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What Is The Nature Of Interactions Between DNA And Nanopores Fabricated In Thin Silicon Nitride Membranes?

What Is The Nature Of Interactions Between DNA And Nanopores Fabricated In Thin Silicon Nitride Membranes?

Authors :
Meni Wanunu
Anatoly B. Kolomeisky
Amit Meller
Source :
Biophysical Journal. 96(3)
Publication Year :
2009
Publisher :
Elsevier BV, 2009.

Abstract

Manipulating the drag force acting on charged biopolymers, such as DNA, during their passage through solid-state nanopores is critical for various single-molecule applications for biotechnology (e.g., sequencing, genotyping, DNA/protein interactions). We have recently shown for solid-state nanopores in silicon nitride (SiN) that small variations in the nanopore diameter, temperature, and voltage, strongly affect the biopolymer's average sliding velocity, indicating that in this size regime DNA transport is governed by DNA/pore attraction[1]. However, the exact nature of these interactions has remained to date unknown. To elucidate the character of these nanopore/DNA interactions, we have performed two independent types of experiments: First, we investigated the capture rate of DNA as a function of temperature. Surprisingly, our temperature measurements reveal anti-Arrhenius behavior, suggesting a two-step capture process. Second, we mapped the spatial distribution of charged biopolymer in the vicinity of the SiN membrane, using a custom confocal microscope equipped with a nano-positioning stage. Our measurements reveal a salt-dependent enhancement of DNA concentration in the vicinity of the SiN. These combined results suggest that electrostatic DNA/pore and DNA/membrane interactions are present between the weakly positive SiN surface and the negatively-charged DNA. In this presentation, these results are discussed and a model that explains these and previously reported observations is presented.[1] Wanunu, M. Sutin, J. McNally, B. Chow, A. and A. Meller (2008) DNA Translocation Governed by Interactions with Solid State Nanopores, Biophys. J., 95 (11), in press.

Details

ISSN :
00063495
Volume :
96
Issue :
3
Database :
OpenAIRE
Journal :
Biophysical Journal
Accession number :
edsair.doi.dedup.....686e9ee3c18a57a043673ee0415ad058
Full Text :
https://doi.org/10.1016/j.bpj.2008.12.3860