Elasticity of a DNA chain dotted with bubbles under force

Cidofovir (CDV) (HPMPC) has potent in vitro and in vivo activity against human cytomegalovirus (HCMV), CDV diphosphate (CDVpp), the putative antiviral metabolite of CDV, is an inhibitor and an alternate substrate of HCMV DNA polymerase. CDV is incorporated with the correct complementation to dGMP in the template, and the incorporated CDV at the primer end is not excised by the 3'-to-5' exonuclease activity of HCMV DNA polymerase. The incorporation of a CDV molecule causes a decrease in the rate of DNA elongation for the addition of the second natural nucleotide from the singly incorporated CDV molecule. The reduction in the rate of DNA (36-mer) synthesis from an 18-mer by one incorporated CDV is 31% that of the control. However, the fidelity of HCMV DNA polymerase is maintained for the addition of the nucleotides following a single incorporated CDV molecule. The rate of DNA synthesis by HCMV DNA polymerase is drastically decreased after the incorporation of two consecutive CDV molecules; the incorporation of a third consecutive CDV molecule is not detectable. Incorporation of two CDV molecules separated by either one or two deoxynucleoside monophosphates (dAMP, dGMP, or dTMP) also drastically decreases the rate of DNA chain elongation by HCMV DNA polymerase. The rate of DNA synthesis decreases by 90% when a template which contains one internally incorporated CDV molecule is used. The inhibition by CDVpp of DNA synthesis by HCMV DNA polymerase and the inability of HCMV DNA polymerase to excise incorporated CDV from DNA may account for the potent and long-lasting anti-CMV activity of CDV.

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A model of nonlinear DNA-protein interaction system with Cornell potential and its stability

Journal of Physics Theories and Applications ◽

10.20961/jphystheor-appl.v1i1.4716 ◽

2017 ◽

Vol 1 (1) ◽

pp. 62

Author(s):

Edy Syahroni ◽

A Suparmi ◽

C Cari ◽

Fuad Anwar

Keyword(s):

Protein Interaction ◽

Interaction Model ◽

The State ◽

Hamiltonian Equation ◽

Single Chain ◽

Cornell Potential ◽

Interaction System ◽

Dna Protein Interaction ◽

Dna Chain ◽

The Stability

<p class="Abstract">The purpose of this study was to determine the model of a interaction system between the DNA with protein. The interaction system consisted of a molecule of protein bound with a single chain of DNA. The interaction between DNA chain, especially adenine and thymine, and DNA-protein bound to glutamine and adenine. The forms of these bonds are adapted from the hydrogen bonds. The Cornell potential was used to describe both of the interactions. We proposed the Hamiltonian equation to describe the general model of interaction. Interaction system is divided into three parts. The interaction model is satisfied when a protein molecule triggers pulses on a DNA chain. An initial shift in position of protein xm should trigger the shift in position of DNA ym, or alter the state. However, an initial shift in DNA, yn, should not alter the state of a rest protein (i.e. xm = 0), otherwise, the protein would not steadily bind. We also investigated the stability of the model from the DNA-protein interaction with Lyapunov function. The stability of system can be determined when we obtained the equilibrium point.</p>

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