Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems

2011 ◽  
pp. 130-144 ◽  
Author(s):  
Matthew R. Lakin ◽  
Andrew Phillips
Keyword(s):  
Strand Displacement

An optical DNA logic gate based on strand displacement and magnetic separation, with response to multiple microRNAs in cancer cell lysates

2017 ◽  
Vol 184 (8) ◽  
pp. 2505-2513 ◽  
Author(s):  
Xiaoting Ji ◽  
Haoyuan Lv ◽  
Minghui Ma ◽  
Binglin Lv ◽  
Caifeng Ding
Keyword(s):  
Magnetic Separation ◽  
Cancer Cell ◽  
Logic Gate ◽  
Strand Displacement ◽  
Cell Lysates

scholarly journals Defective Strand-Displacement DNA Synthesis Due to Accumulation of Thymidine Analogue Resistance Mutations in HIV-2 Reverse Transcriptase

2020 ◽  
Vol 6 (5) ◽  
pp. 1140-1153 ◽  
Author(s):  
Samara Martín-Alonso ◽  
Mar Álvarez ◽  
María Nevot ◽  
Miguel Á. Martínez ◽  
Luis Menéndez-Arias
Keyword(s):  
Reverse Transcriptase ◽  
Dna Synthesis ◽  
Strand Displacement ◽  
Resistance Mutations ◽  
Thymidine Analogue

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 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 Biosensors Based on Isothermal DNA Amplification for Bacterial Detection in Food Safety and Environmental Monitoring

Sensors ◽  
2021 ◽  
Vol 21 (2) ◽  
pp. 602
Author(s):  
Sandra Leonardo ◽  
Anna Toldrà ◽  
Mònica Campàs
Keyword(s):  
Food Safety ◽  
Environmental Monitoring ◽  
Rolling Circle Amplification ◽  
Dna Amplification ◽  
Isothermal Amplification ◽  
In Situ Monitoring ◽  
Strand Displacement ◽  
Strand Displacement Amplification ◽  
Bacterial Detection ◽  
Efficient Detection

The easy and rapid spread of bacterial contamination and the risk it poses to human health makes evident the need for analytical methods alternative to conventional time-consuming laboratory-based techniques for bacterial detection. To tackle this demand, biosensors based on isothermal DNA amplification methods have emerged, which avoid the need for thermal cycling, thus facilitating their integration into small and low-cost devices for in situ monitoring. This review focuses on the breakthroughs made on biosensors based on isothermal amplification methods for the detection of bacteria in the field of food safety and environmental monitoring. Optical and electrochemical biosensors based on loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), strand displacement amplification (SDA), and isothermal strand displacement polymerisation (ISDPR) are described, and an overview of their current advantages and limitations is provided. Although further efforts are required to harness the potential of these emerging analytical techniques, the coalescence of the different isothermal amplification techniques with the wide variety of biosensing detection strategies provides multiple possibilities for the efficient detection of bacteria far beyond the laboratory bench.

Ultra-sensitive MicroRNA-21 detection based on multiple cascaded strand displacement amplification and CRISPR/Cpf1 (MC-SDA/CRISPR/Cpf1)

2021 ◽  
Author(s):  
Xiaolong Chen ◽  
Yuanyi Deng ◽  
Gaihua Cao ◽  
Yifan Xiong ◽  
Danqun Huo ◽  
...  
Keyword(s):  
Cancer Diagnosis ◽  
Analytical Method ◽  
Strand Displacement ◽  
Strand Displacement Amplification ◽  
Diagnosis And Prognosis ◽  
Potential Biomarker ◽  
Cancer Diagnosis And Prognosis

MicroRNA-21 (miR-21) has been considered as a potential biomarker for cancer diagnosis and prognosis due to its highly expressed in tumors. Here, an analytical method which integrates the multiple cascaded...

scholarly journals CRISPR-Associated Primase-Polymerases are implicated in prokaryotic CRISPR-Cas adaptation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Katerina Zabrady ◽  
Matej Zabrady ◽  
Peter Kolesar ◽  
Arthur W. H. Li ◽  
Aidan J. Doherty
Keyword(s):  
Dna Repair ◽  
Dna Synthesis ◽  
Genome Stability ◽  
Dna Polymerases ◽  
Acquired Immunity ◽  
Strand Displacement ◽  
Genetic Studies ◽  
Type Iiia ◽  
Maintain Genome Stability ◽  
Cas Proteins

AbstractCRISPR-Cas pathways provide prokaryotes with acquired “immunity” against foreign genetic elements, including phages and plasmids. Although many of the proteins associated with CRISPR-Cas mechanisms are characterized, some requisite enzymes remain elusive. Genetic studies have implicated host DNA polymerases in some CRISPR-Cas systems but CRISPR-specific replicases have not yet been discovered. We have identified and characterised a family of CRISPR-Associated Primase-Polymerases (CAPPs) in a range of prokaryotes that are operonically associated with Cas1 and Cas2. CAPPs belong to the Primase-Polymerase (Prim-Pol) superfamily of replicases that operate in various DNA repair and replication pathways that maintain genome stability. Here, we characterise the DNA synthesis activities of bacterial CAPP homologues from Type IIIA and IIIB CRISPR-Cas systems and establish that they possess a range of replicase activities including DNA priming, polymerisation and strand-displacement. We demonstrate that CAPPs operonically-associated partners, Cas1 and Cas2, form a complex that possesses spacer integration activity. We show that CAPPs physically associate with the Cas proteins to form bespoke CRISPR-Cas complexes. Finally, we propose how CAPPs activities, in conjunction with their partners, may function to undertake key roles in CRISPR-Cas adaptation.

Biocomputing based on DNA strand displacement reactions

ChemPhysChem ◽  
2021 ◽  
Author(s):  
Hui Lv ◽  
Qian Li ◽  
Jiye Shi ◽  
Fei Wang ◽  
Chunhai Fan
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand
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