Directed evolution: methodologies and applications

Y Wang, P Xue, M Cao, T Yu, ST Lane… - Chemical reviews, 2021 - ACS Publications
Directed evolution aims to expedite the natural evolution process of biological molecules
and systems in a test tube through iterative rounds of gene diversifications and library …

[HTML][HTML] 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 …

Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity

MF Richter, KT Zhao, E Eton, A Lapinaite… - Nature …, 2020 - nature.com
Applications of adenine base editors (ABEs) have been constrained by the limited
compatibility of the deoxyadenosine deaminase component with Cas homologs other than …

[HTML][HTML] Phage-assisted evolution and protein engineering yield compact, efficient prime editors

JL Doman, S Pandey, ME Neugebauer, M An, JR Davis… - Cell, 2023 - cell.com
Prime editing enables a wide variety of precise genome edits in living cells. Here we use
protein evolution and engineering to generate prime editors with reduced size and improved …

Continuous evolution of SpCas9 variants compatible with non-G PAMs

SM Miller, T Wang, PB Randolph, M Arbab… - Nature …, 2020 - nature.com
The targeting scope of Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants
is largely restricted to protospacer-adjacent motif (PAM) sequences containing G bases …

Continuous evolution of base editors with expanded target compatibility and improved activity

BW Thuronyi, LW Koblan, JM Levy, WH Yeh… - Nature …, 2019 - nature.com
Base editors use DNA-modifying enzymes targeted with a catalytically impaired CRISPR
protein to precisely install point mutations. Here, we develop phage-assisted continuous …

Deep mutational scanning: a new style of protein science

DM Fowler, S Fields - Nature methods, 2014 - nature.com
Mutagenesis provides insight into proteins, but only recently have assays that couple
genotype to phenotype been used to assess the activities of as many as 1 million mutant …

Epistasis in protein evolution

TN Starr, JW Thornton - Protein science, 2016 - Wiley Online Library
The structure, function, and evolution of proteins depend on physical and genetic
interactions among amino acids. Recent studies have used new strategies to explore the …

Causes of molecular convergence and parallelism in protein evolution

JF Storz - Nature Reviews Genetics, 2016 - nature.com
To what extent is the convergent evolution of protein function attributable to convergent or
parallel changes at the amino acid level? The mutations that contribute to adaptive protein …

[HTML][HTML] Systematic molecular evolution enables robust biomolecule discovery

EA DeBenedictis, EJ Chory, DW Gretton, B Wang… - Nature …, 2022 - nature.com
Evolution occurs when selective pressures from the environment shape inherited variation
over time. Within the laboratory, evolution is commonly used to engineer proteins and RNA …