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Calaça Serrão A, Wunnava S, Dass AV, Ufer L, Schwintek P, Mast CB, Braun D. High-Fidelity RNA Copying via 2',3'-Cyclic Phosphate Ligation. J Am Chem Soc 2024; 146:8887-8894. [PMID: 38503430 PMCID: PMC10995993 DOI: 10.1021/jacs.3c10813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Templated ligation offers an efficient approach to replicate long strands in an RNA world. The 2',3'-cyclic phosphate (>P) is a prebiotically available activation that also forms during RNA hydrolysis. Using gel electrophoresis and high-performance liquid chromatography, we found that the templated ligation of RNA with >P proceeds in simple low-salt aqueous solutions with 1 mM MgCl2 under alkaline pH ranging from 9 to 11 and temperatures from -20 to 25 °C. No additional catalysts were required. In contrast to previous reports, we found an increase in the number of canonical linkages to 50%. The reaction proceeds in a sequence-specific manner, with an experimentally determined ligation fidelity of 82% at the 3' end and 91% at the 5' end of the ligation site. With splinted oligomers, five ligations created a 96-mer strand, demonstrating a pathway for the ribozyme assembly. Due to the low salt requirements, the ligation conditions will be compatible with strand separation. Templated ligation mediated by 2',3'-cyclic phosphate in alkaline conditions therefore offers a performant replication and elongation reaction for RNA on early Earth.
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Affiliation(s)
- Adriana Calaça Serrão
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Sreekar Wunnava
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Avinash V. Dass
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
- Department
of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4M1, Canada
| | - Lennard Ufer
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Philipp Schwintek
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Christof B. Mast
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Dieter Braun
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
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2
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Zumkeller C, Schindler D, Felder J, Waldminghaus T. Modular Assembly of Synthetic Secondary Chromosomes. Methods Mol Biol 2024; 2819:157-187. [PMID: 39028507 DOI: 10.1007/978-1-0716-3930-6_9] [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: 07/20/2024]
Abstract
The development of novel DNA assembly methods in recent years has paved the way for the construction of synthetic replicons to be used for basic research and biotechnological applications. A learning-by-building approach can now answer questions about how chromosomes must be constructed to maintain genetic information. Here we describe an efficient pipeline for the design and assembly of synthetic, secondary chromosomes in Escherichia coli based on the popular modular cloning (MoClo) system.
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Affiliation(s)
- Celine Zumkeller
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Jennifer Felder
- Technische Universität Darmstadt, Faculty of Biology, Darmstadt, Germany
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3
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Wen WC, Lin YH, Duh TH, Chen CH, Feng CH, Chen YL. Fluorescence detection of apolipoprotein E gene polymorphisms based on oligonucleotide ligation and magnetic separation. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4710-4717. [PMID: 37680175 DOI: 10.1039/d3ay01245j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Alzheimer's disease is a progressive neurodegenerative condition that causes brain cell death and is the leading cause of dementia. Most patients with Alzheimer's disease are diagnosed with late-onset Alzheimer's disease (LOAD), with apolipoprotein E (APOE) genotypes being highly associated with the frequency of LOAD risk. A fluorescence detection system coupled with oligonucleotide ligation and magnetic separation was developed to identify two single-nucleotide polymorphisms (SNPs) for the APOE gene and recognize APOE alleles for LOAD. The system utilized a fluorescence probe with one base-discriminating nucleoside for SNP (F probe) and a perfectly complementary biotin-modified sequence against the target DNA (P probe). When the F and P probes matched the target DNA sequences, DNA ligation occurred, and ligation products were produced. Streptavidin magnetic beads were subsequently employed to remove the ligation products, and a decrease in fluorescence intensity was observed in the supernatant compared to when there was no target DNA. This system detected two SNPs of APOE alleles, namely rs429358 and rs7412. The results indicated that the R-values ((F0 - F1)/F0) for rs429358 were 0.92 ± 0.002 for the T/T target, 0.47 ± 0.004 for the T/C target and 0.11 ± 0.004 for the C/C target, respectively. The R-values for rs7412 were 0.73 ± 0.009 for the C/C target, 0.42 ± 0.001 for the C/T target and 0.16 ± 0.007 for the T/T target, respectively. F0 and F1 represent the fluorescence intensity of the F probe without and with target DNA, respectively. Based on fluorescence intensity, the fluorescence detection system was able to identify the genotypes of the APOE gene accurately to evaluate the risk of Alzheimer's disease.
