Engineering a functional small RNA negative autoregulation network with model-guided design

CY Hu, MK Takahashi, Y Zhang, JB Lucks - ACS synthetic biology, 2018 - ACS Publications
RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand
the repertoire of synthetic gene networks built from these regulators by constructing a …

Tailored synthetic sRNAs dynamically tune multilayer genetic circuits

AK Velazquez Sanchez, B Klopprogge… - ACS synthetic …, 2023 - ACS Publications
Predictable and controllable tuning of genetic circuits to regulate gene expression, including
modulation of existing circuits or constructs without the need for redesign or rebuilding, is a …

Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription–translation (TX-TL) systems

MK Takahashi, J Chappell, CA Hayes… - ACS synthetic …, 2015 - ACS Publications
RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or
rewire existing ones. A potential strength of RNA networks is that they may be able to …

Achieving large dynamic range control of gene expression with a compact RNA transcription–translation regulator

AM Westbrook, JB Lucks - Nucleic Acids Research, 2017 - academic.oup.com
RNA transcriptional regulators are emerging as versatile components for genetic network
construction. However, these regulators suffer from incomplete repression in their OFF state …

Generating effective models and parameters for RNA genetic circuits

CY Hu, JD Varner, JB Lucks - ACS synthetic biology, 2015 - ACS Publications
RNA genetic circuitry is emerging as a powerful tool to control gene expression. However,
little work has been done to create a theoretical foundation for RNA circuit design. A …

Versatile RNA-sensing transcriptional regulators for engineering genetic networks

JB Lucks, L Qi, VK Mutalik, D Wang… - Proceedings of the …, 2011 - National Acad Sciences
The widespread natural ability of RNA to sense small molecules and regulate genes has
become an important tool for synthetic biology in applications as diverse as environmental …

RNA compensation: a positive feedback insulation strategy for RNA-based transcription networks

B Liu, C Cuba Samaniego, M Bennett… - ACS Synthetic …, 2022 - ACS Publications
The lack of signaling modularity of biomolecular systems poses major challenges toward
engineering complex networks. Directional signaling between an upstream and a …

Design rules of synthetic non-coding RNAs in bacteria

YJ Lee, TS Moon - Methods, 2018 - Elsevier
One of the long-term goals of synthetic biology is to develop designable genetic parts with
predictable behaviors that can be utilized to implement diverse cellular functions. The …

An easy-to-use plasmid toolset for efficient generation and benchmarking of synthetic small RNAs in bacteria

TS Köbel, R Melo Palhares, C Fromm… - ACS synthetic …, 2022 - ACS Publications
Synthetic biology approaches life from the perspective of an engineer. Standardized and de
novo design of genetic parts to subsequently build reproducible and controllable modules …

In Silico Design, In Vitro Construction, and In Vivo Application of Synthetic Small Regulatory RNAs in Bacteria

M Brück, BA Berghoff, D Schindler - Synthetic Biology: Methods and …, 2024 - Springer
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-
transcriptional regulation. sRNAs have recently gained attention as tools in basic and …