Dynamics of inserts and simple attachments in DNA polymers

Richard David Beger, Purdue University

Abstract

All life subsisting processes like RNA transcription, growth and reproduction are related to melting (separation of) the DNA helix. In this thesis we study the hydrogen bond stretch of the DNA polymers for various inserts and simple attachments. We find a dramatic change in the hydrogen bond stretch as a function of inserts, attachment position and the resonant frequency of the attachment. Our results depends on the input parameters of the force constants, amplitudes, resonant frequencies and long range interactions. Most of these parameters are extracted from experimental data. The resonant frequency of the enzymes are used as a free parameter to study their effect. The Green's function technique is used to study the dynamics of (TATA)$\sb2$ promoter inserts inside of DNA and the dynamics of simple enzyme-like attachments to DNA. The inserts show that there is a greater thermal hydrogen bond motion near these (TATA)$\sb2$ promoter boxes. The amount that the open base pair probability (i.e. thermal hydrogen bond stretch) changes is dependent on the base pair sequence outside the promoter insert. A rigid simple attachment destabilized the DNA helix by increasing the thermal hydrogen bond stretch. When the rigid attachment was allowed to extend over 70 base pairs the helix almost melted. The simple attachments were given resonant frequencies and the effects of such frequencies on the stability of the DNA was probed. Some frequencies destabilized the helix near the attachment sites and showed effects associated with enzyme enhancers. Some frequencies stabilized the helix near the attachment and behaved like enzyme repressors. Finally the attachments were allowed to bond to the Watson-Crick hydrogen atoms. The hydrogen bonds force constants for the Watson-Crick hydrogen bond atoms were therefore lowered. This produced a state of destabilization that increased as the Watson-Crick hydrogen bond force constant decreased. These effects were also resonant frequency dependent.

Degree

Ph.D.

Advisors

Prohofsky, Purdue University.

Subject Area

Biophysics|Molecules

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