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Affiliation(s)
- Wan-Chen Wen
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
| | - Yi-Hui Lin
- School of Pharmacy, College of Pharmacy, China Medical University, Taichung 406040, Taiwan
| | - Tsai-Hui Duh
- Department of Medicinal and Applied Chemistry, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chun-Hsien Chen
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chia-Hsien Feng
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
- College of Professional Studies, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
| | - Yen-Ling Chen
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 621301, Taiwan.
- Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 621301, Taiwan
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4
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Rodgers ML, O'Brien B, Woodson SA. Small RNAs and Hfq capture unfolded RNA target sites during transcription. Mol Cell 2023; 83:1489-1501.e5. [PMID: 37116495 PMCID: PMC10176597 DOI: 10.1016/j.molcel.2023.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/11/2023] [Accepted: 03/31/2023] [Indexed: 04/30/2023]
Abstract
Small ribonucleoproteins (sRNPs) target nascent precursor RNAs to guide folding, modification, and splicing during transcription. Yet, rapid co-transcriptional folding of the RNA can mask sRNP sites, impeding target recognition and regulation. To examine how sRNPs target nascent RNAs, we monitored binding of bacterial Hfq⋅DsrA sRNPs to rpoS transcripts using single-molecule co-localization co-transcriptional assembly (smCoCoA). We show that Hfq⋅DsrA recursively samples the mRNA before transcription of the target site to poise it for base pairing with DsrA. We adapted smCoCoA to precisely measure when the target site is synthesized and revealed that Hfq⋅DsrA often binds the mRNA during target site synthesis close to RNA polymerase (RNAP). We suggest that targeting transcripts near RNAP allows an sRNP to capture a site before the transcript folds, providing a kinetic advantage over post-transcriptional targeting. We propose that other sRNPs may also use RNAP-proximal targeting to hasten recognition and regulation.
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Affiliation(s)
- Margaret L Rodgers
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Brett O'Brien
- Chemical Biology Interface Program, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
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5
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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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6
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Qin X, Wang X, Xu K, Zhang Y, Tian H, Li Y, Qi B, Yang X. Quantitative analysis of miRNAs using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER)-qPCR. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:241-255. [PMID: 36700047 PMCID: PMC9842969 DOI: 10.1016/j.omtn.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Here, a method using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER) for miRNAs quantification was established. The strategy has two steps: (1) ligation of two DNA probes specifically hybridize to target miRNA and (2) qPCR amplifying the ligated probe. The miRNA-binding regions of the probes are stem-looped, a motif significantly reduces nonspecific ligation at high ligation temperature (65°C). The ends of the probes are designed complementary to form a paired probe, facilitating the recognition of target miRNAs with low concentrations. RNase H proved to be able to stabilize the heteroduplex formed by the probe and target miRNA, contributing to enhanced sensitivity (limit of detection = 60 copies). High specificity (discriminating homology miRNAs differing only one nucleotide), wide dynamic range (seven orders of magnitude) and ability to accurately detect plant miRNAs (immune to hindrance of 2'-O-methyl moiety) enable SPLICER comparable with the commercially available TaqMan and miRCURY assays. SYBR green I, rather than expensive hydrolysis or locked nucleic acid probes indispensable to TaqMan and miRCURY assays, is adequate for SPLICER. The method was efficient (<1 h), economical ($7 per sample), and robust (able to detect xeno-miRNAs in mammalian bodies), making it a powerful tool for molecular diagnosis and corresponding therapy.
