4.6 Article

The Free-Energy Landscape of a Mechanically Bistable DNA Origami

Related references

Note: Only part of the references are listed.
Article Chemistry, Multidisciplinary

Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking

Ian Hamilton et al.

Summary: We developed a disulfide cross-linking approach, xHEED, to measure the distance-dependent encounter frequency of DNA helices in solution. Our measurements define the relevant distances for electrostatic interactions of nucleic-acid helices and provide insights into the impact of different ionic conditions on these forces.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

Article Chemistry, Multidisciplinary

Probing the Mechanical Properties of DNA Nanostructures with Metadynamics

Will T. Kaufhold et al.

Summary: The study utilizes metadynamics to sample the free energy landscapes of DNA nanostructures and demonstrates its ability to predict the mechanical response of DNA nanodevices. These findings are significant for the design and application of DNA nanostructures.

ACS NANO (2022)

Article Chemistry, Multidisciplinary

High-Force Application by a Nanoscale DNA Force Spectrometer

Michael Darcy et al.

Summary: The ability to apply and measure high forces on the nanometer scale is crucial for the development of nanomedicine, molecular robotics, and understanding biological processes. Current force spectroscopy techniques have limitations in applying forces in constrained geometries. DNA-based molecular calipers have shown promise as an alternative, but their force application capabilities are currently limited. This study implemented DNA origami nanocalipers with tunable mechanical properties to demonstrate the ability to apply forces of at least 20 piconewtons with a nanometer-scale dynamic range.

ACS NANO (2022)

Review Biophysics

Advancing Biophysics Using DNA Origami

Wouter Engelen et al.

Summary: DNA origami technology enables the construction of nanoscale objects with user-defined shapes and tailored functionalities, opening up new avenues of exploration in biophysics. By interfacing with biomolecules effectively, added value or new biophysical insights can be generated, showing great potential for applications in more complex environments such as cells or organisms.

ANNUAL REVIEW OF BIOPHYSICS, VOL 50, 2021 (2021)

Article Chemistry, Multidisciplinary

Massively Parallelized Molecular Force Manipulation with On-Demand Thermal and Optical Control

Hanquan Su et al.

Summary: The origami polymer force clamp (OPFC) is a technology that enables parallel operations to be conducted in single-molecule force spectroscopy (SMFS) to address the issue of serial and slow measurements. It allows for the manipulation of multiple molecules under force simultaneously without the need for dedicated instruments or surface tethering.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Chemistry, Multidisciplinary

Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

Ruixin Li et al.

Summary: The study focused on the structural properties of DNA origami and the energy required for deformation. By using molecular dynamics simulations with a coarse-grained model, it was found that approximately 33.1 kcal/mol of energy is needed to complete the deformation of DNA structures. These insights provide valuable information on the mechanics of DNA origami for various applications.

APPLIED SCIENCES-BASEL (2021)

Article Chemistry, Physical

Integrated computer-aided engineering and design for DNA assemblies

Chao-Min Huang et al.

Summary: Recent studies have shown that integrating molecular dynamics-based computer-aided engineering with computer-aided design allows for the rapid construction of large three-dimensional DNA assemblies with control over their geometry, mechanics, and dynamics, expanding the scope of structural complexity and design capabilities for DNA assemblies.

NATURE MATERIALS (2021)

Article Biochemistry & Molecular Biology

A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules

Yuchen Wang et al.

Summary: Single molecule force spectroscopy is a powerful method for studying the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. Researchers have developed a nanoscale DNA force spectrometer that can apply both tensile and compressive forces with tunable mechanical properties, providing a versatile tool for designing nanoscale mechanical devices.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

DNA origami

Swarup Dey et al.

Summary: DNA origami technology, a bottom-up method for constructing nanostructures, offers high precision and controllability. It finds wide applications in nanofabrication, nanophotonics, nanoelectronics, catalysis, computation, bioimaging, and more. However, challenges such as size limits, stability issues, and scale of production need to be addressed for further advancement in the field.

NATURE REVIEWS METHODS PRIMERS (2021)

Article Biochemistry & Molecular Biology

Free energy landscape of salt-actuated reconfigurable DNA nanodevices

Ze Shi et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Chemistry, Multidisciplinary

Meta-DNA structures

Guangbao Yao et al.

NATURE CHEMISTRY (2020)

Article Chemistry, Multidisciplinary

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

Jonathan F. Berengut et al.

