Engineering synthetic RNA devices for cell control

PB Dykstra, M Kaplan, CD Smolke - Nature Reviews Genetics, 2022 - nature.com
The versatility of RNA in sensing and interacting with small molecules, proteins and other
nucleic acids while encoding genetic instructions for protein translation makes it a powerful …

High-throughput determination of RNA structures

EJ Strobel, AM Yu, JB Lucks - Nature Reviews Genetics, 2018 - nature.com
RNA performs and regulates a diverse range of cellular processes, with new functional roles
being uncovered at a rapid pace. Interest is growing in how these functions are linked to …

'Deadman'and'Passcode'microbial kill switches for bacterial containment

CTY Chan, JW Lee, DE Cameron, CJ Bashor… - Nature chemical …, 2016 - nature.com
Biocontainment systems that couple environmental sensing with circuit-based control of cell
viability could be used to prevent escape of genetically modified microbes into the …

Quantifying cellular capacity identifies gene expression designs with reduced burden

F Ceroni, R Algar, GB Stan, T Ellis - Nature methods, 2015 - nature.com
Heterologous gene expression can be a significant burden for cells. Here we describe an in
vivo monitor that tracks changes in the capacity of Escherichia coli in real time and can be …

Creating small transcription activating RNAs

J Chappell, MK Takahashi, JB Lucks - Nature chemical biology, 2015 - nature.com
We expanded the mechanistic capability of small RNAs by creating an entirely synthetic
mode of regulation: small transcription activating RNAs (STARs). Using two strategies, we …

Computational design of small transcription activating RNAs for versatile and dynamic gene regulation

J Chappell, A Westbrook, M Verosloff… - Nature communications, 2017 - nature.com
A longstanding goal of synthetic biology has been the programmable control of cellular
functions. Central to this is the creation of versatile regulatory toolsets that allow for …

RNA–ligand molecular docking: Advances and challenges

Y Zhou, Y Jiang, SJ Chen - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
With rapid advances in computer algorithms and hardware, fast and accurate virtual
screening has led to a drastic acceleration in selecting potent small molecules as drug …

[HTML][HTML] A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future

J Chappell, KE Watters, MK Takahashi… - Current opinion in …, 2015 - Elsevier
Highlights•We review recent progress in RNA synthetic biology.•New advances in synthetic
RNA regulator design have created high-performing/functioning parts.•New generation of …

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 …

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing

D Loughrey, KE Watters, AH Settle… - Nucleic acids …, 2014 - academic.oup.com
RNA structure is a primary determinant of its function, and methods that merge chemical
probing with next generation sequencing have created breakthroughs in the throughput and …