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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

The consistent description of diffusion and kinetic states of the adsorption of ligands on DNA immobilized molecules

Taking into account the design process of DNA-biosensors, the theoretical analysis of physicochemical peculiarities of both diffusion process of ligands to the underlayer and their adsorption process on DNA becomes necessary. It is convenient to divide the kinetics of the adsorption process of ligands on DNA into two states: diffusion state of motion of ligands to the adsorption center on DNA and kinetic state - immediately ligand binding to adsorption center on DNA. It has been studied the case when the characteristic times of both diffusion and kinetic states have the same order (Arakelyan et al., 2014). The theoretical description of the binding kinetics of ligands with DNA immobilized molecules was carried out within the following adsorption model framework. One-dimensional diffusion of ligands perpendicular to the underlayer surface on which DNA molecules are immobilized was observed. DNA immobilized molecules are in some layer out of which there is a well stirring solution of ligands. Because of the fact that the concentration of ligands near to DNA molecules changes due to diffusion of ligands in the solution and their adsorption on DNA, the kinetics of the binding process of ligands to DNA is described by the system of non-linear equations of “reaction-diffusion” type (Hagan & Chakraborty, 2004). The numeric solution of these equations shows that depending on the ratio between the parameters of diffusion and kinetic states of adsorption, different regimes of adsorption of ligands on DNA may be realized. At limitation of kinetic or diffusion states the exponential kinetics of filling of adsorption centers on DNA takes place. If characteristic times of diffusion and kinetic states have the same orders, the kinetics of filling of adsorption centers on DNA by ligands differs from exponential one acquiring a form of S-like curve. It was also shown that the concentration of adsorption centers influences on DNA filling kinetics by ligands only in that case, when the characteristic time of diffusion state is much longer than the characteristic time of kinetic state.

References
    V.B.Arakelyan, P.O.Vardevanyan, Z.E.Navoyan, M.A.Parsadanyan, G.G.Hovhannisyan & A.T.Karapetian. (2014). Kinetics of adsorption of extended ligands on DNA at small fillings. Journal of Biomolecular Structure and Dynamics 32, 330-333.

    M.F. Hagan & A.K. Chakraborty. (2004). Hybridization dynamics of surface immobilized DNA. J. Chem. Phys. 120, 4958-4968.


Valeri B. Arakelyan
Zaven E. Navoyan
Gohar G. Hovhannisyan
Poghos O. Vardevanyan

Chairs of Molecular Physics and Biophysics
Yerevan State University Yerevan, Armenia

Ph: (+37410) 555240
Fx: (+37410) 554641
v.arakelyan@ysu.am