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Madeira F, Madhusoodanan N, Lee J, Eusebi A, Niewielska A, Tivey ARN, Meacham S, Lopez R, Butcher S. Using EMBL-EBI Services via Web Interface and Programmatically via Web Services. Curr Protoc 2024; 4:e1065. [PMID: 38857087 DOI: 10.1002/cpz1.1065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The European Bioinformatics Institute (EMBL-EBI)'s Job Dispatcher framework provides access to a wide range of core databases and analysis tools that are of key importance in bioinformatics. As well as providing web interfaces to these resources, web services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. This article describes the various options available to researchers and bioinformaticians who would like to use our resources via the web interface employing RESTful web services clients provided in Perl, Python, and Java or who would like to use Docker containers to integrate the resources into analysis pipelines and workflows. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Retrieving data from EMBL-EBI using Dbfetch via the web interface Alternate Protocol 1: Retrieving data from EMBL-EBI using WSDbfetch via the REST interface Alternate Protocol 2: Retrieving data from EMBL-EBI using Dbfetch via RESTful web services with Python client Support Protocol 1: Installing Python REST web services clients Basic Protocol 2: Sequence similarity search using FASTA search via the web interface Alternate Protocol 3: Sequence similarity search using FASTA via RESTful web services with Perl client Support Protocol 2: Installing Perl REST web services clients Basic Protocol 3: Sequence similarity search using NCBI BLAST+ RESTful web services with Python client Basic Protocol 4: Sequence similarity search using HMMER3 phmmer REST web services with Perl client and Docker Support Protocol 3: Installing Docker and running the EMBL-EBI client container Basic Protocol 5: Protein functional analysis using InterProScan 5 RESTful web services with the Python client and Docker Alternate Protocol 4: Protein functional analysis using InterProScan 5 RESTful web services with the Java client Support Protocol 4: Installing Java web services clients Basic Protocol 6: Multiple sequence alignment using Clustal Omega via web interface Alternate Protocol 5: Multiple sequence alignment using Clustal Omega with Perl client and Docker Support Protocol 5: Exploring the RESTful API with OpenAPI User Inferface.
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Affiliation(s)
- Fábio Madeira
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nandana Madhusoodanan
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Joonheung Lee
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alberto Eusebi
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ania Niewielska
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Adrian R N Tivey
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stuart Meacham
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Rodrigo Lopez
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sarah Butcher
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Han F, Zhang X, Chen Y, Zhao H, Wu J, Yu Y, Wang Y. A Simple Allelic Exchange Method for Efficient Seamless Knockout of Up to 34-kbp-Long Gene Cassettes in Pseudomonas. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04806-1. [PMID: 38103122 DOI: 10.1007/s12010-023-04806-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Gene knockout is a widely used technique for engineering bacterial genomes, investigating the roles of genes in metabolism, and conferring biological characteristics. Herein, we developed a rapid, efficient, and simple method for the knockout of long gene cassettes in Pseudomonas spp., based on a traditional allelic exchange strategy. The upstream and downstream sequences of the target gene cluster to be deleted were amplified using primers with 5'-end sequences identical to the multiple cloning sites of a suicide plasmid (mutant allele insert vector). The sequences were then fused with the linearized suicide plasmid in one step via seamless cloning. The resulting allelic exchange vector (recombinant plasmid) was introduced from the donor strain (Escherichia coli SM 10) into recipient cells (Pseudomonas putida, P. composti, and P. khazarica) via conjugation. Single-crossover merodiploids (integrates the vector into host chromosome by homologous recombination) were screened based on antibiotic resistance conferred by the plasmid, and double-crossover haploids (deleting the target gene clusters and inserted alien plasmid backbone) were selected using sucrose-mediated counterselection. Unlike other approaches, the method described herein introduces no selective marker genes into the genomes of the knockout mutants. Using our method, we successfully deleted polysaccharide-encoding gene clusters in P. putida, P. composti, and P. khazarica and generated four mutants with single-gene cassette deletions up to 18 kbp and one mutant with double-gene cassette deletion of approximately 34 kbp. Collectively, our results indicate that this method is ideal for the deletion of long genetic sequences, yielding seamless mutants of various Pseudomonas spp.