ACS NANO (2020)

Article Chemistry, Physical

Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures

Hemani Chhabra et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Physical

Measuring Internal Forces in Single-Stranded DNA: Application to a DNA Force Clamp

Megan C. Engel et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Review Chemistry, Physical

Dynamic DNA nanotechnology: toward functional nanoscale devices

Marcello DeLuca et al.

NANOSCALE HORIZONS (2020)

Article Chemistry, Multidisciplinary

TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami

Antonio Suma et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2019)

Editorial Material Multidisciplinary Sciences

Emerging uses of DNA mechanical devices

Aaron T. Blanchard et al.

SCIENCE (2019)

Article Biochemistry & Molecular Biology

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters

Jonathan F. Berengut et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Coarse-grained modelling of the structural properties of DNA origami

Benedict E. K. Snodin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Chemistry, Multidisciplinary

Programmable Multivalent DNA-Origami Tension Probes for Reporting Cellular Traction Forces

Palash K. Dutta et al.

NANO LETTERS (2018)

Article Multidisciplinary Sciences

Quantifying absolute addressability in DNA origami with molecular resolution

Maximilian T. Strauss et al.

NATURE COMMUNICATIONS (2018)

Article Chemistry, Multidisciplinary

Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures

Erik Benson et al.

ACS NANO (2018)

Article Chemistry, Multidisciplinary

Paper Origami-Inspired Design and Actuation of DNA Nanomachines with Complex Motions

Lifeng Zhou et al.

SMALL (2018)

Article Multidisciplinary Sciences

Barcode extension for analysis and reconstruction of structures

Cameron Myhrvold et al.

NATURE COMMUNICATIONS (2017)

Review Chemistry, Multidisciplinary

The Beauty and Utility of DNA Origami

Pengfei Wang et al.

Article Chemistry, Multidisciplinary

Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model

Rahul Sharma et al.

ACS NANO (2017)

Article Chemistry, Multidisciplinary

Dynamic DNA Origami Device for Measuring Compressive Depletion Forces

Michael W. Hudoba et al.

ACS NANO (2017)

Article Chemistry, Multidisciplinary

Probing Nucleosome Stability with a DNA Origami Nanocaliper

Jenny V. Le et al.

ACS NANO (2016)

Article Physics, Multidisciplinary

Directing folding pathways for multi-component DNA origami nanostructures with complex topology

A. E. Marras et al.

NEW JOURNAL OF PHYSICS (2016)

Article Multidisciplinary Sciences

Molecular force spectroscopy with a DNA origami-based nanoscopic force clamp

Philipp C. Nickels et al.

SCIENCE (2016)

Article Multidisciplinary Sciences

Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator

Yonggang Ke et al.

NATURE COMMUNICATIONS (2016)

Article Multidisciplinary Sciences

Uncovering the forces between nucleosomes using DNA origami

Jonas J. Funke et al.

SCIENCE ADVANCES (2016)

Article Chemistry, Physical

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

Benedict E. K. Snodin et al.

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Multidisciplinary

Direct Design of an Energy Landscape with Bistable DNA Origami Mechanisms

Lifeng Zhou et al.

NANO LETTERS (2015)

Article Multidisciplinary Sciences

Programmable motion of DNA origami mechanisms

Alexander E. Marras et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Chemistry, Multidisciplinary

A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs

Lorenzo Rovigatti et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)

Article Chemistry, Multidisciplinary

DNA Origami Compliant Nanostructures with Tunable Mechanical Properties

Lifeng Zhou et al.

ACS NANO (2014)

Article Multidisciplinary Sciences

Quantifying quality in DNA self-assembly

Klaus F. Wagenbauer et al.

NATURE COMMUNICATIONS (2014)

Article Chemistry, Multidisciplinary

Rigid DNA Beams for High-Resolution Single-Molecule Mechanics

Emanuel Pfitzner et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)

Article Chemistry, Physical

Sequence-dependent thermodynamics of a coarse-grained DNA model

Petr Sulc et al.

JOURNAL OF CHEMICAL PHYSICS (2012)

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 Multidisciplinary Sciences

Self-assembly of DNA into nanoscale three-dimensional shapes

Shawn M. Douglas et al.

NATURE (2009)

Article Multidisciplinary Sciences

Folding DNA to create nanoscale shapes and patterns

PWK Rothemund

NATURE (2006)