Alishahi Marzieh, Kamali Reza, Abouali Omid
School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
Eur Phys J E Soft Matter. 2015 Aug;38(8):92. doi: 10.1140/epje/i2015-15092-5. Epub 2015 Aug 31.
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.
通过采用严格的分子动力学（MD）全数值方法，重新审视了限制在纳米通道中的双链DNA（dsDNA）的基本和有效特性。在数值模拟中精确施加了dsDNA的变形和壁-生物分子相互作用，这在高度受限的情况下至关重要。该数值方法已根据现有的理论结果得到验证。从数值模拟中提取了一个关于DNA电泳迁移率与DNA长度的新的通用表达式，由于实际缺陷，该表达式是实验方法无法得到的。新推导的表达式表明，对于小DNA分子的临界情况，先前提出的表达式需要进行必要的修正，并揭示了小DNA迁移率惊人的未知趋势。还研究了在大外力条件下dsDNA解链的亚分子现象。假设施加强电场，MD方法恰当地展示了亚分子尺度下dsDNA的精细解链现象。
