Next Article in Journal
The TORC2‐Dependent Signaling Network in the Yeast Saccharomyces cerevisiae
Previous Article in Journal
Comparative Degradation of a Thiazole Pollutant by an Advanced Oxidation Process and an Enzymatic Approach
Previous Article in Special Issue
TrmL and TusA Are Necessary for rpoS and MiaA Is Required for hfq Expression in Escherichia coli
Article Menu

Export Article

Open AccessArticle
Biomolecules 2017, 7(3), 65; doi:10.3390/biom7030065

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
Received: 21 June 2017 / Revised: 15 August 2017 / Accepted: 21 August 2017 / Published: 25 August 2017
(This article belongs to the Collection RNA Modifications)
View Full-Text   |   Download PDF [2307 KB, uploaded 4 September 2017]   |  

Abstract

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
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

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.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Biomolecules EISSN 2218-273X Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top