Normal mode calculation for triple helical DNA, stability and hydration effects
Abstract
The effective field model for the dynamics of the triple helix $d(T)\sb{n} - d(A)\sb{n} - d(T)\sb{n}$ DNA polymer in solution has been applied to determine the vibrational normal modes of the system for both A and B conformation. The effect of site-bound counterions as compared to the area-bound counterions has been considered specifically by explicitly introducing degrees of freedom for the three counterions associated with a unit cell and coupling these to the DNA degrees of freedom via appropriate interactions. Stability of the system for all vibrational modes (positive eigenvalues for the solution of the dynamics problem) was used as a criterion to find possible equilibrium positions of the site-bound counterions in specific conditions of weak covalent bonding between the counterions and the phosphate free oxygens and distance dependent dielectric constants. Normal mode calculation for the A conformation shows that this type of triple helix is not stable in aqueous solutions unless the counterions are site-bound in certain positions close to the phosphate groups. The equilibrium domains for the positions of the counterions in both conformations have been determined. Free energy calculations for the two triple helices show that the B conformation is more stable than the A conformation. Our calculated normal modes match reasonably well with the experimental IR spectra. The effect of adding structural waters to the triplex DNA in the B conformation have been studied. The results clearly show that there is an inverse proportional relationship between the degree of boundness of the water molecules to the atoms in the triple helix and the relative humidity (RH) of the samples.
Degree
Ph.D.
Advisors
Reifenberger, Purdue University.
Subject Area
Molecules|Biochemistry|Molecular biology
Off-Campus Purdue Users:
To access this dissertation, please log in to our
proxy server.