Modeling DNA-Strand Displacement Reactions in the Presence of Base-Pair Mismatches

Irmisch, Patrick; Ouldridge, Thomas E.; Seidel, Ralf

doi:10.1021/jacs.0c03105

Cited by 93 publications

(128 citation statements)

References 52 publications

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“…The observed slowdown induced by mismatches at different positions for RNA TMSD is hence compatible with the kinetics of TMSD of DNA strands with mismatches that was previously studied computationally and experimentally [26,27,34]. The kinetics of the TMSD can be approximately modeled as a stochastic Markovian process consisting of transitions between states characterized by the number of bonds between respective strands.…”

Section: B Mismatch Effectssupporting

confidence: 82%

Kinetics of RNA and RNA:DNA hybrid strand displacement

Líu

Fan

Smith

et al. 2021

Preprint

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In dynamic nucleic acids nanotechnology, strand displacement is a widely used mechanism where one strand from a hybridized duplex is exchanged with an invading strand which binds to a toehold, a single-stranded region on the duplex. With proper design and kinetic control, strand displacement is used to perform logic operations on molecular level to trigger the conformational change in nanostructures, 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, there has not been a comparable systematic work done for 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. Through comparing the reaction rates, combined with previous theoretical studies, we observed reaction acceleration with increasing toehold length and placement of toehold at 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. Comparison of RNA displacement and DNA displacement with hybrid displacement (RNA invading DNA or DNA invading RNA) is in part explainable by the thermodynamic stabilities of the respective toehold regions, but also suggest that the rearrangement from B-form to A-form helix in case of RNA invading DNA might play a role in the kinetics. The measured kinetics of toehold-mediated strand displacement will be important in understanding and construction of more complex dynamic nucleic acid systems.

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Section: B Mismatch Effectssupporting

confidence: 82%

Kinetics of RNA and RNA:DNA hybrid strand displacement

Líu

Fan

Smith

et al. 2021

Preprint

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“…The rate of DNA strand displacement reactions can be modulated over several orders of magnitude by introducing one or more mismatches between the input strand and the target duplex ( 48 , 60 ). Rational positioning of mismatches provides a useful control mechanism for competitive reaction networks ( 60 , 62 ) and enables the design of strand displacement-based nucleic acid probes having a high-degree of mismatch discrimination ( 63 , 64 ). A common practical application is the detection of single nucleotide polymorphisms (SNPs), which are of great diagnostic value ( 65–67 ).…”

Section: Resultsmentioning

confidence: 99%

“…A series of inputs containing mismatches at a single position (and one input containing two mismatches within the toehold binding domain) were generated from input strand ( d -IN TH 8) having an 8-nucleotide toehold domain (Figure 3A ). Placement of the mismatches were, in part, informed by previous literature on the effects of mismatches on rates of all-DNA strand displacement reactions, as well as PNA–DNA hybridization ( 48 , 58 , 62 , 63 ).…”

Section: Resultsmentioning

confidence: 99%

Kinetics of heterochiral strand displacement from PNA–DNA heteroduplexes

Kundu

Young

Sczepanski

2021

Nucleic Acids Research

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Dynamic DNA nanodevices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation remains challenging due to nuclease degradation and other cellular factors. Use of l-DNA, the nuclease resistant enantiomer of native d-DNA, provides a promising solution. On this basis, we recently developed a strand displacement methodology, referred to as ‘heterochiral’ strand displacement, that enables robust l-DNA nanodevices to be sequence-specifically interfaced with endogenous d-nucleic acids. However, the underlying reaction – strand displacement from PNA–DNA heteroduplexes – remains poorly characterized, limiting design capabilities. Herein, we characterize the kinetics of strand displacement from PNA–DNA heteroduplexes and show that reaction rates can be predictably tuned based on several common design parameters, including toehold length and mismatches. Moreover, we investigate the impact of nucleic acid stereochemistry on reaction kinetics and thermodynamics, revealing important insights into the biophysical mechanisms of heterochiral strand displacement. Importantly, we show that strand displacement from PNA–DNA heteroduplexes is compatible with RNA inputs, the most common nucleic acid target for intracellular applications. Overall, this work greatly improves the understanding of heterochiral strand displacement reactions and will be useful in the rational design and optimization of l-DNA nanodevices that operate at the interface with biology.

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“…Fourth, this metal-ligand complexation mediated strand displacement was also highly sensitive to the mismatched nucleotide in the invaded duplex structure through an asymmetric way as previously observed in the conventional toehold mediated Please do not adjust margins Please do not adjust margins displacement (Figure 4d). 56 Taken together, we revealed that the strand invasion by the metal-ligand complexation also possessed the efficiency, specificity, tunability and sensitivity similarly as the Watson-Crick base-paired toehold DNA, which could potentially achieve all kinds of dynamic stranddisplacement processes like a conventional toehold. Notably, compared with the Watson-Crick base-paired toehold, the metal-ligand paired toehold can present a unique feature of controllability during the dynamic strand displacement.…”

Section: S S Smentioning

confidence: 75%