Slowing down DNA translocation through a nanopore in lithium chloride.
The charge of a DNA molecule is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial reduction of the DNA charge due to counterion binding by means of nanopore translocation experiments and all-atom molecular dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA molecule through a solid-state nanopore strongly increases as the counterions decrease in size from K(+) to Na(+) to Li(+), both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li(+) and Na(+) bind DNA stronger than K(+). These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resolution in nanopore applications.
Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
Stefan W
SW
Kowalczyk
David B
DB
Wells
Aleksei
A
Aksimentiev
Cees
C
Dekker
D004247:DNA / Q000737:chemistry*; D018021:Lithium Chloride / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D036103:Nanotechnology; D010316:Particle Size; D013499:Surface Properties
D004247:DNA; D018021:Lithium Chloride