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Abstract
The thermal denaturation of DNA, i.e. the separation of the two strands is a phenomenon caused by the amplitude of the vibrations of the bases, therefore it is necessary to know how such separation is generated in order to implement alternative model of the melting behavior as a function of nucleotide sequence and therapies to combat the cancer. We propose to use the extended nonlinear Peyrard-Bishop(PB) model of DNA to include an anharmonic potential representing the aromatic stacking interaction between n- and (n-1)-th consecutive base pairs to treat the problem. We use Finite-difference methods for determine the mean value of the displacement for the “hump Morse” potential of the Peyrard-Bishop model of DNA. We show how the extended “pseudo-Schrödinger” combined with finite difference method can be used to obtain the mean value displacements for the thermal denaturation of DNA with “hump” Morse potential.
Highlights
Eclética Química JournalOriginal research publication in all aspects of Chemistry homepage: http://revista.iq.unesp.br/ojs/index.php/ecletica/
We explore the thermodynamic properties solving the pseudo-Schrödinger equation of the transfer integral[1,2,3,4,5,6,7] for the “hump Morse”
The mathematical tools used in the theoretical study of the problem are Finite Difference Method (FDM) and pseudo-Schrödinger equation with anharmonic stacking interactions for the DNA molecule
Summary
Original research publication in all aspects of Chemistry homepage: http://revista.iq.unesp.br/ojs/index.php/ecletica/. Resumo: A desnaturação térmica do DNA, ou seja, a separação das duas cadeias, é um fenômeno causado pela amplitude das vibrações das bases, portanto, é necessário saber como essa separação é gerada para implementar o modelo alternativo do comportamento de fusão como uma função da sequência de nucleotídeos e terapias para combater o câncer. Propomos usar o modelo de Peyrard-Bishop (PB) de DNA não linear estendido para incluir um potencial enarmônico que represente a interação de empilhamento aromático entre n- e (n-1)-enésimos pares de bases consecutivos para tratar o problema. Nós usamos métodos de diferença finita para determinar o valor médio do deslocamento para o potencial “corcunda de Morse” do modelo Peyrard-Bishop do DNA. Mostramos como o “pseudo-Schrödinger” estendido combinado com método de diferença finita pode ser usado para obter os deslocamentos do valor médio para a desnaturação térmica do DNA com o potencial Morse “da corcunda”. Palavras-chave: Método das diferenças finitas, equação pseudo-Schrödinger, “corcunda” do potencial de Morse
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