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Affiliation(s)
- Xinshu Qin
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Xingyu Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China,Corresponding author: Xingyu Wang, College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710054, Shaanxi, China.
| | - Ke Xu
- Department of Joint Surgery, Hong Hui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi, China
| | - Yi Zhang
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hongye Tian
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Yinglei Li
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Bangran Qi
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Xingbin Yang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China,Corresponding author: Xingbin Yang, College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710054, Shaanxi, China.
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7
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Nelson DJ, Shilts MH, Pakala SB, Das SR, Schmitz JE, Haselton FR. Ligation-based assay for variant typing without sequencing: Application to SARS-CoV-2 variants of concern. Influenza Other Respir Viruses 2022; 17:e13083. [PMID: 36510692 PMCID: PMC9835417 DOI: 10.1111/irv.13083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND COVID-19 prevalence has remained high throughout the pandemic with intermittent surges, due largely to the emergence of genetic variants, demonstrating the need for more accessible sequencing technologies for strain typing. METHODS A ligation-based typing assay was developed to detect known variants of severe acute respiratory syndrome virus 2 (SARS-CoV-2) by identifying the presence of characteristic single-nucleotide polymorphisms (SNPs). General principles for extending the strategy to new variants and alternate diseases with SNPs of interest are described. Of note, this strategy leverages commercially available reagents for assay preparation, as well as standard real-time polymerase chain reaction (PCR) instrumentation for assay performance. RESULTS The assay demonstrated a combined sensitivity and specificity of 96.6% and 99.5%, respectively, for the classification of 88 clinical samples of the Alpha, Delta, and Omicron variants relative to the gold standard of viral genome sequencing. It achieved an average limit of detection of 7.4 × 104 genome copies/mL in contrived nasopharyngeal samples. The ligation-based strategy performed robustly in the presence of additional polymorphisms in the targeted regions of interest as shown by the sequence alignment of clinical samples. CONCLUSIONS The assay demonstrates the potential for robust variant typing with performance comparable with next-generation sequencing without the need for the time delays and resources required for sequencing. The reduced resource dependency and generalizability could expand access to variant classification information for pandemic surveillance.
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Affiliation(s)
- Dalton J. Nelson
- Department of Biomedical EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Meghan H. Shilts
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Suman B. Pakala
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Suman R. Das
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA,Vanderbilt Institute for Infection, Immunology and InflammationVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Jonathan E. Schmitz
- Department of Pathology, Microbiology and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA,Vanderbilt Institute for Infection, Immunology and InflammationVanderbilt University Medical CenterNashvilleTennesseeUSA
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8
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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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9
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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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10
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PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction. Nat Commun 2022; 13:2697. [PMID: 35577775 PMCID: PMC9110713 DOI: 10.1038/s41467-022-30355-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/28/2022] [Indexed: 01/01/2023] Open
Abstract
Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments. PlasmidMaker should greatly expand the potential of synthetic biology. Despite their broad utility, design and construction of plasmids remains laborious and time-consuming. Here the authors report a robust, versatile, and automated end-to-end platform that enables scarless construction of virtually any plasmid.
