Biomaterial Database

Forces affecting double-stranded DNA translocation through synthetic nanopores. 2011

Lei Chen, and A T Conlisk

Department of Mechanical Engineering, The Ohio State University, 201 W. 19th Avenue, Columbus, OH 43210, USA. chen.990@osu.edu

One of the recent applications of nanopores is to use them as detectors/analyzers for bio-molecules and nanopore based sequencing has been studied to quickly sequence DNA. In this paper, three categories of forces proposed in the literature to oppose the electrical driving forces in the DNA translocation process are analyzed, (1) the entropic forces of DNA uncoiling/recoiling at the pore entrance/exits, (2) the viscous drag acting on the blob like DNA outside the nanopore, and (3) the viscous drag acting on the linear DNA inside the nanopore. The magnitudes of these forces are calculated based on the parameters used in experiments and it is shown that the first two of the aforementioned categories of forces are usually small compared to the electrical driving force, while the last one is of the same order as the electrical driving force. To evaluate the viscous drag force acting on the linear DNA inside the nanopore, a hydrodynamic model based on the lubrication approximation is used to calculate the flow field and the viscous drag force acting on a DNA immobilized in a nanopore. This model is validated by good agreement with the experimental data for the tethering force used to immobilize a DNA inside the nanopore.

UI	MeSH Term	Description	Entries
D009068	Movement	The act, process, or result of passing from one place or position to another. It differs from LOCOMOTION in that locomotion is restricted to the passing of the whole body from one place to another, while movement encompasses both locomotion but also a change of the position of the whole body or any of its parts. Movement may be used with reference to humans, vertebrate and invertebrate animals, and microorganisms. Differentiate also from MOTOR ACTIVITY, movement associated with behavior.	Movements
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D004247	DNA	A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).	DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D014783	Viscosity	The resistance that a gaseous or liquid system offers to flow when it is subjected to shear stress. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)	Viscosities
D055595	Mechanical Phenomena	The properties and processes of materials that affect their behavior under force.	Mechanical Concepts,Mechanical Processes,Mechanical Phenomenon,Mechanical Process,Concept, Mechanical,Concepts, Mechanical,Mechanical Concept,Phenomena, Mechanical,Phenomenon, Mechanical,Process, Mechanical,Processes, Mechanical
D057446	Hydrodynamics	The motion of fluids, especially noncompressible liquids, under the influence of internal and external forces.	Fluid Dynamics,Dynamic, Fluid,Dynamics, Fluid,Fluid Dynamic,Hydrodynamic
D058608	Nanopores	Small holes of nanometer dimensions in a membrane, that can be used as single molecule detectors. The pores can be biological or synthetic.	Nanopore