In vivo hypermutation and continuous evolution

RS Molina, G Rix, AA Mengiste, B Álvarez… - Nature Reviews …, 2022 - nature.com
Directed evolution has revolutionized biomolecular engineering by applying cycles of
mutation, amplification and selection to genes of interest (GOIs). However, classical directed …

Opportunities and challenges for machine learning-assisted enzyme engineering

J Yang, FZ Li, FH Arnold - ACS Central Science, 2024 - ACS Publications
Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …

High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs

TP Huang, ZJ Heins, SM Miller, BG Wong… - Nature …, 2023 - nature.com
Despite the availability of Cas9 variants with varied protospacer-adjacent motif (PAM)
compatibilities, some genomic loci—especially those with pyrimidine-rich PAM sequences …

Evolution of pyrrolysyl-tRNA synthetase: From methanogenesis to genetic code expansion

NG Koch, N Budisa - Chemical Reviews, 2024 - ACS Publications
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific
archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA …

Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility

L Schmidheini, N Mathis, KF Marquart… - Nature Chemical …, 2024 - nature.com
CRISPR–Cas9 genome engineering is a powerful technology for correcting genetic
diseases. However, the targeting range of Cas9 proteins is limited by their requirement for a …

Computer-aided engineering of lipases solvent tolerance enhanced their applications in sugar esters synthesis: State of the art

Y Qi, M Chen, T Jin, W Chong, Z Zhang, B Nian… - Trends in Food Science & …, 2024 - Elsevier
Abstract Background Sugar esters (SEs) are non-ionic amphiphilic surfactants that possess
excellent emulsifying properties, and consequently have potential applications in the food …

Continuous evolution of compact protein degradation tags regulated by selective molecular glues

JAM Mercer, SJ DeCarlo, SS Roy Burman, V Sreekanth… - Science, 2024 - science.org
Conditional protein degradation tags (degrons) are usually> 100 amino acids long or are
triggered by small molecules with substantial off-target effects, thwarting their use as specific …

Virus-assisted directed evolution of biomolecules

D Jewel, Q Pham, A Chatterjee - Current Opinion in Chemical Biology, 2023 - Elsevier
Directed evolution is a powerful technique that uses principles of natural evolution to enable
the development of biomolecules with novel functions. However, the slow pace of natural …

A high-throughput platform for efficient exploration of functional polypeptide chemical space

G Wu, H Zhou, J Zhang, ZY Tian, X Liu, S Wang… - Nature …, 2023 - nature.com
Rapid and in-depth exploration of the chemical space of high-molecular-weight synthetic
polypeptides via ring-opening polymerization of N-carboxyanhydride allows the discovery of …

Engineering is evolution: a perspective on design processes to engineer biology

SD Castle, M Stock, TE Gorochowski - Nature Communications, 2024 - nature.com
Careful consideration of how we approach design is crucial to all areas of biotechnology.
However, choosing or developing an effective design methodology is not always easy as …