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11
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Ura H, Togi S, Niida Y. A comparison of mRNA sequencing (RNA-Seq) library preparation methods for transcriptome analysis. BMC Genomics 2022; 23:303. [PMID: 35418012 PMCID: PMC9008973 DOI: 10.1186/s12864-022-08543-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND mRNA sequencing is a powerful technique, which is used to investigate the transcriptome status of a gene of interest, such as its transcription level and splicing variants. Presently, several RNA sequencing (RNA-Seq) methods have been developed; however, the relative advantage of each method has remained unknown. Here we used three commercially available RNA-Seq library preparation kits; the traditional method (TruSeq), in addition to full-length double-stranded cDNA methods (SMARTer and TeloPrime) to investigate the advantages and disadvantages of these three approaches in transcriptome analysis. RESULTS We observed that the number of expressed genes detected from the TeloPrime sequencing method was fewer than that obtained using the TruSeq and SMARTer. We also observed that the expression patterns between TruSeq and SMARTer correlated strongly. Alternatively, SMARTer and TeloPrime methods underestimated the expression of relatively long transcripts. Moreover, genes having low expression levels were undetected stochastically regardless of any three methods used. Furthermore, although TeloPrime detected a significantly higher proportion at the transcription start site (TSS), its coverage of the gene body was not uniform. SMARTer is proposed to be yielded for nonspecific genomic DNA amplification. In contrast, the detected splicing event number was highest in the TruSeq. The percent spliced in index (PSI) of the three methods was highly correlated. CONCLUSIONS TruSeq detected transcripts and splicing events better than the other methods and measured expression levels of genes, in addition to splicing events accurately. However, although detected transcripts and splicing events in TeloPrime were fewer, the coverage at TSS was highest. Additionally, SMARTer was better than TeloPrime with regards to the detected number of transcripts and splicing events among the understudied full-length double-stranded cDNA methods. In conclusion, for short-read sequencing, TruSeq has relative advantages for use in transcriptome analysis.
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Affiliation(s)
- Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan. .,Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan.
| | - Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan.,Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan.,Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan
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12
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Zatopek KM, Fossa SL, Bilotti K, Caffrey PJ, Chuzel L, Gehring AM, Lohman GJS, Taron CH, Gardner AF. Capillary Electrophoresis-Based Functional Genomics Screening to Discover Novel Archaeal DNA Modifying Enzymes. Appl Environ Microbiol 2022; 88:e0213721. [PMID: 34788065 PMCID: PMC8788744 DOI: 10.1128/aem.02137-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/13/2021] [Indexed: 12/05/2022] Open
Abstract
It has been predicted that 30 to 80% of archaeal genomes remain annotated as hypothetical proteins with no assigned gene function. Further, many archaeal organisms are difficult to grow or are unculturable. To overcome these technical and experimental hurdles, we developed a high-throughput functional genomics screen that utilizes capillary electrophoresis (CE) to identify nucleic acid modifying enzymes based on activity rather than sequence homology. Here, we describe a functional genomics screening workflow to find DNA modifying enzyme activities encoded by the hyperthermophile Thermococcus kodakarensis (T. kodakarensis). Large DNA insert fosmid libraries representing an ∼5-fold average coverage of the T. kodakarensis genome were prepared in Escherichia coli. RNA-seq showed a high fraction (84%) of T. kodakarensis genes were transcribed in E. coli despite differences in promoter structure and translational machinery. Our high-throughput screening workflow used fluorescently labeled DNA substrates directly in heat-treated lysates of fosmid clones with capillary electrophoresis detection of reaction products. Using this method, we identified both a new DNA endonuclease activity for a previously described RNA endonuclease (Nob1) and a novel AP lyase DNA repair enzyme family (termed 'TK0353') that is found only in a small subset of Thermococcales. The screening methodology described provides a fast and efficient way to explore the T. kodakarensis genome for a variety of nucleic acid modifying activities and may have implications for similar exploration of enzymes and pathways that underlie core cellular processes in other Archaea. IMPORTANCE This study provides a rapid, simple, high-throughput method to discover novel archaeal nucleic acid modifying enzymes by utilizing a fosmid genomic library, next-generation sequencing, and capillary electrophoresis. The method described here provides the details necessary to create 384-well fosmid library plates from Thermococcus kodakarensis genomic DNA, sequence 384-well fosmids plates using Illumina next-generation sequencing, and perform high-throughput functional read-out assays using capillary electrophoresis to identify a variety of nucleic acid modifying activities, including DNA cleavage and ligation. We used this approach to identify a new DNA endonuclease activity for a previously described RNA endonuclease (Nob1) and identify a novel AP lyase enzyme (TK0353) that lacks sequence homology to known nucleic acid modifying enzymes.