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Affiliation(s)
- Feng Han
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xiaoya Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yunfei Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Haixia Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jieer Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China.
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China.
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Kawabe H, Thomas CA, Hoshika S, Kim MJ, Kim MS, Miessner L, Kaplan N, Craig JM, Gundlach JH, Laszlo AH, Benner SA, Marchand JA. Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA. Nat Commun 2023; 14:6820. [PMID: 37884513 PMCID: PMC10603101 DOI: 10.1038/s41467-023-42406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
The 4-letter DNA alphabet (A, T, G, C) as found in Nature is an elegant, yet non-exhaustive solution to the problem of storage, transfer, and evolution of biological information. Here, we report on strategies for both writing and reading DNA with expanded alphabets composed of up to 12 letters (A, T, G, C, B, S, P, Z, X, K, J, V). For writing, we devise an enzymatic strategy for inserting a singular, orthogonal xenonucleic acid (XNA) base pair into standard DNA sequences using 2'-deoxy-xenonucleoside triphosphates as substrates. Integrating this strategy with combinatorial oligos generated on a chip, we construct libraries containing single XNA bases for parameterizing kmer basecalling models for commercially available nanopore sequencing. These elementary steps are combined to synthesize and sequence DNA containing 12 letters - the upper limit of what is accessible within the electroneutral, canonical base pairing framework. By introducing low-barrier synthesis and sequencing strategies, this work overcomes previous obstacles paving the way for making expanded alphabets widely accessible.
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Affiliation(s)
- Hinako Kawabe
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | | | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Logan Miessner
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nicholas Kaplan
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Jorge A Marchand
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA.
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Liu ZJ, Yang LY, Lu TC, Huang C, Liang YQ, Xu XW, Xu YF, Liu MM, Lin XH, Chen JY. Precise Differentiation of Wobble-Type Allele via Ratiometric Design of a Ligase Chain Reaction-Based Electrochemical Biosensor for CYP2C19*2 Genotyping of Clinical Samples. Anal Chem 2023; 95:14592-14599. [PMID: 37683102 DOI: 10.1021/acs.analchem.3c01907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
Due to the comparable stability between the perfect-base pair and the wobble-base pair, a precise differentiation of the wobble-type allele has remained a challenge, often leading to false results. Herein, we proposed a ligase chain reaction (LCR)-based ratiometric electrochemical DNA sensor, namely, R-eLCR, for a precise typing of the wobble-type allele, in which the traditionally recognized "negative" signal of wobble-base pair-mediated amplification was fully utilized as a "positive" one and a ratiometric readout mode was employed to ameliorated the underlying potential external influence and improved its detection accuracy in the typing of the wobble-type allele. The results showed that the ratio between current of methylene blue (IMB) and current of ferrocene (IFc) was partitioned in three regions and three types of wobble-type allele were thus precisely differentiated (AA homozygote: IMB/IFc > 2; GG homozygote: IMB/IFc < 1; GA heterozygote: 1 < IMB/IFc < 2); the proposed R-eLCR successfully discriminated the three types of CYP2C19*2 allele in nine cases of human whole blood samples, which was consistent with those of the sequencing method. These results evidence that the proposed R-eLCR can serve as an accurate and robust alternative for the identification of wobble-type allele, which lays a solid foundation and holds great potential for precision medicine.
