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Single Molecule Oscillations of an RNA/DNA Duplex in a Plasmonic Nanocavity | OMICS International | Abstract
ISSN: 2157-7439

Journal of Nanomedicine & Nanotechnology
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Research Article

Single Molecule Oscillations of an RNA/DNA Duplex in a Plasmonic Nanocavity

Sagnik Basuray1, Avinash Pathak1, Biyan Chen1, Drew Menke2, Charles M Darr3, Keshab Gangopadhyay1,4, Peter V Cornish2* and Shubhra Gangopadhyay1*

1Department of Electrical and Computer Engineering, 349 Engineering Building West, University of Missouri, Columbia, MO 65211, USA

2Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA

3Department of Bioengineering, 349 Engineering Building West, University of Missouri, Columbia, MO 65211, USA

4Author Contributions Equality

*Corresponding Author:
Shubhra Gangopadhyay
141A Engineering Building West
University of Missouri
Columbia, MO 65211-2300, USA
Tel: 1-573-882- 4070
Fax: 1-573-884-0312
E-mail: [email protected]
 
Peter V Cornish
117 Schweitzer Hall
University of Missouri
Columbia, MO 65211, USA
Tel: 1-573-882-0443
Fax: 1-573-882-5635
E-mail: [email protected]

Received Date: April 06, 2015; Accepted Date: May 05, 2015; Published Date: May 15, 2015

Citation: Basuray S, Pathak A, Chen B, Menke D, Darr CM, et al. (2015) Single Molecule Oscillations of an RNA/DNA Duplex in a Plasmonic Nanocavity. J Nanomed Nanotechnol 6:293. doi:10.4172/2157-7439.1000293

Copyright: © 2015 Basuray S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

We report the visualization of single molecule dynamics in epifluorescence mode through extraordinary plasmonic enhancement provided by silver grating with embedded nanocavities. Cy3/Cy5-labeled DNA/RNA hybrid duplexes were affixed to SiO2-capped silver gratings produced by soft lithography process. Tracking single-molecule fluorescence revealed damped sub-1 Hz periodic Cy3 intensity fluctuations with strong dependence on the bulk MgCl2 concentration. Extreme concentration of electric field at the nanocavity edge induces plasmonic heating, which sets up convection deep within the nanocavity. Local fluctuations in Mg2+ ion concentration promote a bent or unbent duplex conformational state, respectively, by varying degrees of negative charge screening along the duplex backbone. These oscillations continue until the duplex conformational state stabilizes or the dyes bleach. This unique molecular behavior in the nanocavity could be used to study duplex complementarity, structural polymorphisms, and protein-nucleic acid interactions at the single molecule level.

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