Kinetics of RNA and RNA:DNA Hybrid Strand Displacement

Hao Liu, Fan Hong, Francesca Smith, John Goertz, Thomas Ouldridge, Molly M. Stevens, Hao Yan, Petr Šulc

Research output: Contribution to journalArticlepeer-review

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 forin vivodiagnostics 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.

Original languageEnglish (US)
Pages (from-to)3066-3073
Number of pages8
JournalACS Synthetic Biology
Volume10
Issue number11
DOIs
StatePublished - Nov 19 2021
Externally publishedYes

Keywords

  • DNA nanotechnology
  • DNA:RNA hybrid duplex
  • Kinetics
  • RNA nanotechnology
  • Strand displacement

ASJC Scopus subject areas

  • Biomedical Engineering
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

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