Biocomputing based on DNA strand displacement reactions

H Lv, Q Li, J Shi, C Fan, F Wang - ChemPhysChem, 2021 - Wiley Online Library
The high sequence specificity and precise base complementary pairing principle of DNA
provides a rich orthogonal molecular library for molecular programming, making it one of the …

Prediction and control in DNA nanotechnology

M DeLuca, S Sensale, PA Lin, G Arya - ACS applied bio materials, 2023 - ACS Publications
DNA nanotechnology is a rapidly develo** field that uses DNA as a building material for
nanoscale structures. Key to the field's development has been the ability to accurately …

Enzyme-free nucleic acid dynamical systems

N Srinivas, J Parkin, G Seelig, E Winfree, D Soloveichik - Science, 2017 - science.org
INTRODUCTION Embedded controllers enable complex functionality in man-made
mechanical and electronic devices. Similarly, intricate regulatory networks within living …

Programmable chemical controllers made from DNA

YJ Chen, N Dalchau, N Srinivas, A Phillips… - Nature …, 2013 - nature.com
Biological organisms use complex molecular networks to navigate their environment and
regulate their internal state. The development of synthetic systems with similar capabilities …

Modeling DNA-strand displacement reactions in the presence of base-pair mismatches

P Irmisch, TE Ouldridge, R Seidel - Journal of the American …, 2020 - ACS Publications
Toehold-mediated strand displacement is the most abundantly used method to achieve
dynamic switching in DNA-based nanotechnology. An “invader” strand binds to the “toehold” …

Visual DSD: a design and analysis tool for DNA strand displacement systems

MR Lakin, S Youssef, F Polo, S Emmott… - …, 2011 - academic.oup.com
The Visual DSD (DNA Strand Displacement) tool allows rapid prototy** and analysis of
computational devices implemented using DNA strand displacement, in a convenient web …

A secure communication scheme of three-variable chaotic coupling synchronization based on DNA chemical reaction networks

J Sun, M Zang, P Liu, Y Wang - IEEE Transactions on Signal …, 2022 - ieeexplore.ieee.org
Three-variable chaotic synchronization has been implemented based on DNA chemical
reaction networks (CRNs) in previous works. However, it is still difficult to realize the …

Computational design of nucleic acid feedback control circuits

B Yordanov, J Kim, RL Petersen, A Shudy… - ACS synthetic …, 2014 - ACS Publications
The design of synthetic circuits for controlling molecular-scale processes is an important
goal of synthetic biology, with potential applications in future in vitro and in vivo …

Supervised learning in adaptive DNA strand displacement networks

MR Lakin, D Stefanovic - ACS synthetic biology, 2016 - ACS Publications
The development of engineered biochemical circuits that exhibit adaptive behavior is a key
goal of synthetic biology and molecular computing. Such circuits could be used for long-term …

Computing with biological switches and clocks

N Dalchau, G Szép, R Hernansaiz-Ballesteros… - Natural computing, 2018 - Springer
The complex dynamics of biological systems is primarily driven by molecular interactions
that underpin the regulatory networks of cells. These networks typically contain positive and …