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Kinetics of RNA and RNA:DNA hybrid strand displacement

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Title: Kinetics of RNA and RNA:DNA hybrid strand displacement
Authors: Liu, H
Hong, F
Smith, F
Goertz, J
Ouldridge, T
Stevens, MM
Yan, H
Šulc, P
Item Type: Journal Article
Abstract: In nucleic acid nanotechnology, strand displacement is a widely used mechanism where one strand from a hybridized duplex is exchanged with an invading strand that binds to a toehold, a single-stranded region on the duplex. It is used to perform logic operations on a molecular level, initiate cascaded reactions, or even for in vivo diagnostics and treatments. While systematic experimental studies have been carried out to probe the kinetics of strand displacement in DNA with different toehold lengths, sequences, and mismatch positions, there has not been a comparable investigation of RNA or RNA-DNA hybrid systems. Here, we experimentally study how toehold length, toehold location (5' or 3' end of the strand), and mismatches influence the strand displacement kinetics. We observe reaction acceleration with increasing toehold length and placement of the toehold at the 5' end of the substrate. We find that mismatches closer to the interface of toehold and duplex slow down the reaction more than remote mismatches. A comparison of RNA and DNA displacement with hybrid displacement (RNA invading DNA or DNA invading RNA) is partly explainable by the thermodynamic stabilities of the respective toehold regions, but also suggests that the rearrangement from B-form to A-form helix in the case of RNA invading DNA might play a role in the kinetics.
Issue Date: 19-Nov-2021
Date of Acceptance: 26-Oct-2021
URI: http://hdl.handle.net/10044/1/92445
DOI: 10.1021/acssynbio.1c00336
ISSN: 2161-5063
Publisher: American Chemical Society
Start Page: 3066
End Page: 3073
Journal / Book Title: ACS Synthetic Biology
Volume: 10
Issue: 11
Copyright Statement: © 2021 American Chemical Society. This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Synthetic Biology, after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acssynbio.1c00336
Sponsor/Funder: Engineering & Physical Science Research Council (EPSRC)
Funder's Grant Number: EP/R018707/1
Keywords: DNA nanotechnology
DNA:RNA hybrid duplex
Kinetics
RNA nanotechnology
Strand displacement
DNA nanotechnology
DNA:RNA hybrid duplex
Kinetics
RNA nanotechnology
Strand displacement
0304 Medicinal and Biomolecular Chemistry
0601 Biochemistry and Cell Biology
0903 Biomedical Engineering
Publication Status: Published
Conference Place: United States
Embargo Date: 2022-11-09
Online Publication Date: 2021-11-09
Appears in Collections:Materials
Bioengineering
Faculty of Natural Sciences
Faculty of Engineering