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Affiliation(s)
- Zhou-Jie Liu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Liang-Yong Yang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Tai-Cheng Lu
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Chen Huang
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Yu-Qi Liang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Xiong-Wei Xu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Yan-Fang Xu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Meng-Meng Liu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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Bai J, Zou J, Cao Y, Du Y, Chen T. Recognition of an Unnatural Base Pair by Tool Enzymes from Bacteriophages and Its Application in the Enzymatic Preparation of DNA with an Expanded Genetic Alphabet. ACS Synth Biol 2023; 12:2676-2690. [PMID: 37590442 DOI: 10.1021/acssynbio.3c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Unnatural base pairs (UBPs) have been developed to expand the genetic alphabet in vitro and in vivo. UBP dNaM-dTPT3 and its analogues have been successfully used to construct the first set of semi-synthetic organisms, which suggested the great potential of UBPs to be used for producing novel synthetic biological parts. Two prerequisites for doing so are the facile manipulation of DNA containing UBPs with common tool enzymes, including DNA polymerases and ligases, and the easy availability of UBP-containing DNA strands. Besides, for the application of UBPs in phage synthetic biology, the recognition of UBPs by phage enzymes is essential. Here, we first explore the recognition of dNaM-dTPT3 by a family B DNA polymerase from bacteriophage, T4 DNA polymerase D219A. Results from primer extension, steady-state kinetics, and gap-filling experiments suggest that T4 DNA polymerase D219A can efficiently and faithfully replicate dNaM-dTPT3, and efficiently fill a gap by inserting dTPT3TP or its analogues opposite dNaM. We then systematically explore the recognition of dNaM-dTPT3 and its analogues by different DNA ligases from bacteriophages and find that these DNA ligases are generally able to efficiently ligate the DNA nick next to dNaM-dTPT3 or its analogues, albeit with slightly different efficiencies. These results suggest more enzymatic tools for the manipulation of dNaM-dTPT3 and indicate the potential use of dNaM-dTPT3 for expanding the genetic alphabet in bacteriophages. Based on these results, we next develop and comprehensively optimize an upgraded method for enzymatic preparation of unnatural nucleobase (UB)-containing DNA oligonucleotides with good simplicity and universality.
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Affiliation(s)
- Jingsi Bai
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jinrong Zou
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yijun Cao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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6
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Sikkema AP, Tabatabaei SK, Lee YJ, Lund S, Lohman GJS. High-Complexity One-Pot Golden Gate Assembly. Curr Protoc 2023; 3:e882. [PMID: 37755329 DOI: 10.1002/cpz1.882] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Golden Gate Assembly is a flexible method of DNA assembly and cloning that permits the joining of multiple fragments in a single reaction through predefined connections. The method depends on cutting DNA using a Type IIS restriction enzyme, which cuts outside its recognition site and therefore can generate overhangs of any sequence while separating the recognition site from the generated fragment. By choosing compatible fusion sites, Golden Gate permits the joining of multiple DNA fragments in a defined order in a single reaction. Conventionally, this method has been used to join five to eight fragments in a single assembly round, with yield and accuracy dropping off rapidly for more complex assemblies. Recently, we demonstrated the application of comprehensive measurements of ligation fidelity and bias data using data-optimized assembly design (DAD) to enable a high degree of assembly accuracy for very complex assemblies with the simultaneous joining of as many as 52 fragments in one reaction. Here, we describe methods for applying DAD principles and online tools to evaluate the fidelity of existing fusion site sets and assembly standards, selecting new optimal sets, and adding fusion sites to existing assemblies. We further describe the application of DAD to divide known sequences at optimal points, including designing one-pot assemblies of small genomes. Using the T7 bacteriophage genome as an example, we present a protocol that includes removal of native Type IIS sites (domestication) simultaneously with parts generation by PCR. Finally, we present recommended cycling protocols for assemblies of medium to high complexity (12-36 fragments), methods for producing high-quality parts, examples highlighting the importance of DNA purity and fragment stoichiometric balance for optimal assembly outcomes, and methods for assessing assembly success. © 2023 New England Biolabs, Inc. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assessing the fidelity of an overhang set using the NEBridge Ligase Fidelity Viewer Basic Protocol 2: Generating a high-fidelity overhang set using the NEBridge GetSet Tool Alternate Protocol 1: Expanding an existing overhang set using the NEBridge GetSet Tool Basic Protocol 3: Dividing a genomic sequence with optimal fusion sites using the NEBridge SplitSet Tool Basic Protocol 4: One-pot Golden Gate Assembly of 12 fragments into a destination plasmid Alternate Protocol 2: One-pot Golden Gate Assembly of 24+ fragments into a destination plasmid Basic Protocol 5: One-pot Golden Gate Assembly of the T7 bacteriophage genome from 12+ parts Support Protocol 1: Generation of high-purity amplicons for assembly Support Protocol 2: Cloning assembly parts into a holding vector Support Protocol 3: Quantifying DNA concentration using a Qubit 4 fluorometer Support Protocol 4: Visualizing large assemblies via TapeStation Support Protocol 5: Validating phage genome assemblies via ONT long-read sequencing.
