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Lindenburg L, Huovinen T, van de Wiel K, Herger M, Snaith MR, Hollfelder F. Split & mix assembly of DNA libraries for ultrahigh throughput on-bead screening of functional proteins. Nucleic Acids Res 2020; 48:e63. [PMID: 32383757 PMCID: PMC7293038 DOI: 10.1093/nar/gkaa270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Site-saturation libraries reduce protein screening effort in directed evolution campaigns by focusing on a limited number of rationally chosen residues. However, uneven library synthesis efficiency leads to amino acid bias, remedied at high cost by expensive custom synthesis of oligonucleotides, or through use of proprietary library synthesis platforms. To address these shortcomings, we have devised a method where DNA libraries are constructed on the surface of microbeads by ligating dsDNA fragments onto growing, surface-immobilised DNA, in iterative split-and-mix cycles. This method-termed SpliMLiB for Split-and-Mix Library on Beads-was applied towards the directed evolution of an anti-IgE Affibody (ZIgE), generating a 160,000-membered, 4-site, saturation library on the surface of 8 million monoclonal beads. Deep sequencing confirmed excellent library balance (5.1% ± 0.77 per amino acid) and coverage (99.3%). As SpliMLiB beads are monoclonal, they were amenable to direct functional screening in water-in-oil emulsion droplets with cell-free expression. A FACS-based sorting of the library beads allowed recovery of hits improved in Kd over wild-type ZIgE by up to 3.5-fold, while a consensus mutant of the best hits provided a 10-fold improvement. With SpliMLiB, directed evolution workflows are accelerated by integrating high-quality DNA library generation with an ultra-high throughput protein screening platform.
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Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Tuomas Huovinen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Kayleigh van de Wiel
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Michael Herger
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
- AstraZeneca Medimmune Cambridge, Antibody Discovery and Protein Engineering, Cambridge, UK
| | - Michael R Snaith
- AstraZeneca Medimmune Cambridge, Antibody Discovery and Protein Engineering, Cambridge, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
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2
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Contreras-Llano LE, Tan C. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 2018; 3:ysy012. [PMID: 32995520 PMCID: PMC7445777 DOI: 10.1093/synbio/ysy012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023] Open
Abstract
The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
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Affiliation(s)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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3
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Wei SJ, Chee S, Yurlova L, Lane D, Verma C, Brown C, Ghadessy F. Avoiding drug resistance through extended drug target interfaces: a case for stapled peptides. Oncotarget 2016; 7:32232-46. [PMID: 27057630 PMCID: PMC5078010 DOI: 10.18632/oncotarget.8572] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/18/2016] [Indexed: 11/25/2022] Open
Abstract
Cancer drugs often fail due to the emergence of clinical resistance. This can manifest through mutations in target proteins that selectively exclude drug binding whilst retaining aberrant function. A priori knowledge of resistance-inducing mutations is therefore important for both drug design and clinical surveillance. Stapled peptides represent a novel class of antagonists capable of inhibiting therapeutically relevant protein-protein interactions. Here, we address the important question of potential resistance to stapled peptide inhibitors. HDM2 is the critical negative regulator of p53, and is often overexpressed in cancers that retain wild-type p53 function. Interrogation of a large collection of randomly mutated HDM2 proteins failed to identify point mutations that could selectively abrogate binding by a stapled peptide inhibitor (PM2). In contrast, the same interrogation methodology has previously uncovered point mutations that selectively inhibit binding by Nutlin, the prototypical small molecule inhibitor of HDM2. Our results demonstrate both the high level of structural p53 mimicry employed by PM2 to engage HDM2, and the potential resilience of stapled peptide antagonists to mutations in target proteins. This inherent feature could reduce clinical resistance should this class of drugs enter the clinic.
