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J. Biol. Chem., Vol. 279, Issue 40, 42041-42054, October 1, 2004

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Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis^*

Amin Ahmed Ouameur and Heidar-Ali Tajmir-Riahi

From the Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada

Biogenic polyamines, such as putrescine, spermidine, and spermine are small organic polycations involved in numerous diverse biological processes. These compounds play an important role in nucleic acid function due to their binding to DNA and RNA. It has been shown that biogenic polyamines cause DNA condensation and aggregation similar to that of inorganic cobalt(III)hexamine cation, which has the ability to induce DNA conformational changes. However, the nature of the polyamine·DNA binding at the molecular level is not clearly established and is the subject of much controversy. In the present study the effects of spermine, spermidine, putrescine, and cobalt(III)hexamine on the solution structure of calf-thymus DNA were investigated using affinity capillary electrophoresis, Fourier transform infrared, and circular dichroism spectroscopic methods. At low polycation concentrations, putrescine binds preferentially through the minor and major grooves of double strand DNA, whereas spermine, spermidine, and cobalt(III)hexamine bind to the major groove. At high polycation concentrations, putrescine interaction with the bases is weak, whereas strong base binding occurred for spermidine in the major and minor grooves of DNA duplex. However, major groove binding is preferred by spermine and cobalt(III)hexamine cations. Electrostatic attractions between polycation and the backbone phosphate group were also observed. No major alterations of B-DNA were observed for biogenic polyamines, whereas cobalt(III)hexamine induced a partial B A transition. DNA condensation was also observed for cobalt(III)hexamine cation, whereas organic polyamines induced duplex stabilization. The binding constants calculated for biogenic polyamines are K_Spm = 2.3 x 10⁵ M^-1, K_Spd = 1.4 x 10⁵ M^-1, and K_Put = 1.02 x 10⁵ M^-1. Two binding constants have been found for cobalt(III)hexamine with K₁ = 1.8 x 10⁵ M^-1 and K₂ = 9.2 x 10⁴ M^-1. The Hill coefficients indicate a positive cooperativity binding for biogenic polyamines and a negative cooperativity for cobalt(III)hexamine.

Received for publication, June 1, 2004 , and in revised form, July 26, 2004.

^* This work was supported by the Natural Sciences and Engineering Research Council of Canada and Fonds pour la formation de Chercheurs et l'Aide à la Recherche (Québec). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

To whom correspondence should be addressed. Tel.: 819-376-5052 (ext. 3310); Fax: 819-376-5084; E-mail: tajmirri{at}uqtr.ca.

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