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Affiliation(s)
| | | | | | | | - Léa Chuzel
- New England Biolabs, Inc., Ipswich, Massachusetts, USA
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13
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Bilotti K, Potapov V, Pryor JM, Duckworth AT, Keck J, Lohman GJS. OUP accepted manuscript. Nucleic Acids Res 2022; 50:4647-4658. [PMID: 35438779 PMCID: PMC9071435 DOI: 10.1093/nar/gkac241] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 03/07/2022] [Accepted: 03/31/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - John M Pryor
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Alexander T Duckworth
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Gregory J S Lohman
- To whom correspondence should be addressed. Tel: +1 978 998 7916; Fax: +1 978 921 1350;
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14
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Li T, Zou H, Zhang J, Ding H, Li C, Chen X, Li Y, Feng W, Kageyama K. High-efficiency and high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases to assist LR-LAMP for the genotyping of single-nucleotide polymorphisms. Analyst 2022; 147:3993-3999. [DOI: 10.1039/d2an01042a] [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
A high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases was developed to assist LR-LAMP for genotyping of SNPs.
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Affiliation(s)
- Taiwen Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Huayan Zou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Jing Zhang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Haixia Ding
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Cheng Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Xiangru Chen
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Yunzhou Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Wenzhuo Feng
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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15
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Structured sequences emerge from random pool when replicated by templated ligation. Proc Natl Acad Sci U S A 2021; 118:2018830118. [PMID: 33593911 PMCID: PMC7923349 DOI: 10.1073/pnas.2018830118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The structure of life emerged from randomness. This is attributed to selection by molecular Darwinian evolution. This study found that random templated ligation led to the simultaneous elongation and sequence selection of oligomers. Product strands showed highly structured sequence motifs which inhibited self-folding and built self-templating reaction networks. By the reduction of the sequence space, the kinetics of duplex formation increased and led to a faster replication through the ligation process. These findings imply that elementary binding properties of nucleotides can lead to an early selection of sequences even before the onset of Darwinian evolution. This suggests that such a simplification of sequence space could result in faster downstream selection for sequence-based function for the origin of life. The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen, Naturwissenschaften 58 (10), 465–523 (1971)]. Here, we showed that linking short oligomers from a random sequence pool in a templated ligation reaction reduced the sequence space of product strands. We started from 12-mer oligonucleotides with two bases in all possible combinations and triggered enzymatic ligation under temperature cycles. Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed. However, between the ligation sites, we found either an A-rich or a T-rich sequence within a single oligonucleotide. Our modeling suggests that avoidance of hairpins was the likely cause for these two complementary sequence pools. What emerged was a network of complementary sequences that acted both as templates and substrates of the reaction. This self-selecting ligation reaction could be restarted by only a few majority sequences. The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool. This is a favorable starting point for a subsequent Darwinian evolution searching for higher catalytic functions in an RNA world scenario.
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16
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Vaisvila R, Hunault L, Saleh L. Detection of TET-Oxidized 5-Methylcytosine Bases by Capillary Gel Electrophoresis. Methods Mol Biol 2021; 2198:137-144. [PMID: 32822028 DOI: 10.1007/978-1-0716-0876-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The oxidation activity of the mammalian ten-eleven translocation dioxygenase (TET) on 5-methylcytosine (5mC) of DNA is usually monitored by analytical methods such as dot blotting and liquid chromatography-mass spectrometry (LC-MS). Herein, we describe a high throughput capillary gel electrophoresis assay for monitoring the in vitro oxidation of 5mC by TET. The method is rapid and quantitative, and can serve as a powerful tool in mechanistic studies of TET.
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Affiliation(s)
| | - Lise Hunault
- New England Biolabs, Inc., Ipswich, MA, USA.,ESPCI Paris, Paris, France
| | - Lana Saleh
- New England Biolabs, Inc., Ipswich, MA, USA.
