scholarly journals Handhold-Mediated Strand Displacement: A Nucleic Acid Based Mechanism for Generating Far-from-Equilibrium Assemblies through Templated Reactions

ACS Nano ◽  
2021 ◽  
Vol 15 (2) ◽  
pp. 3272-3283
Author(s):  
Javier Cabello-Garcia ◽  
Wooli Bae ◽  
Guy-Bart V. Stan ◽  
Thomas E. Ouldridge
Keyword(s):  
Nucleic Acid ◽  
Strand Displacement ◽  
Far From Equilibrium

scholarly journals Handhold-mediated strand displacement: a nucleic acid-based mechanism for generating far-from-equilibrium assemblies through templated reactions

2020 ◽  
Author(s):  
Javier Cabello-Garcia ◽  
Wooli Bae ◽  
Guy-Bart V. Stan ◽  
Thomas E. Ouldridge
Keyword(s):  
Nucleic Acid ◽  
Biological Systems ◽  
Dna Nanotechnology ◽  
Central Mechanism ◽  
Dna Duplexes ◽  
Strand Displacement ◽  
Target Strand ◽  
Far From Equilibrium ◽  
Kinetics Of ◽  
Moderate Length

Toehold-mediated strand displacement (TMSD) is a nucleic acid-based reaction wherein an invader strand (I) replaces an incumbent strand (N) in a duplex with a target strand (T). TMSD is driven by toeholds, overhanging single-stranded domains in T recognised by I. Although TMSD is responsible for the outstanding potential of dynamic DNA nanotechnology1, 2, TMSD cannot implement templating, the central mechanism by which biological systems generate complex, far-from equilibrium assemblies like RNA or proteins3, 4. Therefore, we introduce handhold-mediated strand displacement (HMSD). Handholds are toehold analogues located in N and capable of implementing templating. We measure the kinetics of 98 different HMSD systems to demonstrate that handholds can accelerate the rate of invader-target (IT) binding by more than 4 orders of magnitude. Furthermore, handholds of moderate length accelerate reactions whilst allowing detachment of the product IT from N. We are thus able to experimentally demonstrate the use of HMSD-based templating to produce highly-specific far-from-equilibrium DNA duplexes.

scholarly journals Nucleic Acid Strand Displacement with Synthetic mRNA Inputs in Living Mammalian Cells

2018 ◽  
Vol 7 (12) ◽  
pp. 2737-2741 ◽  
Author(s):  
Gourab Chatterjee ◽  
Yuan-Jyue Chen ◽  
Georg Seelig
Keyword(s):  
Nucleic Acid ◽  
Mammalian Cells ◽  
Strand Displacement ◽  
Synthetic Mrna

scholarly journals Conditional guide RNA through two intermediate hairpins for programmable CRISPR/Cas9 function: building regulatory connections between endogenous RNA expressions

2020 ◽  
Vol 48 (20) ◽  
pp. 11773-11784
Author(s):  
Jiao Lin ◽  
Yan Liu ◽  
Peidong Lai ◽  
Huixia Ye ◽  
Liang Xu
Keyword(s):  
Nucleic Acid ◽  
Genetic Regulation ◽  
Binding Activity ◽  
Strand Displacement ◽  
Genetic Circuits ◽  
Reporter System ◽  
Gene Expressions ◽  
Guide Rna ◽  
Naturally Occurring ◽  
Novel Approach

Abstract A variety of nanodevices developed for nucleic acid computation provide great opportunities to construct versatile synthetic circuits for manipulation of gene expressions. In our study, by employing a two-hairpin mediated nucleic acid strand displacement as a processing joint for conditional guide RNA, we aim to build artificial connections between naturally occurring RNA expressions through programmable CRISPR/Cas9 function. This two-hairpin joint possesses a sequence-switching machinery, in which a random trigger strand can be processed to release an unconstrained sequence-independent strand and consequently activate the self-inhibitory guide RNA for conditional gene regulation. This intermediate processor was characterized by the fluorescence reporter system and applied for regulation of the CRISPR/Cas9 binding activity. Using plasmids to generate this sequence-switching machinery in situ, we achieved the autonomous genetic regulation of endogenous RNA expressions controlled by other unrelated endogenous RNAs in both E. coli and human cells. Unlike previously reported strand-displacement genetic circuits, this advanced nucleic acid nanomachine provides a novel approach that can establish regulatory connections between naturally occurring endogenous RNAs. In addition to CRISPR systems, we anticipate this two-hairpin machine can serve as a general processing joint for wide applications in the development of other RNA-based genetic circuits.

