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Article

tRNA Modification Detection Using Graphene Nanopores: A Simulation Study

1
SUNY Polytechnic Institute, Colleges of Nanoscale Science and Engineering, 257 Fuller Road, Albany, NY, 12203, USA
2
Department of Biology, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
3
The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
4
Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Valérie de Crécy-Lagard
Biomolecules 2017, 7(3), 65; https://doi.org/10.3390/biom7030065
Received: 21 June 2017 / Revised: 15 August 2017 / Accepted: 21 August 2017 / Published: 25 August 2017
(This article belongs to the Collection RNA Modifications)
There are over 100 enzyme-catalyzed modifications on transfer RNA (tRNA) molecules. The levels and identity of wobble uridine (U) modifications are affected by environmental conditions and diseased states, making wobble U detection a potential biomarker for exposures and pathological conditions. The current detection of RNA modifications requires working with nucleosides in bulk samples. Nanopore detection technology uses a single-molecule approach that has the potential to detect tRNA modifications. To evaluate the feasibility of this approach, we have performed all-atom molecular dynamics (MD) simulation studies of a five-layered graphene nanopore by localizing canonical and modified uridine nucleosides. We found that in a 1 M KCl solution with applied positive and negative biases not exceeding 2 V, nanopores can distinguish U from 5-carbonylmethyluridine (cm5U), 5-methoxycarbonylmethyluridine (mcm5U), 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), and 5-methoxycarbonylmethyl-2′-O-methyluridine (mcm5Um) based on changes in the resistance of the nanopore. Specifically, we observed that in nanopores with dimensions less than 3 nm diameter, a localized mcm5Um and mcm5U modifications could be clearly distinguished from the canonical uridine, while the other modifications showed a modest yet detectable decrease in their respective nanopore conductance. We have compared the results between nanopores of various sizes to aid in the design, optimization, and fabrication of graphene nanopores devices for tRNA modification detection. View Full-Text
Keywords: tRNA modification; graphene; nanopore; wobble uridine tRNA modification; graphene; nanopore; wobble uridine
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MDPI and ACS Style

Onanuga, K.; Begley, T.J.; Chen, A.A.; Ranganathan, S.V. tRNA Modification Detection Using Graphene Nanopores: A Simulation Study. Biomolecules 2017, 7, 65. https://doi.org/10.3390/biom7030065

AMA Style

Onanuga K, Begley TJ, Chen AA, Ranganathan SV. tRNA Modification Detection Using Graphene Nanopores: A Simulation Study. Biomolecules. 2017; 7(3):65. https://doi.org/10.3390/biom7030065

Chicago/Turabian Style

Onanuga, Khadijah, Thomas J. Begley, Alan A. Chen, and Srivathsan V. Ranganathan 2017. "tRNA Modification Detection Using Graphene Nanopores: A Simulation Study" Biomolecules 7, no. 3: 65. https://doi.org/10.3390/biom7030065

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