Journal
ACS NANO
Volume 9, Issue 11, Pages 10598-10611Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acsnano.5b04173
Keywords
nanopore; DNA sequencing; nanoplasmonics; molecular dynamics; plasmonic tweezers
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Funding
- National Institutes of Health [R01-HG007406, P41-RR005969]
- National Science Foundation [DMR-0955959]
- Wenner-Gren Foundations
- Netherlands Organisation for Scientific Research
- XSEDE Allocation Grant [MCA05S028]
- Division Of Materials Research
- Direct For Mathematical & Physical Scien [955959] Funding Source: National Science Foundation
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With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.
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