On the biophysics and kinetics of toehold-mediated DNA strand displacement (Q37528778)

20 August 2017

On the biophysics and kinetics of toehold-mediated DNA strand displacement (English)

1 reference

20 August 2017

0 references

Erik Winfree

1 reference

20 August 2017

Thomas E Ouldridge

0 references

Ard A Louis

0 references

Bernard Yurke

1 reference

20 August 2017

Jonathan P K Doye

1 reference

20 August 2017

Niranjan Srinivas

1 reference

20 August 2017

Petr Sulc

series ordinal

1 reference

20 August 2017

Joseph M Schaeffer

series ordinal

1 reference

20 August 2017

language of work or name

English

0 references

publication date

9 September 2013

1 reference

20 August 2017

Nucleic Acids Research

1 reference

20 August 2017

1 reference

20 August 2017

1 reference

20 August 2017

10641-10658

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

20 August 2017

start time

10 November 2016

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

The role of collective motion in examples of coarsening and self-assembly.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Expanding the rule set of DNA circuitry with associative toehold activation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Challenges and opportunities for structural DNA nanotechnology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Scaling up digital circuit computation with DNA strand displacement cascades

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Dynamic DNA nanotechnology using strand-displacement reactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

DNA as a universal substrate for chemical kinetics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Robustness and modularity properties of a non-covalent DNA catalytic reaction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Programming biomolecular self-assembly pathways

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

An overview of structural DNA nanotechnology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Enzyme-free nucleic acid logic circuits

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Folding DNA to create nanoscale shapes and patterns

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Triggered amplification by hybridization chain reaction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Stacked-unstacked equilibrium at the nick site of DNA

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

The thermodynamics of DNA structural motifs

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Vienna RNA secondary structure server

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Mfold web server for nucleic acid folding and hybridization prediction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

A DNA-fuelled molecular machine made of DNA

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

RNA folding at elementary step resolution

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Design and self-assembly of two-dimensional DNA crystals

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

The kinetics of spontaneous DNA branch migration

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Reassociation rate limited displacement of DNA strands by branch migration

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Forward flux sampling for rare event simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Nucleic acid based molecular devices

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

The kinetics of oligonucleotide replacements

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Hybridization and renaturation kinetics of nucleic acids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Thermodynamic parameters for DNA sequences with dangling ends

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Hybridization kinetics and thermodynamics of molecular beacons

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Dissociation of long-chain duplex RNA can occur via strand displacement in vitro: biological implications

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

The effect of topology on the structure and free energy landscape of DNA kissing complexes.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Kinetics of renaturation of DNA

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

A direct measurement of the unzippering rate of a nucleic acid double helix.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Absorbance melting curves of RNA.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Implication of RNA structure on antisense oligonucleotide hybridization kinetics

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Coarse-grained simulations of DNA overstretching.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Complex shapes self-assembled from single-stranded DNA tiles

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Programmable in situ amplification for multiplexed imaging of mRNA expression

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

NUPACK: Analysis and design of nucleic acid systems

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

DNA nanotweezers studied with a coarse-grained model of DNA.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Control of DNA strand displacement kinetics using toehold exchange.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Langevin thermostat for rigid body dynamics

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Engineering entropy-driven reactions and networks catalyzed by DNA.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Deoxyribozyme-based ligase logic gates and their initial circuits.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+), deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3905871

Thermodynamic Analysis of Interacting Nucleic Acid Strands

2 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT801

Two-domain DNA strand displacement

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT801

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT801

Exact stochastic simulation of coupled chemical reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT801

An immobile nucleic acid junction constructed from oligonucleotides

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT801

Relaxation kinetics of dimer formation by self complementary oligonucleotides

21 January 2018

1 reference

12 December 2020

Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution

1 reference

12 December 2020

Behavior of polycatalytic assemblies in a substrate-displaying matrix

1 reference

12 December 2020

New Monte Carlo technique for studying phase transitions

1 reference

12 December 2020

1 reference

12 December 2020

Thermodynamics of (dG-dC)3 double-helix formation in water and deuterium oxide

1 reference

12 December 2020

Uptake of homologous single-stranded fragments by superhelical DNA. IV. Branch migration

1 reference

12 December 2020

Improved nearest-neighbor parameters for predicting DNA duplex stability

1 reference

12 December 2020

Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy

1 reference

12 December 2020

Elementary steps of base recognition and helix-coil transitions in nucleic acids

1 reference

12 December 2020

Sampling Rare Switching Events in Biochemical Networks

1 reference

12 December 2020

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

1 reference

12 December 2020

Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKT801

1 reference

20 August 2017

1 reference

20 August 2017

PubMed publication ID

24019238

1 reference