Date of Award
Master of Science
Electrical and Computer Engr
Single molecule DNA sequencing, commonly referred as the third generation sequencing, requires new approaches to identify nucleotide bases. Based on molecular dynamics (MD) simulations, we investigate a prospective direct electronic sequencing approach of nucleotides using the electrostatics of single-stranded DNA (ssDNA). To study the intrinsic electrostatic of ssDNA, electrostatic potentials have been calculated by solving the nonlinear Poisson-Boltzmann equation using visual molecular dynamics (VMD) for 25 base pair (bp) of polymers. The results show that the molecular electrostatic potential (MEP) differs for various bases within 3 nm from the center of the sugar backbone, with suitably differentiable variations at 1.4 nm distance. The MEP variations among four nucleotide bases are the most significant near ~33.7° and ~326.3° from the center of the nucleotide base, while the influences of the neighboring bases on MEPs become insignificant after the 3rd-nearest neighbors. With simulation of ssDNA under an applied electric field using NAMD MD simulator, the results suggest that the translocation rate of the ssDNA is dependent on the size of the nucleotides. These results demonstrate the potential to develop novel single molecule electronic DNA sequencing technology. Ability of proximal probing, vibration of nucleotides, ionic interference and sequencing of polymers are some of the challenges to be resolved.
dissertation or thesis originally submitted to the local University of Memphis Electronic Theses & dissertation (ETD) Repository.
Abu Saude, Mohammad Jomah I., "Molecular Dynamic Analysis of Electrostatics of Single-Stranded DNA with a Prospective Towards Single Molecule Sequencing" (2013). Electronic Theses and Dissertations. 719.