scholarly journals A nucleic acid strand displacement system for the multiplexed detection of tuberculosis-specific mRNA using quantum dots

Nanoscale ◽  
2016 ◽  
Vol 8 (19) ◽  
pp. 10087-10095 ◽  
Author(s):  
H. D. Gliddon ◽  
P. D. Howes ◽  
M. Kaforou ◽  
M. Levin ◽  
M. M. Stevens
Keyword(s):  
Quantum Dots ◽  
Nucleic Acid ◽  
Strand Displacement ◽  
Multiplexed Detection ◽  
Mrna Detection ◽  
Dna Strand Displacement ◽  
Displacement System ◽  
Dna Strand ◽  
Specific Mrna

On the development of a novel multiplexed assay for Tuberculosis-specific mRNA detection using DNA strand displacement and quantum dots.

scholarly journals Mismatches Improve the Performance of Strand-Displacement Nucleic Acid Circuits

2014 ◽  
Vol 126 (7) ◽  
pp. 1876-1879 ◽  
Author(s):  
Yu Sherry Jiang ◽  
Sanchita Bhadra ◽  
Bingling Li ◽  
Andrew D. Ellington
Keyword(s):  
Nucleic Acid ◽  
Strand Displacement

Ultraselective electrochemiluminescence biosensor based on locked nucleic acid modified toehold-mediated strand displacement reaction and junction-probe

The Analyst ◽  
2014 ◽  
Vol 139 (23) ◽  
pp. 6109-6112 ◽  
Author(s):  
Xi Zhang ◽  
Jing Zhang ◽  
Dongzhi Wu ◽  
Zhijing Liu ◽  
Shuxian Cai ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Locked Nucleic Acid ◽  
Displacement Reaction ◽  
Strand Displacement ◽  
Junction Probe ◽  
Strand Displacement Reaction

scholarly journals A simple DNA gate motif for synthesizing large-scale circuits

2011 ◽  
Vol 8 (62) ◽  
pp. 1281-1297 ◽  
Author(s):  
Lulu Qian ◽  
Erik Winfree
Keyword(s):  
Nucleic Acid ◽  
Large Scale ◽  
Strand Displacement ◽  
Molecular Systems ◽  
Displacement Reactions ◽  
Analogue Circuits ◽  
Practical Synthesis

The prospects of programming molecular systems to perform complex autonomous tasks have motivated research into the design of synthetic biochemical circuits. Of particular interest to us are cell-free nucleic acid systems that exploit non-covalent hybridization and strand displacement reactions to create cascades that implement digital and analogue circuits. To date, circuits involving at most tens of gates have been demonstrated experimentally. Here, we propose a simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates.

scholarly journals Availability: A Metric for Nucleic Acid Strand Displacement Systems

2016 ◽  
Vol 6 (1) ◽  
pp. 84-93 ◽  
Author(s):  
Xiaoping Olson ◽  
Shohei Kotani ◽  
Jennifer E. Padilla ◽  
Natalya Hallstrom ◽  
Sara Goltry ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Strand Displacement

scholarly journals Ultrasensitive electrochemical detection of nucleic acid based on the isothermal strand-displacement polymerase reaction and enzyme dual amplification

2010 ◽  
Vol 12 (7) ◽  
pp. 985-988 ◽  
Author(s):  
Yuqing He ◽  
Kang Zeng ◽  
Xibao Zhang ◽  
Anant S. Gurung ◽  
Meenu Baloda ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Electrochemical Detection ◽  
Strand Displacement ◽  
Dual Amplification
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