Customizing cellular signal processing by synthetic multi-level regulatory circuits

Y Gao, L Wang, B Wang - Nature Communications, 2023 - nature.com
As synthetic biology permeates society, the signal processing circuits in engineered living
systems must be customized to meet practical demands. Towards this mission, novel …

Predictive biology: modelling, understanding and harnessing microbial complexity

AJ Lopatkin, JJ Collins - Nature Reviews Microbiology, 2020 - nature.com
Predictive biology is the next great chapter in synthetic and systems biology, particularly for
microorganisms. Tasks that once seemed infeasible are increasingly being realized such as …

Application of combinatorial optimization strategies in synthetic biology

G Naseri, MAG Koffas - Nature communications, 2020 - nature.com
In the first wave of synthetic biology, genetic elements, combined into simple circuits, are
used to control individual cellular functions. In the second wave of synthetic biology, the …

Supercoiling-mediated feedback rapidly couples and tunes transcription

CP Johnstone, KE Galloway - Cell reports, 2022 - cell.com
Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA
polymerases and resha** the biochemical landscape of gene regulation. As supercoiling …

Bottom-up construction of complex biomolecular systems with cell-free synthetic biology

N Laohakunakorn, L Grasemann… - … in bioengineering and …, 2020 - frontiersin.org
Cell-free systems offer a promising approach to engineer biology since their open nature
allows for well-controlled and characterized reaction conditions. In this review, we discuss …

Multistable and dynamic CRISPRi-based synthetic circuits

J Santos-Moreno, E Tasiudi, J Stelling… - Nature …, 2020 - nature.com
Gene expression control based on CRISPRi (clustered regularly interspaced short
palindromic repeats interference) has emerged as a powerful tool for creating synthetic gene …

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 …

Context-dependent redesign of robust synthetic gene circuits

A Stone, A Youssef, S Rijal, R Zhang, XJ Tian - Trends in Biotechnology, 2024 - cell.com
Cells provide dynamic platforms for executing exogenous genetic programs in synthetic
biology, resulting in highly context-dependent circuit performance. Recent years have seen …

An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells

RD Jones, Y Qian, V Siciliano, B DiAndreth… - Nature …, 2020 - nature.com
Synthetic biology has the potential to bring forth advanced genetic devices for applications
in healthcare and biotechnology. However, accurately predicting the behavior of engineered …

Engineering AraC to make it responsive to light instead of arabinose

E Romano, A Baumschlager, EB Akmeric… - Nature chemical …, 2021 - nature.com
The l-arabinose-responsive AraC and its cognate PBAD promoter underlie one of the most
often used chemically inducible prokaryotic gene expression systems in microbiology and …