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Literature DB >> 27723752

Plasmid-based one-pot saturation mutagenesis.

Emily E Wrenbeck¹, Justin R Klesmith², James A Stapleton¹, Adebola Adeniran³, Keith E J Tyo³, Timothy A Whitehead^1,4.

Abstract

Deep mutational scanning is a foundational tool for addressing the functional consequences of large numbers of mutants, but a more efficient and accessible method for construction of user-defined mutagenesis libraries is needed. Here we present nicking mutagenesis, a robust, single-day, one-pot saturation mutagenesis method performed on routinely prepped plasmid dsDNA. The method can be used to produce comprehensive or single- or multi-site saturation mutagenesis libraries.

Entities: CellLine Chemical Disease Gene Mutation Species

Mesh：

Substances：

Year: 2016 PMID： 27723752 PMCID： PMC5666567 DOI： 10.1038/nmeth.4029

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

21 in total

1. Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.

Authors: Daniel F Heiter; Keith D Lunnen; Geoffrey G Wilson
Journal: J Mol Biol Date: 2005-05-06 Impact factor: 5.469

2. A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library.

Authors: Pankaj C Jain; Raghavan Varadarajan
Journal: Anal Biochem Date: 2013-12-09 Impact factor: 3.365

3. The Sequence Alignment/Map format and SAMtools.

Authors: Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal: Bioinformatics Date: 2009-06-08 Impact factor: 6.937

4. Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli.

Authors: Justin R Klesmith; John-Paul Bacik; Ryszard Michalczyk; Timothy A Whitehead
Journal: ACS Synth Biol Date: 2015-09-22 Impact factor: 5.110

5. Deep mutational scanning: a new style of protein science.

Authors: Douglas M Fowler; Stanley Fields
Journal: Nat Methods Date: 2014-08 Impact factor: 28.547

6. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing.

Authors: Caitlin A Kowalsky; Matthew S Faber; Aritro Nath; Hailey E Dann; Vince W Kelly; Li Liu; Purva Shanker; Ellen K Wagner; Jennifer A Maynard; Christina Chan; Timothy A Whitehead
Journal: J Biol Chem Date: 2015-08-20 Impact factor: 5.157

Review 7. Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.

Authors: Siu-Hong Chan; Barry L Stoddard; Shuang-Yong Xu
Journal: Nucleic Acids Res Date: 2010-08-30 Impact factor: 16.971

8. High-resolution sequence-function mapping of full-length proteins.

Authors: Caitlin A Kowalsky; Justin R Klesmith; James A Stapleton; Vince Kelly; Nolan Reichkitzer; Timothy A Whitehead
Journal: PLoS One Date: 2015-03-19 Impact factor: 3.240

9. PFunkel: efficient, expansive, user-defined mutagenesis.

Authors: Elad Firnberg; Marc Ostermeier
Journal: PLoS One Date: 2012-12-17 Impact factor: 3.240

10. The interrelationship between promoter strength, gene expression, and growth rate.

Authors: Matthew S Bienick; Katherine W Young; Justin R Klesmith; Emily E Detwiler; Kyle J Tomek; Timothy A Whitehead
Journal: PLoS One Date: 2014-10-06 Impact factor: 3.240

52 in total

1. Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering.

Authors: Sean A Higgins; Sorel V Y Ouonkap; David F Savage
Journal: ACS Synth Biol Date: 2017-07-24 Impact factor: 5.110

2. User-defined single pot mutagenesis using unamplified oligo pools.

Authors: Angélica V Medina-Cucurella; Paul J Steiner; Matthew S Faber; Jesús Beltrán; Alexandra N Borelli; Monica B Kirby; Sean R Cutler; Timothy A Whitehead
Journal: Protein Eng Des Sel Date: 2019-09-10 Impact factor: 1.650

3. Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody.

Authors: Bharat Madan; Baoshan Zhang; Kai Xu; Cara W Chao; Sijy O'Dell; Jacy R Wolfe; Gwo-Yu Chuang; Ahmed S Fahad; Hui Geng; Rui Kong; Mark K Louder; Thuy Duong Nguyen; Reda Rawi; Arne Schön; Zizhang Sheng; Rajani Nimrania; Yiran Wang; Tongqing Zhou; Bob C Lin; Nicole A Doria-Rose; Lawrence Shapiro; Peter D Kwong; Brandon J DeKosky
Journal: Proc Natl Acad Sci U S A Date: 2021-03-09 Impact factor: 11.205

Plasmid-based one-pot saturation mutagenesis.

1. Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.

2. A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library.

3. The Sequence Alignment/Map format and SAMtools.

4. Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli.

5. Deep mutational scanning: a new style of protein science.

6. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing.

Review 7. Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.

8. High-resolution sequence-function mapping of full-length proteins.

9. PFunkel: efficient, expansive, user-defined mutagenesis.

10. The interrelationship between promoter strength, gene expression, and growth rate.

1. Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering.

2. User-defined single pot mutagenesis using unamplified oligo pools.

3. Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody.

Review 4. Emerging strategies to bridge the gap between pharmacogenomic research and its clinical implementation.

5. Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning.

6. Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit.

Review 7. Deep sequencing methods for protein engineering and design.

8. Feline Interleukin-31 Shares Overlapping Epitopes with the Oncostatin M Receptor and IL-31RA.

9. Protein interaction perturbation profiling at amino-acid resolution.

10. Hedgehog pathway activation through nanobody-mediated conformational blockade of the Patched sterol conduit.