title: Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores.
abstract: Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4-8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
authors.forename: Maxim
authors.initials: M
authors.lastname: Belkin
authors.forename: Christopher
authors.initials: C
authors.lastname: Maffeo
authors.forename: David B
authors.initials: DB
authors.lastname: Wells
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
mesh_terms: D015374:Biosensing Techniques; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry*; D015195:Drug Design; D006046:Gold / Q000737:chemistry; D006358:Hot Temperature; D053768:Metal Nanoparticles / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009038:Motion; D058608:Nanopores; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D013314:Stress, Mechanical; D013696:Temperature
chemical_list: D004277:DNA, Single-Stranded; D006046:Gold; D004247:DNA