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- W2294328198 abstract "The best-characterized epigenetic modification is DNA methylation, which was found to shapesignificantly gene expression in mammalian cells, though bacteria and plants display less sequencespecificity. The cytosine methylation of DNA sequence here was studied by the molecular dynamic(MD) method. We found that the optimized structures are not significantly altered betweenunmethylated, methylated sequences. However, sampling of the molecule dynamical landscape vialong MD simulations showed that the altered sequences could adopt different conformations(revealed in the twist and roll angles) from the unmodified DNA, which are dependent on the§sequence environment. We propose that this conformational diversity may play a role on proteinrecognition.The G-rich sequences are studied with MD simulations to check the propensity of the sequence toadopt to A-form or B-form of DNA. The results showed that the DNA sequence adopts most of thetime in A-form and also spend sometime in between A-form and B-form. The groove widthsshowed the conformation in B-form. By analyzing the DNA in different contexts usingcomputational methods we were able to test limits that force field methods offer for these systems.We propose that this conformational diversity may play a role in protein recognition.Finally, we have studied the conformational changes of DNA sequence with uracil as a base.Sometimes in the replication process uracil can be formed and the mismatch base pair in the DNAsequence is removed by the enzyme UDG (Uracil-DNA sequence). In the present work MDsimulations were used to study the structure, dynamics and base pair kinetics of DNA sequence.The opening and closing kinetics of the T-A base pair were studied. A fast base pair opening wasobserved and also additionally base flipping was spotted. A very fast opening of the bases may beresponsible for the fast closing of the bases. In order to characterize the complete study of base pairkinetics in relation to T-A versus U-A base pairs is currently under way." @default.
- W2294328198 created "2016-06-24" @default.
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- W2294328198 date "2016-01-13" @default.
- W2294328198 modified "2023-09-27" @default.
- W2294328198 title "Computational studies on DNA: insights into structure and dynamics" @default.
- W2294328198 hasPublicationYear "2016" @default.
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