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Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores
Published on: October 31, 2013
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Slowing single-stranded DNA translocation through a solid-state nanopore by decreasing the nanopore diameter
Rena Akahori1, Takanobu Haga, Toshiyuki Hatano
1Central Research Laboratory, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan.
Nanotechnology
|June 25, 2014
Summary
Narrowing nanopore size significantly slows single-stranded DNA (ssDNA) translocation, enabling precise control for DNA sequencing applications. This research optimizes nanopore technology for faster, more accurate DNA analysis.
Area of Science:
- Nanotechnology
- Biophysics
- Genomics
Background:
- Controlling DNA translocation speed through nanopores is crucial for DNA sequencing.
- Solid-state nanopores offer a platform for DNA analysis, but translocation speed requires optimization.
Purpose of the Study:
- To investigate the effect of nanopore diameter on single-stranded DNA (ssDNA) translocation speed.
- To explore methods for slowing ssDNA translocation for improved nanopore DNA sequencing.
Main Methods:
- Synthesized long, uniform ssDNA (5.3 kb ss-poly(dA)).
- Fabricated nanopores with controlled diameters (4.5 nm to 2.3 nm) using transmission electron microscopy and atomic-layer deposition.
- Measured ssDNA translocation speed under an applied voltage (300 mV).
- Utilized molecular-dynamics (MD) simulations for theoretical validation.
Main Results:
- Reducing nanopore diameter from 4.5 nm to 2.3 nm slowed ssDNA translocation over 16-fold.
- ssDNA translocated significantly faster (over two orders of magnitude) than dsDNA through similar-sized nanopores.
- MD simulations accurately predicted measured translocation speeds and suggested further slowing at 1.4 nm nanopore diameter.
Conclusions:
- Nanopore diameter is a critical factor in controlling ssDNA translocation speed.
- Nanopore narrowing is an effective strategy for achieving the controlled translocation necessary for DNA sequencing.
- Understanding ssDNA-dsDNA translocation differences can refine nanopore sequencing technologies.
