Dynamic and scalable DNA-based information storage

KN Lin, K Volkel, JM Tuck, AJ Keung - Nature communications, 2020 - nature.com
The physical architectures of information storage systems often dictate how information is
encoded, databases are organized, and files are accessed. Here we show that a simple …

BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts

W Poole, A Pandey, A Shur, ZA Tuza… - PLOS Computational …, 2022 - journals.plos.org
Biochemical interactions in systems and synthetic biology are often modeled with chemical
reaction networks (CRNs). CRNs provide a principled modeling environment capable of …

Dynamic DNA assembly by programmable hybridization chain reaction mimicking tubulin

L Zhang, Y Fu, Y Tong, G **e, S Deng - Nano Letters, 2024 - ACS Publications
Dynamic biological structures involve the continual turnover of molecules within
supramolecular assemblies such as tubulin. Inspired by dynamic biology self-organizing …

[HTML][HTML] Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network

AG Becerra, M Gutiérrez, R Lahoz-Beltra - Biosystems, 2022 - Elsevier
In nature, bacteria exhibit a limited repertoire of behaviors in response to environmental
changes. Synthetic biology has now opened up the possibility of programming cells or …

Domain-specific programming languages for computational nucleic acid systems

MR Lakin, A Phillips - ACS Synthetic Biology, 2020 - ACS Publications
The construction of models of system behavior is of great importance throughout science
and engineering. In bioengineering and bionanotechnology, these often take the form of …

Solving 0–1 integer programming problem based on DNA strand displacement reaction network

Z Tang, Z Yin, L Wang, J Cui, J Yang… - ACS Synthetic …, 2021 - ACS Publications
Chemical reaction networks (CRNs) based on DNA strand displacement (DSD) can be used
as an effective programming language for solving various mathematical problems. In this …

A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

S Badelt, C Grun, KV Sarma… - Journal of the …, 2020 - royalsocietypublishing.org
Information technologies enable programmers and engineers to design and synthesize
systems of startling complexity that nonetheless behave as intended. This mastery of …

Molecular communication relays for dynamic cross-regulation of self-sorting fibrillar self-assemblies

S Groeer, K Schumann, S Loescher, A Walther - Science Advances, 2021 - science.org
Structures in living systems cross-regulate via exchange of molecular information to
assemble or disassemble on demand and in a coordinated, signal-triggered fashion. DNA …

Design of a single-channel chaotic secure communication system implemented by DNA strand displacement

X An, Z Meng, Y Wang, J Sun - ACS Synthetic Biology, 2022 - ACS Publications
DNA strand displacement (DSD) is regarded as a foundation for the construction of
biological computing systems because of the predictability of DNA molecular behaviors …

Automated leak analysis of nucleic acid circuits

I Zarubiieva, C Spaccasassi, V Kulkarni… - ACS Synthetic …, 2022 - ACS Publications
Nucleic acids are a powerful engineering material that can be used to implement a broad
range of computational circuits at the nanoscale, with potential applications in high-precision …