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

Integrating DNA-Strand-Displacement Circuitry with Self-Assembly of Spherical Nucleic Acids

2015 ◽  
Vol 137 (44) ◽  
pp. 14107-14113 ◽  
Author(s):  
Dongbao Yao ◽  
Tingjie Song ◽  
Xianbao Sun ◽  
Shiyan Xiao ◽  
Fujian Huang ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Self Assembly ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Spherical Nucleic Acids

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 Controllable DNA strand displacement by independent metal-ligand complexation

2021 ◽  
Author(s):  
Liang-Liang Wang ◽  
Qiu-Long Zhang ◽  
Yang Wang ◽  
Yan Liu ◽  
Jiao Lin ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Structural Diversity ◽  
Strand Displacement ◽  
Base Pairs ◽  
Novel Approach ◽  
Ligand Type ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Metal Ligand

Introduction of artificial metal-ligand base pairs can enrich the structural diversity and functional controllability of nucleic acids. In this work, we revealed a novel approach by placing a ligand-type nucleoside...

Proximity aptasensor for protein detection based on an enzyme-free amplification strategy

2017 ◽  
Vol 13 (10) ◽  
pp. 1936-1939 ◽  
Author(s):  
Dawei Yang ◽  
Yuguo Tang ◽  
Zhenzhen Guo ◽  
Xifeng Chen ◽  
Peng Miao
Keyword(s):  
Protein Detection ◽  
Hybridization Chain Reaction ◽  
Strand Displacement ◽  
Chain Reaction ◽  
Protein Sensing ◽  
Free Protein ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Amplification Strategy ◽  
Kinetics Of

An enzyme-free protein sensing strategy based on the kinetics of proximity-induced DNA strand displacement and hybridization chain reaction is developed.

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