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Affiliation(s)
- Siau Jia Wei
- P53 Laboratory (A*STAR), #06-04/05 Neuros, 138648, Singapore
| | - Sharon Chee
- P53 Laboratory (A*STAR), #06-04/05 Neuros, 138648, Singapore
| | | | - David Lane
- P53 Laboratory (A*STAR), #06-04/05 Neuros, 138648, Singapore
| | - Chandra Verma
- Bioinformatics Institute (A*STAR), 07-01 Matrix, 138671, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | | | - Farid Ghadessy
- P53 Laboratory (A*STAR), #06-04/05 Neuros, 138648, Singapore
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4
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Iwao C, Shidoji Y. Induction of nuclear translocation of mutant cytoplasmic p53 by geranylgeranoic acid in a human hepatoma cell line. Sci Rep 2014; 4:4419. [PMID: 24658405 PMCID: PMC3963086 DOI: 10.1038/srep04419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 03/05/2014] [Indexed: 02/01/2023] Open
Abstract
Mutant p53 proteins in human hepatoma cell lines such as HuH-7 (Y220C) and PLC/PRF/5 (R249S) accumulate in the cytoplasm, and lose their transcriptional function. Geranylgeranoic acid (GGA) is a naturally occurring acyclic diterpenoid that induces cell death in both cell lines, but not in HepG2 cells harboring wild-type p53. Here, we demonstrate that micromolar concentrations of GGA induce a rapid nuclear translocation of cytoplasmic p53 in both p53-mutant cell lines and p53 knockdown attenuates GGA-induced cell death in HuH-7 cells. Cell-free experiments demonstrate that GGA is able to release 670-kD p53-containing complexes from putative huge macromolecular aggregates in post-mitochondrial fractions as revealed on blue-native gradient PAGE. Among several p53-target genes tested, GGA upregulates PUMA gene expression, and ivermectin, an inhibitor for importin α/β, blocks GGA-induced nuclear translocation of cytoplasmic p53 and suppresses GGA-induced upregulation of PUMA mRNA levels in HuH-7 cells. Taken together, these data suggest that GGA treatment stimulates a nuclear translocation of mutant p53 through its dissociation from cytoplasmic aggregates, which may be essential for GGA-induced cell death.
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Affiliation(s)
- Chieko Iwao
- Molecular and Cellular Biology, Graduate School of Human Health Science, University of Nagasaki, Academy Hills 1-1-1, Nagayo, Nagasaki 851-2195, Japan
| | - Yoshihiro Shidoji
- Molecular and Cellular Biology, Graduate School of Human Health Science, University of Nagasaki, Academy Hills 1-1-1, Nagayo, Nagasaki 851-2195, Japan
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5
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Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics. PLoS One 2013; 8:e80221. [PMID: 24324553 PMCID: PMC3855832 DOI: 10.1371/journal.pone.0080221] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 09/30/2013] [Indexed: 11/19/2022] Open
Abstract
The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD). In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs). Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3). Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart). Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1) a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2) possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.
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6
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Gaj T, Sirk SJ, Barbas CF. Expanding the scope of site-specific recombinases for genetic and metabolic engineering. Biotechnol Bioeng 2013; 111:1-15. [PMID: 23982993 DOI: 10.1002/bit.25096] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 12/20/2022]
Abstract
Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, 92037
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Powell BC, Jiang L, Muzny DM, Treviño LR, Dreyer ZE, Strong LC, Wheeler DA, Gibbs RA, Plon SE. Identification of TP53 as an acute lymphocytic leukemia susceptibility gene through exome sequencing. Pediatr Blood Cancer 2013; 60:E1-3. [PMID: 23255406 PMCID: PMC3926299 DOI: 10.1002/pbc.24417] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 11/03/2012] [Indexed: 11/10/2022]
Abstract
Although acute lymphocytic leukemia (ALL) is the most common childhood cancer, genetic predisposition to ALL remains poorly understood. Whole-exome sequencing was performed in an extended kindred in which five individuals had been diagnosed with leukemia. Analysis revealed a nonsense variant of TP53 which has been previously reported in families with sarcomas and other typical Li Fraumeni syndrome-associated cancers but never in a familial leukemia kindred. This unexpected finding enabled identification of an appropriate sibling bone marrow donor and illustrates that exome sequencing will reveal atypical clinical presentations of even well-studied genes.
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Affiliation(s)
- Bradford C. Powell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lichun Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Lisa R. Treviño
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - ZoAnn E. Dreyer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX,Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX
| | - Louise C. Strong
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX
| | - David A. Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX,Department of Pediatrics, Baylor College of Medicine, Houston, TX,Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX
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8
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Wei SJ, Joseph T, Sim AYL, Yurlova L, Zolghadr K, Lane D, Verma C, Ghadessy F. In vitro selection of mutant HDM2 resistant to Nutlin inhibition. PLoS One 2013; 8:e62564. [PMID: 23653682 PMCID: PMC3641235 DOI: 10.1371/journal.pone.0062564] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/22/2013] [Indexed: 11/25/2022] Open
Abstract
HDM2 binds to the p53 tumour suppressor and targets it for proteosomal degradation. Presently in clinical trials, the small molecule Nutlin-3A competitively binds to HDM2 and abrogates its repressive function. Using a novel in vitro selection methodology, we simulated the emergence of resistance by evolving HDM2 mutants capable of binding p53 in the presence of Nutlin concentrations that inhibit the wild-type HDM2-p53 interaction. The in vitro phenotypes were recapitulated in ex vivo assays measuring both p53 transactivation function and the direct p53-HDM2 interaction in the presence of Nutlin. Mutations conferring drug resistance were not confined to the N-terminal p53/Nutlin–binding domain, and were additionally seen in the acidic, zinc finger and RING domains. Mechanistic insights gleaned from this broad spectrum of mutations will aid in future drug design and further our understanding of the complex p53-HDM2 interaction.
