scholarly journals Kinetics of RNA and RNA:DNA Hybrid Strand Displacement

2021 ◽  
Author(s):  
Hao Liu ◽  
Fan Hong ◽  
Francesca Smith ◽  
John Goertz ◽  
Thomas Ouldridge ◽  
...  
Keyword(s):  
Strand Displacement ◽  
Rna:Dna Hybrid ◽  
Kinetics Of

scholarly journals Kinetics of RNA and RNA:DNA hybrid strand displacement

2021 ◽  
Author(s):  
Hao Liu ◽  
Fan Hong ◽  
Francesca Smith ◽  
John Goertz ◽  
Thomas E Ouldridge ◽  
...  
Keyword(s):  
Experimental Studies ◽  
Reaction Rates ◽  
Strand Displacement ◽  
Single Stranded Region ◽  
In Vivo Diagnostics ◽  
Rna:Dna Hybrid ◽  
Logic Operations ◽  
Work Done ◽  
Kinetics Of

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.

scholarly journals Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids

2017 ◽  
Vol 121 (12) ◽  
pp. 2594-2602 ◽  
Author(s):  
Xiaoping Olson ◽  
Shohei Kotani ◽  
Bernard Yurke ◽  
Elton Graugnard ◽  
William L. Hughes
Keyword(s):  
Nucleic Acids ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Locked Nucleic Acids ◽  
Dna Strand ◽  
Kinetics Of

scholarly journals Kinetics of Toehold-Mediated DNA Strand Displacement Depend on FeII4L4 Tetrahedron Concentration

Nano Letters ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 1368-1374
Author(s):  
Jinbo Zhu ◽  
Filip Bošković ◽  
Bao-Nguyen T. Nguyen ◽  
Jonathan R. Nitschke ◽  
Ulrich F. Keyser
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Kinetics Of

scholarly journals Kinetics of DNA Strand Displacement

2019 ◽  
Vol 116 (3) ◽  
pp. 499a
Author(s):  
Alexander W. Cook ◽  
Bo Broadwater ◽  
Harold Kim
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Kinetics Of

scholarly journals On the biophysics and kinetics of toehold-mediated DNA strand displacement

2013 ◽  
Vol 41 (22) ◽  
pp. 10641-10658 ◽  
Author(s):  
Niranjan Srinivas ◽  
Thomas E. Ouldridge ◽  
Petr Šulc ◽  
Joseph M. Schaeffer ◽  
Bernard Yurke ◽  
...  
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Kinetics Of

scholarly journals First passage time study of DNA strand displacement

2020 ◽  
Author(s):  
D. W. Bo Broadwater ◽  
Alexander W. Cook ◽  
Harold D. Kim
Keyword(s):  
Single Molecule ◽  
First Passage Time ◽  
Resonance Energy ◽  
Passage Time ◽  
Single Step ◽  
Strand Displacement ◽  
First Passage ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Kinetics Of

AbstractDNA strand displacement, where a single-stranded nucleic acid invades a DNA duplex, is pervasive in genomic processes and DNA engineering applications. The kinetics of strand displacement have been studied in bulk; however, the kinetics of the underlying strand exchange were obfuscated by a slow bimolecular association step. Here, we use a novel single-molecule Fluorescence Resonance Energy Transfer (smFRET) approach termed the “fission” assay to obtain the full distribution of first passage times of unimolecular strand displacement. At a frame time of 4.4 ms, the first passage time distribution for a 14-nt displacement domain exhibited a nearly monotonic decay with little delay. Among the eight different sequences we tested, the mean displacement time was on average 35 ms and varied by up to a factor of 13. The measured displacement kinetics also varied between complementary invaders and between RNA and DNA invaders of the same base sequence except for T→U substitution. However, displacement times were largely insensitive to the monovalent salt concentration in the range of 0.25 M to 1 M. Using a one-dimensional random walk model, we infer that the single-step displacement time is in the range of ∼30 µs to ∼300 µs depending on the base identity. The framework presented here is broadly applicable to the kinetic analysis of multistep processes investigated at the single-molecule level.

Kinetics of Proximity-Induced Intramolecular DNA Strand Displacement

2016 ◽  
Vol 88 (16) ◽  
pp. 8152-8157 ◽  
Author(s):  
Feng Li ◽  
Yanan Tang ◽  
Sarah M. Traynor ◽  
Xing-Fang Li ◽  
X. Chris Le
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Kinetics Of

scholarly journals Measurement of Kinetics of Hammerhead Ribozyme Cleavage Reactions using Toehold Mediated Strand Displacement

2020 ◽  
Author(s):  
Jay Bhakti Kapadia ◽  
Nawwaf Kharma ◽  
Alen Nellikulam Davis ◽  
Nicolas Kamel ◽  
Jonathan Perreault
Keyword(s):  
Hammerhead Ribozyme ◽  
Polyacrylamide Gels ◽  
Strand Displacement ◽  
Rna Molecules ◽  
Starting Point ◽  
Dna Strands ◽  
Regular Sampling ◽  
Cleavage Reactions ◽  
Labeled Rna ◽  
Kinetics Of

ABSTRACTThis paper presents a probe comprising a fluorophore and a quencher, enabling measurement of hammerhead ribozyme cleavage reactions, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two DNA strands; one strand is labelled with a fluorophore at its 5’-end, while the other strand is labelled with a quencher at its 3’-end. These two DNA strands are perfectly complementary, but with a 3’-overhang of the fluorophore strand. These unpaired nucleotides act as a toehold, which is utilized by a detached cleaved fragment (coming from a self-cleaving hammerhead ribozyme) as the starting point for a strand displacement reaction. This reaction causes the separation of the fluorophore strand from the quencher strand, culminating in fluorescence, detectable in a plate reader. Notably, the emitted fluorescence is proportional to the amount of detached cleaved-off RNAs, displacing the DNA quencher strand. This method can replace or complement radio-hazardous unstable 32P as a method of measurement of the kinetics of ribozyme cleavage reactions; it also eliminates the need for polyacrylamide gels, for the same purpose. Critically, this method allows to distinguish between the total amount of cleaved ribozymes and the amount of detached fragments, resulting from that cleavage reaction.

scholarly journals DNA dynamics and computation based on toehold-free strand displacement

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hong Kang ◽  
Tong Lin ◽  
Xiaojin Xu ◽  
Qing-Shan Jia ◽  
Richard Lakerveld ◽  
...  
Keyword(s):  
Information Processing ◽  
Boolean Functions ◽  
The Other ◽  
Dna Nanostructures ◽  
Dna Dynamics ◽  
Strand Displacement ◽  
Equilibrium Control ◽  
Target Strand ◽  
Excess Amount ◽  
Kinetics Of

AbstractWe present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics.

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