Rigorous study of molecular dynamics of a single dsDNA confined in a nanochannel: Introduction of a critical mobility...

The essential and effective characteristics of a double-stranded DNA (dsDNA) confined in a nanochannel is revisited by employing the rigorous full numerical approach of Molecular Dynamics (MD). The deformation of dsDNA and wall-biomolecule interaction which is critical in highly confined regime has been precisely imposed in numerical simulations. The numerical approach has been justified against available theoretical outcomes. A new and general expression for DNA electrophoretic mobility versus DNA length is extracted from numerical simulation which is out of reach of experimental methods due to practical shortcomings. The newly derived expression suggests an essential correction in the previously proposed expression for the critical case of small DNA molecules and reveals an astonishingly unbeknown trend of small DNA's mobility. Sub-molecular phenomenon of dsDNA melting under the condition of large external force is also studied. Assuming strong electric field exertion, the MD approach aptly demonstrates the elaborate melting phenomenon for dsDNA in sub-molecular scale.