Ionic liquid prolongs DNA translocation through graphene nanopores

Kulkarni, Mandar; Mukherjee, Arnab

doi:10.1039/c6ra07017e

Cited by 18 publications

(19 citation statements)

References 53 publications

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“…A cell contains only two copies of each DNA molecule, and its preservation during the sequencing procedure is of utmost importance ( 109–112 ). [C 4 Mim][Cl] decelerates dsDNA translocation through a graphene nanopore which can be advantageous in genome sequencing techniques ( 113 ).…”

Section: Nucleic Acids In Ionic Liquidsmentioning

confidence: 99%

Ionic liquids: prospects for nucleic acid handling and delivery

Egorova

Posvyatenko

Larin

et al. 2021

Nucleic Acids Research

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Operations with nucleic acids are among the main means of studying the mechanisms of gene function and developing novel methods of molecular medicine and gene therapy. These endeavours usually imply the necessity of nucleic acid storage and delivery into eukaryotic cells. In spite of diversity of the existing dedicated techniques, all of them have their limitations. Thus, a recent notion of using ionic liquids in manipulations of nucleic acids has been attracting significant attention lately. Due to their unique physicochemical properties, in particular, their micro-structuring impact and tunability, ionic liquids are currently applied as solvents and stabilizing media in chemical synthesis, electrochemistry, biotechnology, and other areas. Here, we review the current knowledge on interactions between nucleic acids and ionic liquids and discuss potential advantages of applying the latter in delivery of the former into eukaryotic cells.

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Section: Nucleic Acids In Ionic Liquidsmentioning

confidence: 99%

Ionic liquids: prospects for nucleic acid handling and delivery

Egorova

Posvyatenko

Larin

et al. 2021

Nucleic Acids Research

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show abstract

“…In the latter case, novel magnetic ILs turn out to be particularly interesting for the purpose of effective extraction and preservation of DNA (Clark et al 2015a(Clark et al , b, 2016. For industrial purposes, ILs are being currently applied in DNA-based biosensors (Chen et al 2013;Sun et al 2013;Machado et al 2014), or to assist a vast variety of methods in genetic manipulations, including genomic sequencing (Kulkarni and Mukherjee 2016), cloning (Li et al 2013b), or gene delivery and transformation (Zhang et al 2009;Soni et al 2015). Moreover, replacement of standard aqueous solutions by ILs as solvents and catalysts for laboratory purposes enabled to overcome certain technological limitations associated with DNA nanotechnology (Nishimura et al 2005;Dandia et al 2013) due to enhanced DNA stability and solubility in ILs (Zhang et al 2009;Sharma et al 2015;Jumbri et al 2016;Mishra et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Aqueous ionic liquids in comparison with standard co-solutes

Oprzeska-Zingrebe

Smiatek

2018

Biophys Rev

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Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes. In this review article, we highlight common principles and differences between aqueous ILs and standard co-solutes with a specific focus on their underlying macromolecular stabilization or destabilization behavior. In combination with statistical thermodynamics theories, we present an efficient framework, which is used to classify structure modification effects consistently. The crucial importance of enthalpic and entropic contributions to the free energy change upon IL-assisted macromolecular unfolding in combination with a complex destabilization mechanism is described in detail. A special focus is also set on aqueous IL-DNA interactions, for which experimental and simulation outcomes are summarized and discussed in the context of previous findings.

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“…3D, there was a brief surge of ionic current (∼1.3

\times

of baseline value) at the entrance of 10‐nt ssDNA, followed by multiple resistive pulses from the nucleobase translocations and another current surge flagging the exit of the molecule. The abrupt current surges at the molecular entrance and exit could be due to the brief ionic crowding effect near the translocating strand [60]. The current surges by the exiting and entering molecules occurred almost concurrently in ∼30 μs range (inter‐molecular duration) due to the continuous back‐to‐back molecular translocations (Fig.…”

Section: Resultsmentioning

confidence: 99%

Detection of nucleotides in hydrated ssDNA via 2D h‐BN nanopore with ionic‐liquid/salt–water interface

et al. 2021

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Accomplishing slow translocation speed with high sensitivity has been the most critical mission for solid‐state nanopore (SSN) device to electrically detect nucleobases in ssDNA. In this study, a method to detect nucleobases of ssDNA using a 2D SSN is introduced by considerably reducing the translocation speed and effectively increasing its sensitivity. The ultra‐thin titanium dioxide coated hexagonal boron nitride nanopore was fabricated, along with an ionic‐liquid 1‐butyl‐3‐methylimidazolium hexafluorophosphate/2.0 M KCl aqueous (cis/trans) interface, for increasing both the spatial and the temporal resolutions. As the ssDNA molecules entered the nanopore, a brief surge of electrical conductivity occurred, which was followed by multiple resistive pulses from nucleobases during the translocation of ssDNA and another brief current surge flagging the exit of the molecule. The continuous detection of nucleobases using a 2D SSN device is a novel achievement: the water molecules bound to ssDNA increased the molecular conductivity and amplified electrical signals during the translocation. Along with the experiment, computational simulations using COMSOL Multiphysics are presented to explain the pivotal role of water molecules bound to ssDNA to detect nucleobases using a 2D SSN.

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Ionic liquid prolongs DNA translocation through graphene nanopores

Abstract: Ionic liquid molecules interact strongly with DNA and effectively reduce its translocation speed via graphene nanopore.

Cited by 18 publications

References 53 publications

Ionic liquids: prospects for nucleic acid handling and delivery

Ionic liquids: prospects for nucleic acid handling and delivery

Aqueous ionic liquids in comparison with standard co-solutes

Detection of nucleotides in hydrated ssDNA via 2D h‐BN nanopore with ionic‐liquid/salt–water interface

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