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Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Spectral Density of DNA-ligand Complexes Fluctuation

The binding of a ligand with DNA is described in the framework of quasichemical approach, representing binding as quasichemical reaction between a ligand and a free binding site on DNA (1). Markoff equation was derived, describing the probabilistic binding process between the ligand and the DNA. The suggested model will allow to gain more detailed information on DNA-ligand binding parameters. This model describes the kinetics of DNA-ligand binding and can give the following statistical characteristics of number of ligands, bound to DNA -- the average number of ligands, their dispersion, the correlation function, and the spectral density of number of bound ligands. "Double-sided" spectral density of ligands, adsorbed on DNA is calculated. It is shown, that spectrum density has Lorentzian view. The analysis of the obtained expression allows to distinguish the ?fast? adsorption of ligands on DNA from the ?slow? adsorption. The characteristic feature of spectral density fluctuation's dependence on the frequency is that along with increase of speed constants of adsorption/desorption the sharp decrease of spectral density fluctuation occurs at large values of frequency. The stochastic description of adsorption allows describe ligand-DNA binding using kinetic parameters. First through the comparison of theoretical and experimental isotherms the DNA-ligand binding constant, number of adsorption sites and the number of nucleotide pairs, binding one ligand is determined, then at known values of thermodynamical adsorption parameters the values for adsorption and desorption rates are obtained from the comparison of theoretical and experimental curves of spectral density fluctuation dependence on the frequency.

References and Footnotes
  1. V. Arakelyan, Yu. Babayan, G. Potikyan. Biomol. Str. Dyn. 18, 231-235 (2000).

V. B. Arakelyan1
S. Yu. Babayan2
V. I. Tairyan2
A. V. Arakelyan3
P. O. Vardevanyan3,*

1Yerevan Physics Institute
375036 Yerevan, Armenia
2Russian-Armenian State University
Yerevan, 375051
Hovsep Emin St.
123, Armenia
3Department of Biophysics
Yerevan State University
375025 Yerevan, Armenia

*Phone: 3741 57 10 61
Email: simvar@arminco.com