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Affiliation(s)
- Siau Jia Wei
- p53Lab, Agency for Science, Technology and Research, Singapore, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singpore
| | - Thomas Joseph
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singpore
| | - Adelene Y. L. Sim
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singpore
| | | | | | - David Lane
- p53Lab, Agency for Science, Technology and Research, Singapore, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singpore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail: (CV); sg (FG)
| | - Farid Ghadessy
- p53Lab, Agency for Science, Technology and Research, Singapore, Singapore
- * E-mail: (CV); sg (FG)
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9
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Ong HJ, Siau JW, Zhang JB, Hong M, Flotow H, Ghadessy F. Analysis of p53 binding to DNA by fluorescence imaging microscopy. Micron 2012; 43:996-1000. [PMID: 22537717 DOI: 10.1016/j.micron.2012.03.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/27/2012] [Accepted: 03/29/2012] [Indexed: 11/19/2022]
Abstract
Transcription factors play a central role in cell biology through binding to target DNA elements and regulating gene expression. In this study, we used the p53 tumour suppressor as a model transcription factor to develop an imaging based assay to measure DNA binding. The assay utilizes fluorescence imaging microscopy to detect labelled p53 bound to DNA coated on microbeads. We demonstrate the ability to multiplex the assay by interrogating simultaneous binding to variant DNA sequences present on tractable beads. Additionally, the assay measures activation of p53 for increased DNA binding by a known peptide in addition to reactivation of mutant p53 by a small molecule. It may therefore be adaptable to a high-content imaging screen for compounds capable of restoring the function of mutant p53 associated with cancer.
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Affiliation(s)
- Hwee Jing Ong
- Experimental Therapeutics Centre, Agency for Science and Technology and Research, Singapore 138669, Singapore
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10
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Lu WC, Ellington AD. In vitro selection of proteins via emulsion compartments. Methods 2012; 60:75-80. [PMID: 22491026 DOI: 10.1016/j.ymeth.2012.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 12/23/2011] [Accepted: 03/09/2012] [Indexed: 11/25/2022] Open
Abstract
In vitro compartmentalization (IVC) is a method to generate numerous, small, aqueous compartments (up to 10(10) compartments per ml) by mixing water, surfactants, and oil. The water phase is surrounded by surfactants and an oil phase, and to a first approximation each water-in-oil compartment is like an artificial cell. By introducing single genes into compartments that are competent for transcription and translation, these cell-like compartments can synthesize RNA protein variants in libraries. Screening or selecting for function has in turn led to schemes for the directed evolution of biomolecules. However, IVC selections can cover larger library sizes, and provide greater control over selection conditions and stringencies. The key issue in designing and executing IVC selections is how to couple genotype and phenotype, and in this review we have organized and presented a variety of mechanisms by which proteins and RNA can attach to or amplify their own templates following emulsification and selection.
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Affiliation(s)
- Wei-Cheng Lu
- Institute of Cellular and Molecule Biology, University of Texas at Austin, TX 78712, USA
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11
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Mutants of the tumour suppressor p53 L1 loop as second-site suppressors for restoring DNA binding to oncogenic p53 mutations: structural and biochemical insights. Biochem J 2010; 427:225-36. [DOI: 10.1042/bj20091888] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
To assess the potential of mutations from the L1 loop of the tumour suppressor p53 as second-site suppressors, the effect of H115N and S116M on the p53 ‘hot spot’ mutations has been investigated using the double-mutant approach. The effects of these two mutants on the p53 hot spots in terms of thermal stability and DNA binding were evaluated. The results show that: (i) the p53 mutants H115N and S116M are thermally more stable than wild-type p53; (ii) H115N but not S116M is capable of rescuing the DNA binding of one of the most frequent p53 mutants in cancer, R248Q, as shown by binding of R248Q/H115N to gadd45 (the promoter of a gene involved in cell-cycle arrest); (iii) the double mutant R248Q/H115N is more stable than wild-type p53; (iv) the effect of H115N as a second-site suppressor to restore DNA-binding activity is specific to R248Q, but not to R248W; (v) molecular-dynamics simulations indicate that R248Q/H115N has a conformation similar to wild-type p53, which is distinct from that of R248Q. These findings could be exploited in designing strategies for cancer therapy to identify molecules that could mimic the effect of H115N in restoring function to oncogenic p53 mutants.