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Affiliation(s)
- Andrew P Sikkema
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
| | | | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
| | - Sean Lund
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
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7
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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8
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Duckworth AT, Bilotti K, Potapov V, Lohman GJS. Profiling DNA Ligase Substrate Specificity with a Pacific Biosciences Single-Molecule Real-Time Sequencing Assay. Curr Protoc 2023; 3:e690. [PMID: 36880776 PMCID: PMC10494924 DOI: 10.1002/cpz1.690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA ligases catalyze the joining of breaks in nucleic acid backbones and are essential enzymes for in vivo genome replication and repair across all domains of life. These enzymes are also critically important to in vitro manipulation of DNA in applications such as cloning, sequencing, and molecular diagnostics. DNA ligases generally catalyze the formation of a phosphodiester bond between an adjacent 5'-phosphate and 3'-hydroxyl in DNA, but they exhibit different substrate structure preferences, sequence-dependent biases in reaction kinetics, and variable tolerance for mismatched base pairs. Information on substrate structure and sequence specificity can inform both biological roles and molecular biology applications of these enzymes. Given the high complexity of DNA sequence space, testing DNA ligase substrate specificity on individual nucleic acid sequences in parallel rapidly becomes impractical when a large sequence space is investigated. Here, we describe methods for investigating DNA ligase sequence bias and mismatch discrimination using Pacific Biosciences Single-Molecule Real-Time (PacBio SMRT) sequencing technology. Through its rolling-circle amplification methodology, SMRT sequencing can give multiple reads of the same insert. This feature permits high-quality top- and bottom-strand consensus sequences to be determined while preserving information on top-bottom strand mismatches that can be obfuscated or lost when using other sequencing methods. Thus, PacBio SMRT sequencing is uniquely suited to measuring substrate bias and enzyme fidelity through multiplexing a diverse set of sequences in a single reaction. The protocols describe substrate synthesis, library preparation, and data analysis methods suitable for measuring fidelity and bias of DNA ligases. The methods are easily adapted to different nucleic acid substrate structures and can be used to characterize many enzymes under a variety of reaction conditions and sequence contexts in a rapid and high-throughput manner. © 2023 New England Biolabs and The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of overhang DNA substrates for ligation Basic Protocol 2: Preparation of ligation fidelity libraries Support Protocol 1: Preparation of ligation libraries for PacBio Sequel II sequencing Support Protocol 2: Loading and sequencing of a prepared library on the Sequel II instrument Basic Protocol 3: Computational processing of ligase fidelity sequencing data.
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9
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Advances in ligase-based nucleic acid amplification technology for detecting gene mutations: a review. Mol Cell Biochem 2022; 478:1621-1631. [DOI: 10.1007/s11010-022-04615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022]
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10
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Stevenson LJ, Robins KJ, Sharma JK, Williams EM, Sharrock AV, Williamson AK, Arcus VL, Patrick WM, Ackerley DF. Development of a compartmentalised self-replication protocol for selection of superior blunt-end DNA ligases. Enzyme Microb Technol 2022; 163:110153. [DOI: 10.1016/j.enzmictec.2022.110153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/06/2022]
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Luo J, Chen H, An R, Liang X. Efficient preparation of AppDNA/AppRNA by T4 DNA ligase aided by a DNA involving mismatched mini-hairpin structure at its 3′ side. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jian Luo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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12
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Park H, Gibbs JM. Selectivity and efficiency in the ligation of the pyrene:abasic base pair by T4 and PBCV-1 DNA ligases. Chem Commun (Camb) 2022; 58:9072-9075. [PMID: 35876431 DOI: 10.1039/d2cc03079a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Remarkable selectivity was observed in the ligation of 5'-phosphate 1-pyrene nucleotide terminated strands across from an abasic lesion in a DNA-templated ligation reaction by two different ligases suggesting that pyrene-terminated strands could be used in abasic site detection. Increasing ATP concentration was critical to enhancing the selectivity for this base pair with T4 DNA ligase.
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Affiliation(s)
- Hansol Park
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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