4.8 Article

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Multidisciplinary

Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

Thomas E. Ouldridge et al.

ACS NANO (2013)

Article Biochemistry & Molecular Biology

Molecular machines

Ron Elber et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)

Article Chemistry, Physical

Coarse-grained simulations of DNA overstretching

Flavio Romano et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Computer Science, Theory & Methods

Two-domain DNA strand displacement

Luca Cardelli

MATHEMATICAL STRUCTURES IN COMPUTER SCIENCE (2013)

Article Biochemistry & Molecular Biology

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

Thomas E. Ouldridge et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Chemistry, Physical

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

Flavio Romano et al.

JOURNAL OF CHEMICAL PHYSICS (2012)

Article Chemistry, Multidisciplinary

Expanding the Rule Set of DNA Circuitry with Associative Toehold Activation

Xi Chen

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Multidisciplinary Sciences

Complex shapes self-assembled from single-stranded DNA tiles

Bryan Wei et al.

NATURE (2012)

Review Chemistry, Multidisciplinary

Nucleic Acid Based Molecular Devices

Yamuna Krishnan et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2011)

Article Chemistry, Physical

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

Thomas E. Ouldridge et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Chemistry, Multidisciplinary

NUPACK: Analysis and Design of Nucleic Acid Systems

Joseph N. Zadeh et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Chemistry, Multidisciplinary

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

Anthony J. Genot et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Review Nanoscience & Nanotechnology

Challenges and opportunities for structural DNA nanotechnology

Andre V. Pinheiro et al.

NATURE NANOTECHNOLOGY (2011)

Article Multidisciplinary Sciences

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

Lulu Qian et al.

SCIENCE (2011)

Article Biotechnology & Applied Microbiology

Programmable in situ amplification for multiplexed imaging of mRNA expression

Harry M. T. Choi et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemistry & Molecular Biology

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

David Yu Zhang et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Physics, Multidisciplinary

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

Thomas E. Ouldridge et al.

PHYSICAL REVIEW LETTERS (2010)

Article Multidisciplinary Sciences

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators

Jarred M. Callura et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

DNA as a universal substrate for chemical kinetics

David Soloveichik et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Chemistry, Physical

Langevin thermostat for rigid body dynamics

Ruslan L. Davidchack et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Review Physics, Condensed Matter

Forward flux sampling for rare event simulations

Rosalind J. Allen et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2009)

Article Chemistry, Multidisciplinary

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

David Yu Zhang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

Article Chemistry, Physical

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

Stephen Whitelam et al.

SOFT MATTER (2009)

Article Biochemistry & Molecular Biology

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

Richard Owczarzy et al.

BIOCHEMISTRY (2008)

Article Multidisciplinary Sciences

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra

Yu He et al.

NATURE (2008)

Article Multidisciplinary Sciences

Programming biomolecular self-assembly pathways

Peng Yin et al.

NATURE (2008)

Article Physics, Multidisciplinary

Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion

S. J. Green et al.

PHYSICAL REVIEW LETTERS (2008)

Article Multidisciplinary Sciences

Engineering entropy-driven reactions and networks catalyzed by DNA

David Yu Zhang et al.

SCIENCE (2007)

Review Biochemistry & Molecular Biology

An overview of structural DNA Nanotechnology

Nadrian C. Seeman

MOLECULAR BIOTECHNOLOGY (2007)

Article Chemistry, Physical

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

Stephen Whitelam et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Review Nanoscience & Nanotechnology

DNA nanomachines

Jonathan Bath et al.

NATURE NANOTECHNOLOGY (2007)

Article Mathematics, Applied

Thermodynamic analysis of interacting nucleic acid strands

Robert M. Dirks et al.

SIAM REVIEW (2007)

Article Multidisciplinary Sciences

Enzyme-free nucleic acid logic circuits

Georg Seelig et al.

SCIENCE (2006)

Article Chemistry, Multidisciplinary

Behavior of polycatalytic assemblies in a substrate-displaying matrix

Renjun Pei et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Multidisciplinary Sciences

Folding DNA to create nanoscale shapes and patterns

PWK Rothemund

NATURE (2006)

Article Biochemistry & Molecular Biology

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

P Yakovchuk et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

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

Yang Gao et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biotechnology & Applied Microbiology

Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes

R Penchovsky et al.

NATURE BIOTECHNOLOGY (2005)

Article Chemistry, Multidisciplinary

Deoxyribozyme-based ligase logic gates and their initial circuits

MN Stojanovic et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Physics, Multidisciplinary

Sampling rare switching events in biochemical networks

RJ Allen et al.

PHYSICAL REVIEW LETTERS (2005)

Article Biochemistry & Molecular Biology

Stacked-unstacked equilibrium at the nick site of DNA

E Protozanova et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Biochemistry & Molecular Biology

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

C Joo et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Multidisciplinary Sciences

Triggered amplification by hybridization chain reaction

RM Dirks et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Multidisciplinary Sciences

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

DH Mathews et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

Mfold web server for nucleic acid folding and hybridization prediction

M Zuker

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Vienna RNA secondary structure server

IL Hofacker

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Hybridization kinetics and thermodynamics of molecular beacons

A Tsourkas et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Chemistry, Multidisciplinary

Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides

DV Pyshnyi et al.

RUSSIAN CHEMICAL BULLETIN (2002)

Article Chemistry, Multidisciplinary

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

H Kuhn et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)

Article Multidisciplinary Sciences

A DNA-fuelled molecular machine made of DNA

B Yurke et al.

NATURE (2000)

Article Biochemistry & Molecular Biology

Thermodynamic parameters for DNA sequences with dangling ends

S Bommarito et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Biochemistry & Molecular Biology

The kinetics of oligonucleotide replacements

LP Reynaldo et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)

Article Biochemistry & Molecular Biology

RNA folding at elementary step resolution

C Flamm et al.