scholarly journals Single-Molecule Kinetics and Thermodynamics Analysis of DNA-Bound Crown Ether/Cation Interactions within the Alpha-Hemolysin Ion Channel

2012 ◽  
Vol 102 (3) ◽  
pp. 728a
Author(s):  
Na An ◽  
Aaron M. Fleming ◽  
Henry S. White ◽  
Cynthia J. Burrows
Keyword(s):  
Crown Ether ◽  
Ion Channel ◽  
Single Molecule ◽  
Kinetics And Thermodynamics ◽  
Thermodynamics Analysis ◽  
Alpha Hemolysin

scholarly journals Single-molecule detection of a guanine(C8)-thymine(N3) cross-link using ion channel recording

2013 ◽  
Vol 27 (4) ◽  
pp. 247-251 ◽  
Author(s):  
Anna H. Wolna ◽  
Aaron M. Fleming ◽  
Cynthia J. Burrows
Keyword(s):  
Ion Channel ◽  
Single Molecule ◽  
Single Molecule Detection ◽  
Cross Link

scholarly journals Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Yong Wang ◽  
Bin-Quan Luan ◽  
Zhiyu Yang ◽  
Xinyue Zhang ◽  
Brandon Ritzo ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Single Molecule ◽  
Metal Ion ◽  
Detection Method ◽  
Direct Detection ◽  
Alpha Hemolysin ◽  
Duplex Stability ◽  
Dynamics Simulations ◽  
Direct Detection Method

Abstract Both cytosine-Ag-cytosine interactions and cytosine modifications in a DNA duplex have attracted great interest for research. Cytosine (C) modifications such as methylcytosine (mC) and hydroxymethylcytosine (hmC) are associated with tumorigenesis. However, a method for directly discriminating C, mC and hmC bases without labeling, modification and amplification is still missing. Additionally, the nature of coordination of Ag+ with cytosine-cytosine (C-C) mismatches is not clearly understood. Utilizing the alpha-hemolysin nanopore, we show that in the presence of Ag+, duplex stability is most increased for the cytosine-cytosine (C-C) pair, followed by the cytosine-methylcytosine (C-mC) pair and the cytosine-hydroxymethylcytosine (C-hmC) pair, which has no observable Ag+ induced stabilization. Molecular dynamics simulations reveal that the hydrogen-bond-mediated paring of a C-C mismatch results in a binding site for Ag+. Cytosine modifications (such as mC and hmC) disrupted the hydrogen bond, resulting in disruption of the Ag+ binding site. Our experimental method provides a novel platform to study the metal ion-DNA interactions and could also serve as a direct detection method for nucleobase modifications.

scholarly journals Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Madiha Sultan ◽  
Anastassia Kanavarioti
Keyword(s):  
Solid State ◽  
Nucleotide Sequence ◽  
Nucleic Acids ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Selective Labeling ◽  
Base Calling ◽  
Alpha Hemolysin ◽  
Oxford Nanopore ◽  
Single Molecule Analysis

Abstract Protein and solid-state nanopores are used for DNA/RNA sequencing as well as for single molecule analysis. We proposed that selective labeling/tagging may improve base-to-base resolution of nucleic acids via nanopores. We have explored one specific tag, the Osmium tetroxide 2,2′-bipyridine (OsBp), which conjugates to pyrimidines and leaves purines intact. Earlier reports using OsBp-tagged oligodeoxyribonucleotides demonstrated proof-of-principle during unassisted voltage-driven translocation via either alpha-Hemolysin or a solid-state nanopore. Here we extend this work to RNA oligos and a third nanopore by employing the MinION, a commercially available device from Oxford Nanopore Technologies (ONT). Conductance measurements demonstrate that the MinION visibly discriminates oligoriboadenylates with sequence A15PyA15, where Py is an OsBp-tagged pyrimidine. Such resolution rivals traditional chromatography, suggesting that nanopore devices could be exploited for the characterization of RNA oligos and microRNAs enhanced by selective labeling. The data also reveal marked discrimination between a single pyrimidine and two consecutive pyrimidines in OsBp-tagged AnPyAn and AnPyPyAn. This observation leads to the conjecture that the MinION/OsBp platform senses a 2-nucleotide sequence, in contrast to the reported 5-nucleotide sequence with native nucleic acids. Such improvement in sensing, enabled by the presence of OsBp, may enhance base-calling accuracy in enzyme-assisted DNA/RNA sequencing.

Discriminating single-molecule sensing by crown-ether-based molecular junctions

2017 ◽  
Vol 146 (6) ◽  
pp. 064704 ◽  
Author(s):  
Ali K. Ismael ◽  
Alaa Al-Jobory ◽  
Iain Grace ◽  
Colin J. Lambert
Keyword(s):  
Crown Ether ◽  
Single Molecule ◽  
Molecular Junctions

scholarly journals Complex formation dynamics in a single-molecule electronic device

2016 ◽  
Vol 2 (11) ◽  
pp. e1601113 ◽  
Author(s):  
Huimin Wen ◽  
Wengang Li ◽  
Jiewei Chen ◽  
Gen He ◽  
Longhua Li ◽  
...  
Keyword(s):  
Crown Ether ◽  
Single Molecule ◽  
Electronic Device ◽  
Device Fabrication ◽  
Point Contacts ◽  
Host Guest Complex ◽  
Guest Binding ◽  
Molecule Junction ◽  
Single Molecule Junction ◽  
Thermodynamic Processes

Single-molecule electronic devices offer unique opportunities to investigate the properties of individual molecules that are not accessible in conventional ensemble experiments. However, these investigations remain challenging because they require (i) highly precise device fabrication to incorporate single molecules and (ii) sufficient time resolution to be able to make fast molecular dynamic measurements. We demonstrate a graphene-molecule single-molecule junction that is capable of probing the thermodynamic and kinetic parameters of a host-guest complex. By covalently integrating a conjugated molecular wire with a pendent crown ether into graphene point contacts, we can transduce the physical [2]pseudorotaxane (de)formation processes between the electron-rich crown ether and a dicationic guest into real-time electrical signals. The conductance of the single-molecule junction reveals two-level fluctuations that are highly dependent on temperature and solvent environments, affording a nondestructive means of quantitatively determining the binding and rate constants, as well as the activation energies, for host-guest complexes. The thermodynamic processes reveal the host-guest binding to be enthalpy-driven and are consistent with conventional 1H nuclear magnetic resonance titration experiments. This electronic device opens up a new route to developing single-molecule dynamics investigations with microsecond resolution for a broad range of chemical and biochemical applications.

Sign in / Sign up

Export Citation Format

Share Document