Heteropolymer translocation through nanopores

Abstract

Effect of charge distribution on the translocation of an inhomogeneously charged polymer through a nanopore J. Chem. Phys. 128, 125104 (2008) The authors investigate the translocation dynamics of heteropolymers driven through a nanopore using a constant temperature Langevin thermostat. Specifically, they consider heteropolymers consisting of two types of monomers labeled A and B, which are distinguished by the magnitude of the driving force that they experience inside the pore. From a series of studies on polymers with sequences A m B n the authors identify both universal as well as specific sequence properties of the translocating chains. They find that the scaling of the average translocation time as a function of the chain length N remains unaffected by the heterogeneity, while the residence time of each bead is a strong function of the sequence for short repeat units. They further discover that for a symmetric heteropolymer A n B n of fixed length, the pattern exhibited by the residence times of the individual monomers has striking similarity with a double slit interference pattern where the total number of repeat units N /2n controls the number of interference fringes. These results are relevant for designing nanopore based sequencing techniques.

Modeling the separation of macromolecules: A review of current computer simulation methods

“…Additionally, the dependence on the nature of the polymer has been studied by simulating charged polymers [212] and heteropolymers [213,214]. Furthermore, considering application to sequencing, it is not surprising that a great number of studies have also examined driven translocation by implementing a pulling force [215], an adsorption force [196], or an external field (discussed below).…”

Nondriven polymer translocation through a nanopore: Computational evidence that the escape and relaxation processes are coupled

“…Moreover, recent advances in manipulating and analyzing DNA moving through natural [1,2] or synthetic nanopores [3] strongly suggest that such mechanical systems could eventually lead to the development of new ultrafast sequencing techniques [1,4,5,6,7,8,9,10,11]. However, even though a great number of theoretical [12,13,14,15,16,17,18,19,20,21,22,23] and computational [24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42] studies have been published on the subject, there are still many unanswered questions concerning the fundamental physics behind such a process.…”

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

“…This model is very successful in capturing chain properties on scales larger than ℓ p , for instance the force-extension relation 14 , but carries no information about the internal structure of the double strand. Slightly more refined models approximate single-stranded DNA as a semiflexible chain of sterically repulsive spheres 15,16 , which may carry charge and thus interact with an external field, although Coulombic monomer-monomer interactions were neglected in these models. One bead per nucleotide representations of DNA have also been used to describe supercoiling and local denaturation in plasmids 17 .…”