Next Article in Journal
Cysteine-Functionalized Chitosan Magnetic Nano-Based Particles for the Recovery of Light and Heavy Rare Earth Metals: Uptake Kinetics and Sorption Isotherms
Next Article in Special Issue
DNA-Protected Silver Clusters for Nanophotonics
Previous Article in Journal
Alumina Matrix Composites with Non-Oxide Nanoparticle Addition and Enhanced Functionalities
Previous Article in Special Issue
Cellular Uptake of Tile-Assembled DNA Nanotubes
Article Menu

Export Article

Open AccessCommunication
Nanomaterials 2015, 5(1), 144-153; doi:10.3390/nano5010144

The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
*
Author to whom correspondence should be addressed.
Academic Editor: Stephen Ralph
Received: 26 November 2014 / Revised: 7 January 2015 / Accepted: 12 January 2015 / Published: 27 January 2015
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
View Full-Text   |   Download PDF [3293 KB, uploaded 27 January 2015]   |  

Abstract

Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein. View Full-Text
Keywords: alpha-hemolysin; exonuclease sequencing; molecular dynamics; nanopore sequencing alpha-hemolysin; exonuclease sequencing; molecular dynamics; nanopore sequencing
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).

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

Manara, R.M.A.; Tomasio, S.; Khalid, S. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations. Nanomaterials 2015, 5, 144-153.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Nanomaterials EISSN 2079-4991 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top