DNA Sequencing Using Graphene Nanopore: A Molecular Dynamics Simulation Study
کد مقاله : 1085-PHYSCHEM20
فهیمه اکبری *، معصومه فروتن
استاد شیمی فیزیک دانشکده شیمی دانشگاه تهران
چکیده مقاله:
In this paper, we used steered molecular dynamics (SMD) simulations to investigate the neighbor nucleotide effect on DNA sequencing using irreversible pulling of a single stranded DNA (ssDNA) molecule through circular graphene nanopore. Specific sequences of purines and pyrimidines ( poly (CT)6, poly (CG)6, poly (GA)6 and poly (TA)6 molecules) were examined. Effect of the neighbor nucleotide was recognized by time passing and force profile in nonequilibrium DNA pulling. Results showed, when purines and pyrimidines frequently lie in a ssDNA molecule, purines passing time is longer than pyrimidines. The difference in the passing time of purines and pyrimidines causes the ssDNA molecule to recognize easier and faster at single nucleotide resolution.
کلیدواژه ها:
Molecular dynamics simulation; DNA sequencing; Purines; Pyrimidines
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