Literature DB >> 29096324

Modern methods for laboratory diversification of biomolecules.

Sinisa Bratulic1, Ahmed H Badran2.   

Abstract

Genetic variation fuels Darwinian evolution, yet spontaneous mutation rates are maintained at low levels to ensure cellular viability. Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering applications, prompting scientists to develop methods for efficient and targeted diversification of nucleic acid sequences. Directed evolution of biomolecules relies upon the generation of unbiased genetic diversity to discover variants with desirable properties, whereas genome-engineering applications require selective modifications on a genomic scale with minimal off-targets. Here, we review the current toolkit of mutagenesis strategies employed in directed evolution and genome engineering. These state-of-the-art methods enable facile modifications and improvements of single genes, multicomponent pathways, and whole genomes for basic and applied research, while simultaneously paving the way for genome editing therapeutic interventions.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 29096324      PMCID: PMC6062405          DOI: 10.1016/j.cbpa.2017.10.010

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  74 in total

1.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

Authors:  K A Datsenko; B L Wanner
Journal:  Proc Natl Acad Sci U S A       Date:  2000-06-06       Impact factor: 11.205

2.  SeSaM-Tv-II generates a protein sequence space that is unobtainable by epPCR.

Authors:  Hemanshu Mundhada; Jan Marienhagen; Andreea Scacioc; Alexander Schenk; Danilo Roccatano; Ulrich Schwaneberg
Journal:  Chembiochem       Date:  2011-06-10       Impact factor: 3.164

3.  PCR-based random mutagenesis using manganese and reduced dNTP concentration.

Authors:  J L Lin-Goerke; D J Robbins; J D Burczak
Journal:  Biotechniques       Date:  1997-09       Impact factor: 1.993

4.  The power of multiplexed functional analysis of genetic variants.

Authors:  Molly Gasperini; Lea Starita; Jay Shendure
Journal:  Nat Protoc       Date:  2016-09-01       Impact factor: 13.491

5.  Rapid and efficient site-specific mutagenesis without phenotypic selection.

Authors:  T A Kunkel
Journal:  Proc Natl Acad Sci U S A       Date:  1985-01       Impact factor: 11.205

6.  Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I.

Authors:  Manel Camps; Jussi Naukkarinen; Ben P Johnson; Lawrence A Loeb
Journal:  Proc Natl Acad Sci U S A       Date:  2003-08-08       Impact factor: 11.205

7.  In vivo continuous evolution of genes and pathways in yeast.

Authors:  Nathan Crook; Joseph Abatemarco; Jie Sun; James M Wagner; Alexander Schmitz; Hal S Alper
Journal:  Nat Commun       Date:  2016-10-17       Impact factor: 14.919

8.  TrimerDimer: an oligonucleotide-based saturation mutagenesis approach that removes redundant and stop codons.

Authors:  Paul Gaytán; Casandra Contreras-Zambrano; Mónica Ortiz-Alvarado; Alfredo Morales-Pablos; Jorge Yáñez
Journal:  Nucleic Acids Res       Date:  2009-09-25       Impact factor: 16.971

9.  CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri.

Authors:  Jee-Hwan Oh; Jan-Peter van Pijkeren
Journal:  Nucleic Acids Res       Date:  2014-07-29       Impact factor: 16.971

10.  In vitro template-change PCR to create single crossover libraries: a case study with B. thuringiensis Cry2A toxins.

Authors:  Changlong Shu; Jianqiao Zhou; Neil Crickmore; Xianchun Li; Fuping Song; Gemei Liang; Kanglai He; Dafang Huang; Jie Zhang
Journal:  Sci Rep       Date:  2016-04-21       Impact factor: 4.379

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  4 in total

1.  Engineering Proteins Containing Noncanonical Amino Acids on the Yeast Surface.

Authors:  Rebecca L Hershman; Arlinda Rezhdo; Jessica T Stieglitz; James A Van Deventer
Journal:  Methods Mol Biol       Date:  2022

2.  Transient AID expression for in situ mutagenesis with improved cellular fitness.

Authors:  Talal Salem Al-Qaisi; Yu-Cheng Su; Steve R Roffler
Journal:  Sci Rep       Date:  2018-06-20       Impact factor: 4.379

Review 3.  Genome editor-directed in vivo library diversification.

Authors:  Cristina Cheng; Mi Zhou; Qiwen Su; Alexandra Steigmeyer; Jia Niu
Journal:  Cell Chem Biol       Date:  2021-06-08       Impact factor: 9.039

Review 4.  Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes.

Authors:  Denis Shepelin; Anne Sofie Lærke Hansen; Rebecca Lennen; Hao Luo; Markus J Herrgård
Journal:  Genes (Basel)       Date:  2018-05-11       Impact factor: 4.096

  4 in total

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