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Literature DB >> 26970191

Studies of RNA Sequence and Structure Using Nanopores.

Robert Y Henley¹, Spencer Carson¹, Meni Wanunu².

Abstract

Nanopores are powerful single-molecule sensors with nanometer scale dimensions suitable for detection, quantification, and characterization of nucleic acids and proteins. Beyond sequencing applications, both biological and solid-state nanopores hold great promise as tools for studying the biophysical properties of RNA. In this review, we highlight selected landmark nanopore studies with regards to RNA sequencing, microRNA detection, RNA/ligand interactions, and RNA structural/conformational analysis.

Entities: Chemical Disease Gene Mutation Species

Keywords: RNA; RNA conformation; RNA sequencing; RNA–protein interaction; drug screening assay; microRNA; nanopore; single-molecule

Mesh：

Substances：
RNA

Year: 2016 PMID： 26970191 PMCID： PMC5146985 DOI： 10.1016/bs.pmbts.2015.10.020

Source DB: PubMed Journal: Prog Mol Biol Transl Sci ISSN： 1877-1173 Impact factor: 3.622

57 in total

1. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors.

Authors: Meni Wanunu; Tali Dadosh; Vishva Ray; Jingmin Jin; Larry McReynolds; Marija Drndić
Journal: Nat Nanotechnol Date: 2010-10-24 Impact factor: 39.213

2. Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results.

Authors: Jin-Der Wen; Maria Manosas; Pan T X Li; Steven B Smith; Carlos Bustamante; Felix Ritort; Ignacio Tinoco
Journal: Biophys J Date: 2007-02-09 Impact factor: 4.033

3. Direct force measurements on double-stranded RNA in solid-state nanopores.

Authors: Michiel van den Hout; Igor D Vilfan; Susanne Hage; Nynke H Dekker
Journal: Nano Lett Date: 2010-02-10 Impact factor: 11.189

4. Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore.

Authors: Adam R Hall; Stijn van Dorp; Serge G Lemay; Cees Dekker
Journal: Nano Lett Date: 2009-12 Impact factor: 11.189

5. The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine.

Authors: Joseph E Reiner; Arvind Balijepalli; Joseph W F Robertson; Bryon S Drown; Daniel L Burden; John J Kasianowicz
Journal: J Chem Phys Date: 2012-12-07 Impact factor: 3.488

6. Helix-coil kinetics of individual polyadenylic acid molecules in a protein channel.

Authors: Jianxun Lin; Anatoly Kolomeisky; Amit Meller
Journal: Phys Rev Lett Date: 2010-04-15 Impact factor: 9.161

7. 2-Aminobenzoxazole ligands of the hepatitis C virus internal ribosome entry site.

Authors: Kevin D Rynearson; Brian Charrette; Christopher Gabriel; Jesus Moreno; Mark A Boerneke; Sergey M Dibrov; Thomas Hermann
Journal: Bioorg Med Chem Lett Date: 2014-06-04 Impact factor: 2.823

Review 8. The potential and challenges of nanopore sequencing.

Authors: Daniel Branton; David W Deamer; Andre Marziali; Hagan Bayley; Steven A Benner; Thomas Butler; Massimiliano Di Ventra; Slaven Garaj; Andrew Hibbs; Xiaohua Huang; Stevan B Jovanovich; Predrag S Krstic; Stuart Lindsay; Xinsheng Sean Ling; Carlos H Mastrangelo; Amit Meller; John S Oliver; Yuriy V Pershin; J Michael Ramsey; Robert Riehn; Gautam V Soni; Vincent Tabard-Cossa; Meni Wanunu; Matthew Wiggin; Jeffery A Schloss
Journal: Nat Biotechnol Date: 2008-10 Impact factor: 54.908

5. RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration.

Authors: Matteo Becchi; Pietro Chiarantoni; Antonio Suma; Cristian Micheletti
Journal: J Phys Chem B Date: 2021-01-26 Impact factor: 2.991

5 in total

Studies of RNA Sequence and Structure Using Nanopores.

1. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors.

2. Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results.

3. Direct force measurements on double-stranded RNA in solid-state nanopores.

4. Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore.

5. The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine.

6. Helix-coil kinetics of individual polyadenylic acid molecules in a protein channel.

7. 2-Aminobenzoxazole ligands of the hepatitis C virus internal ribosome entry site.

Review 8. The potential and challenges of nanopore sequencing.

9. Nanopore-based detection of circulating microRNAs in lung cancer patients.

10. High-throughput optical sensing of nucleic acids in a nanopore array.

1. Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification.

2. Wavelet Denoising of High-Bandwidth Nanopore and Ion-Channel Signals.

Review 3. Next-Generation Sequencing Technologies in Blood Group Typing.

4. Ribosome Fingerprinting with a Solid-State Nanopore.

5. RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration.