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Molecular Dynamics of DNA Translocation through Nanoelectrode Gaps

Xiongce Zhao1, Christina M. Payne2, Peter T. Cummings2, and James W. Lee3. (1) Nanomaterials Theory Institute, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, (2) Chemical Engineering, Vanderbilt University, 24th and Garland Ave., 118 Olin Hall, Nashville, TN 37235, (3) Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831

We have performed molecular dynamics simulations of DNA molecules translocating through a nanoscale electrode gap under the action of constant forces. The application behind this theoretical study is a proposal to use nanoelectrodes as part of a fast gene-sequencing device. We investigate situations where DNA segment is pulled mechanically or driven by voltage through metallic nanoelectrode gaps. By simulating the pulling process through various gaps, we found that a gap width of 1.5 nm is approaching the lower limit of width through which a single strand DNA can pass. The necessary force to be applied to the DNA segment in order to initiate a translocation within nanoseconds is in the range of hundreds of picoNewtons. The minimum amount of force required to initiate translocation appears to be insensitive to the length of ssDNA. Significant deformation was observed for the DNA during the translocation. DNA molecules deform in such ways to fit the gap width. Our simulation indicates that it is very difficult to force a single strand DNA through a gap less than 1.5 nm by electric field force. In addition, we found that it is virtually impossible to drive or pull a single strand DNA segment through a nanogap narrower than 1.0 nm. Simulations show that translocation movements of DNA segments through a nanoscale electrode gap can be well controlled by applying biased voltages in desired directions. Oscillating electric fields along the translocation direction results in oscillatory movements of DNA. Under the same voltage influence, the translocation speeds of DNA depend on the type of nucleotides in the chain. The orientation of bases depends on the gap width and type of nucleotides. Our study indicates that controlled translocation of DNA in a nano electrode gap is approachable, and results from this study can be used for designing novel sequencing devices.