Journal
NANO LETTERS
Volume 12, Issue 2, Pages 1038-1044Publisher
AMER CHEMICAL SOC
DOI: 10.1021/nl204273h
Keywords
Nanopore; DNA; effective charge; lithium chloride; single molecule; molecular dynamics
Categories
Funding
- NanoSci-E+ program
- European Union [201418]
- ERC [247072]
- National Institutes of Health [R01-HG005115, P41-RR005969]
- National Science Foundation [PHY-0822613, DMR-0955959]
- Teragrid [MCA05S028]
- Division Of Materials Research
- Direct For Mathematical & Physical Scien [955959] Funding Source: National Science Foundation
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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.
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