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12
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Joerger AC, Fersht AR. The tumor suppressor p53: from structures to drug discovery. Cold Spring Harb Perspect Biol 2010; 2:a000919. [PMID: 20516128 DOI: 10.1101/cshperspect.a000919] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Even 30 years after its discovery, the tumor suppressor protein p53 is still somewhat of an enigma. p53's intimate and multifaceted role in the cell cycle is mirrored in its equally complex structural biology that is being unraveled only slowly. Here, we discuss key structural aspects of p53 function and its inactivation by oncogenic mutations. Concerted action of folded and intrinsically disordered domains of the highly dynamic p53 protein provides binding promiscuity and specificity, allowing p53 to process a myriad of cellular signals to maintain the integrity of the human genome. Importantly, progress in elucidating the structural biology of p53 and its partner proteins has opened various avenues for structure-guided rescue of p53 function in tumors. These emerging anticancer strategies include targeting mutant-specific lesions on the surface of destabilized cancer mutants with small molecules and selective inhibition of p53's degradative pathways.
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Affiliation(s)
- Andreas C Joerger
- MRC Centre for Protein Engineering, Hills Road, Cambridge, United Kingdom.
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13
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Tay Y, Ho C, Droge P, Ghadessy FJ. Selection of bacteriophage lambda integrases with altered recombination specificity by in vitro compartmentalization. Nucleic Acids Res 2009; 38:e25. [PMID: 19966270 PMCID: PMC2831311 DOI: 10.1093/nar/gkp1089] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In vitro compartmentalization (IVC) was employed for the first time to select for novel bacteriophage λ integrase variants displaying significantly enhanced recombination activity on a non-cognate target DNA sequence. These variants displayed up to 9-fold increased recombination activity over the parental enzyme, and one mutant recombined the chosen non-cognate substrate more efficiently than the parental enzyme recombined the wild-type DNA substrate. The in vitro specificity phenotype extended to the intracellular recombination of episomal vectors in HEK293 cells. Surprisingly, mutations conferring the strongest phenotype do not occur in the λ integrase core-binding domain, which is known to interact directly with cognate target sequences. Instead, they locate to the N-terminal domain which allosterically modulates integrase activity, highlighting a previously unknown role for this domain in directing integrase specificity. The method we describe provides a robust, completely in vitro platform for the development of novel integrase reagent tools for in vitro DNA manipulation and other biotechnological applications.
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Affiliation(s)
- Yvonne Tay
- p53 Laboratory, 8A Biomedical Grove, #06-06, Immunos, Singapore 138648
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Davidson EA, Dlugosz PJ, Levy M, Ellington AD. Directed evolution of proteins in vitro using compartmentalization in emulsions. ACTA ACUST UNITED AC 2009; Chapter 24:Unit 24.6. [PMID: 19575478 DOI: 10.1002/0471142727.mb2406s87] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This unit describes a protocol for the directed evolution of proteins utilizing in vitro compartmentalization. This method uses a large number of independent in vitro transcription and translation (IVTT) reactions in water droplets suspended in an oil emulsion to enable selection of proteins that bind a target molecule. Protein variants that bind the target also bind to and allow recovery of the genes that encoded them. This protocol serves as a basis for carrying out selections in emulsions, and can potentially be modified to select for other functionalities, including catalysis. This selection method is advantageous compared to alternative selection protocols due to the ability to screen through very large-size libraries and the ability to express and screen or select for functions that would otherwise be toxic or inaccessible to in vivo selections and screens.
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15
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Stein V, Hollfelder F. An efficient method to assemble linear DNA templates for in vitro screening and selection systems. Nucleic Acids Res 2009; 37:e122. [PMID: 19617373 PMCID: PMC2764453 DOI: 10.1093/nar/gkp589] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A method is presented to assemble a gene of interest into a linear DNA template with all the components necessary for in vitro transcription and translation in ∼90 min. Assembly is achieved using a coupled uracil excision–ligation strategy based on USER Enzyme and T4 DNA ligase, which allows the simultaneous and seamless assembly of three different PCR products. The method is suitable for screening and selection systems of very high throughput as up to 1011 molecules can be efficiently assembled and purified in reaction volumes of 100 μl. The method is exemplified with the gene coding for a mutant version of O6-alkylguanine alkyltransferase, which is efficiently assembled with an N-terminal peptide tag and its 5′- and 3′-untranslated regions that include a T7 promoter, ribosome binding site and T7 terminator. The utility of the method is further corroborated by assembling error-prone PCR libraries and regenerating templates following model affinity selections. This fast and robust method should find widespread application in directed evolution for the assembly of gene libraries and the regeneration of linear DNA templates between successive screening and selection cycles.
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Affiliation(s)
- Viktor Stein
- Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
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