasedatelev and S.A. Streltsov

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia. email: almicheikin@mail.ru, fax: 7(095)135-1405 , ph.: 7(095)135-9718