Related papers: DNA nanotechnology: understanding and optimisation…
Nanofabrication techniques for achieving dimensional control at the nanometer scale are generally equipment-intensive and time-consuming. The use of energetic beams of electrons or ions has placed the fabrication of nanopores in thin…
We present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform Gaussian curvature. This approach features a core structure that completely…
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The…
DNA has the potential to realize a controllable liquid-liquid phase separation (LLPS) system, because the design of its base sequences results in programmable interactions. Here, we have developed a novel DNA-based LLPS system which enables…
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
Being a dual purpose enzyme, the DNA polymerase is responsible for elongation of the newly formed DNA strand as well as cleaving the erroneous growth in case of a misincorporation. The efficiency of replication depends on the coordination…
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…
Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50mer agree with theoretical predictions, and the DNA…
Innovative methodologies for reliably and inexpensively sequencing DNA can lead to a new era of personalized medicine. In this work, we performed a theoretical investigation of a nanogap-based all electronic DNA sequencing device. To do so,…
Tile displacement is a newly-recognized mechanism in DNA nanotechnology that exploits principles analogous to toehold-mediated strand displacement but within the context of self-assembled DNA origami tile arrays. Here, we formulate an…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…