Literature DB >> 27694911

Massively parallel single-nucleotide mutagenesis using reversibly terminated inosine.

Gabe Haller1, David Alvarado1, Kevin McCall1, Robi D Mitra2, Matthew B Dobbs1,3, Christina A Gurnett1,4,5.   

Abstract

Large-scale mutagenesis of target DNA sequences allows researchers to comprehensively assess the effects of single-nucleotide changes. Here we demonstrate the construction of a systematic allelic series (SAS) using massively parallel single-nucleotide mutagenesis with reversibly terminated deoxyinosine triphosphates (rtITP). We created a mutational library containing every possible single-nucleotide mutation surrounding the active site of the TEM-1 β-lactamase gene. When combined with high-throughput functional assays, SAS mutational libraries can expedite the functional assessment of genetic variation.

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Year:  2016        PMID: 27694911      PMCID: PMC5327618          DOI: 10.1038/nmeth.4015

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


  11 in total

1.  Generating mutant libraries using error-prone PCR.

Authors:  Patrick C Cirino; Kimberly M Mayer; Daisuke Umeno
Journal:  Methods Mol Biol       Date:  2003

2.  Random mutagenesis by error-prone PCR.

Authors:  Elizabeth O McCullum; Berea A R Williams; Jinglei Zhang; John C Chaput
Journal:  Methods Mol Biol       Date:  2010

3.  Massively Parallel Functional Analysis of BRCA1 RING Domain Variants.

Authors:  Lea M Starita; David L Young; Muhtadi Islam; Jacob O Kitzman; Justin Gullingsrud; Ronald J Hause; Douglas M Fowler; Jeffrey D Parvin; Jay Shendure; Stanley Fields
Journal:  Genetics       Date:  2015-03-30       Impact factor: 4.562

4.  Evolvability as a function of purifying selection in TEM-1 β-lactamase.

Authors:  Michael A Stiffler; Doeke R Hekstra; Rama Ranganathan
Journal:  Cell       Date:  2015-02-26       Impact factor: 41.582

5.  Error-prone PCR and effective generation of gene variant libraries for directed evolution.

Authors:  Janine N Copp; Paulina Hanson-Manful; David F Ackerley; Wayne M Patrick
Journal:  Methods Mol Biol       Date:  2014

6.  [A simple error-prone PCR method through dATP reduction].

Authors:  Yiping Gao; He Zhao; Mengyu Lv; Guozhong Sun; Xueju Yang; Haibo Wang
Journal:  Wei Sheng Wu Xue Bao       Date:  2014-01-04

7.  Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.

Authors:  Robin P Smith; Leila Taher; Rupali P Patwardhan; Mee J Kim; Fumitaka Inoue; Jay Shendure; Ivan Ovcharenko; Nadav Ahituv
Journal:  Nat Genet       Date:  2013-07-28       Impact factor: 38.330

8.  High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.

Authors:  Rupali P Patwardhan; Choli Lee; Oren Litvin; David L Young; Dana Pe'er; Jay Shendure
Journal:  Nat Biotechnol       Date:  2009-12       Impact factor: 54.908

9.  Massively parallel functional dissection of mammalian enhancers in vivo.

Authors:  Rupali P Patwardhan; Joseph B Hiatt; Daniela M Witten; Mee J Kim; Robin P Smith; Dalit May; Choli Lee; Jennifer M Andrie; Su-In Lee; Gregory M Cooper; Nadav Ahituv; Len A Pennacchio; Jay Shendure
Journal:  Nat Biotechnol       Date:  2012-02-26       Impact factor: 54.908

10.  Saturation editing of genomic regions by multiplex homology-directed repair.

Authors:  Gregory M Findlay; Evan A Boyle; Ronald J Hause; Jason C Klein; Jay Shendure
Journal:  Nature       Date:  2014-09-04       Impact factor: 49.962

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  6 in total

1.  Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19.

Authors:  Sandhya Devarajan; Irene Moon; Ming-Fen Ho; Nicholas B Larson; Drew R Neavin; Ann M Moyer; John L Black; Suzette J Bielinski; Steven E Scherer; Liewei Wang; Richard M Weinshilboum; Joel M Reid
Journal:  Drug Metab Dispos       Date:  2019-02-11       Impact factor: 3.922

Review 2.  Modern methods for laboratory diversification of biomolecules.

Authors:  Sinisa Bratulic; Ahmed H Badran
Journal:  Curr Opin Chem Biol       Date:  2017-11-02       Impact factor: 8.822

3.  The evolution of substrate discrimination in macrolide antibiotic resistance enzymes.

Authors:  Andrew C Pawlowski; Peter J Stogios; Kalinka Koteva; Tatiana Skarina; Elena Evdokimova; Alexei Savchenko; Gerard D Wright
Journal:  Nat Commun       Date:  2018-01-09       Impact factor: 14.919

4.  Boosting the efficiency of site-saturation mutagenesis for a difficult-to-randomize gene by a two-step PCR strategy.

Authors:  Aitao Li; Carlos G Acevedo-Rocha; Manfred T Reetz
Journal:  Appl Microbiol Biotechnol       Date:  2018-05-21       Impact factor: 4.813

Review 5.  Current and Future Approaches to Classify VUSs in LGMD-Related Genes.

Authors:  Chengcheng Li; Gabe Haller; Conrad C Weihl
Journal:  Genes (Basel)       Date:  2022-02-19       Impact factor: 4.096

Review 6.  Targeted mutagenesis of multiple chromosomal regions in microbes.

Authors:  Bálint Csörgő; Akos Nyerges; Csaba Pál
Journal:  Curr Opin Microbiol       Date:  2020-06-26       Impact factor: 7.584

  6 in total

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