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 …

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 …

Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR

K Jiang, J Koob, XD Chen, RN Krajeski, Y Zhang… - Nature …, 2023 - nature.com
Programmable approaches to sense and respond to the presence of specific RNAs in
biological systems have broad applications in research, diagnostics, and therapeutics. Here …

A deep learning approach to programmable RNA switches

NM Angenent-Mari, AS Garruss, LR Soenksen… - Nature …, 2020 - nature.com
Engineered RNA elements are programmable tools capable of detecting small molecules,
proteins, and nucleic acids. Predicting the behavior of these synthetic biology components …

RNA-responsive elements for eukaryotic translational control

EM Zhao, AS Mao, H de Puig, K Zhang… - Nature …, 2022 - nature.com
The ability to control translation of endogenous or exogenous RNAs in eukaryotic cells
would facilitate a variety of biotechnological applications. Current strategies are limited by …

Sequence-to-function deep learning frameworks for engineered riboregulators

JA Valeri, KM Collins, P Ramesh, MA Alcantar… - Nature …, 2020 - nature.com
While synthetic biology has revolutionized our approaches to medicine, agriculture, and
energy, the design of completely novel biological circuit components beyond naturally …

Multi-arm RNA junctions encoding molecular logic unconstrained by input sequence for versatile cell-free diagnostics

D Ma, Y Li, K Wu, Z Yan, AA Tang… - Nature biomedical …, 2022 - nature.com
Applications of RNA-based molecular logic have been hampered by sequence constraints
imposed on the input and output of the circuits. Here we show that the sequence constraints …

Precise and programmable detection of mutations using ultraspecific riboregulators

F Hong, D Ma, K Wu, LA Mina, RC Luiten, Y Liu, H Yan… - Cell, 2020 - cell.com
The ability to identify single-nucleotide mutations is critical for probing cell biology and for
precise detection of disease. However, the small differences in hybridization energy …

Toehold-mediated biosensors: Types, mechanisms and biosensing strategies

S Li, L Zhu, S Lin, W Xu - Biosensors and Bioelectronics, 2023 - Elsevier
Toehold-mediated strand displacement (TMSD) reactions between double-stranded DNA
and single-stranded oligonucleotides, which use a toehold structure as a switch, enable …

A survey of molecular communication in cell biology: Establishing a new hierarchy for interdisciplinary applications

D Bi, A Almpanis, A Noel, Y Deng… - … Surveys & Tutorials, 2021 - ieeexplore.ieee.org
Molecular communication (MC) engineering is inspired by the use of chemical signals as
information carriers in cell biology. The biological nature of chemical signaling makes MC a …