Kinetics of RNA and RNA:DNA hybrid strand displacement
File(s)
Accepted version
Author(s)
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.
Date Issued
2021-11-19
Date Acceptance
2021-10-26
Citation
ACS Synthetic Biology, 2021, 10 (11), pp.3066-3073
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
Engineering & Physical Science Research Council (EPSRC)
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/34752075
Grant Number
EP/R018707/1
Subjects
DNA nanotechnology
DNA:RNA hybrid duplex
Kinetics
RNA nanotechnology
Strand displacement
Publication Status
Published
Coverage Spatial
United States
Date Publish Online
2021-11-09