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17
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Williamson A, Leiros HKS. Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds. Nucleic Acids Res 2020; 48:8225-8242. [PMID: 32365176 PMCID: PMC7470946 DOI: 10.1093/nar/gkaa307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
DNA ligases are diverse enzymes with essential functions in replication and repair of DNA; here we review recent advances in their structure and distribution and discuss how this contributes to understanding their biological roles and technological potential. Recent high-resolution crystal structures of DNA ligases from different organisms, including DNA-bound states and reaction intermediates, have provided considerable insight into their enzymatic mechanism and substrate interactions. All cellular organisms possess at least one DNA ligase, but many species encode multiple forms some of which are modular multifunctional enzymes. New experimental evidence for participation of DNA ligases in pathways with additional DNA modifying enzymes is defining their participation in non-redundant repair processes enabling elucidation of their biological functions. Coupled with identification of a wealth of DNA ligase sequences through genomic data, our increased appreciation of the structural diversity and phylogenetic distribution of DNA ligases has the potential to uncover new biotechnological tools and provide new treatment options for bacterial pathogens.
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Affiliation(s)
- Adele Williamson
- School of Science, University of Waikato, Hamilton 3240, New Zealand.,Department of Chemistry, UiT The Arctic University of Norway, Tromsø N-9037, Norway
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18
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Kimoto M, Soh SHG, Tan HP, Okamoto I, Hirao I. Cognate base-pair selectivity of hydrophobic unnatural bases in DNA ligation by T4 DNA ligase. Biopolymers 2020; 112:e23407. [PMID: 33156531 PMCID: PMC7900958 DOI: 10.1002/bip.23407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/28/2022]
Abstract
We present cognate base pair selectivity in template-dependent ligation by T4 DNA ligase using a hydrophobic unnatural base pair (UBP), Ds-Pa. T4 DNA ligase efficiently recognizes the Ds-Pa pairing at the conjugation position, and Ds excludes the noncognate pairings with the natural bases. Our results indicate that the hydrophobic base pairing is allowed in enzymatic ligation with higher cognate base-pair selectivity, relative to the hydrogen-bond interactions between pairing bases. The efficient ligation using Ds-Pa can be employed in recombinant DNA technology using genetic alphabet expansion, toward the creation of semi-synthetic organisms containing UBPs.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Si Hui Gabriella Soh
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore.,Raffles Institution, Singapore, Singapore
| | - Hui Pen Tan
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Itaru Okamoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
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19
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Osman EA, Alladin-Mustan BS, Hales SC, Matharu GK, Gibbs JM. Enhanced mismatch selectivity of T4 DNA ligase far above the probe: Target duplex dissociation temperature. Biopolymers 2020; 112:e23393. [PMID: 32896905 DOI: 10.1002/bip.23393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 11/06/2022]
Abstract
T4 DNA ligase is a widely used ligase in many applications; yet in single nucleotide polymorphism analysis, it has been found generally lacking owing to its tendency to ligate mismatches quite efficiently. To address this lack of selectivity, we explored the effect of temperature on the selectivity of the ligase in discriminating single base pair mismatches at the 3'-terminus of the ligating strand using short ligation probes (9-mers). Remarkably, we observe outstanding selectivities when the assay temperature is increased to 7 °C to 13 °C above the dissociation temperature of the matched probe:target duplexes using commercially available enzyme at low concentration. Higher enzyme concentration shifts the temperature range to 13 °C to 19 °C above the probe:target dissociation temperatures. Finally, substituting the 5'-phosphate terminus with an abasic nucleotide decreases the optimal temperature range to 7 °C to 10 °C above the matched probe:target duplex. We compare the temperature dependence of the T4 DNA ligase catalyzed ligation and a nonenzymatic ligation system to contrast the origin of their modes of selectivity. For the latter, temperatures above the probe:target duplex dissociation lead to lower ligation conversions even for the perfect matched system. This difference between the two ligation systems reveals the uniqueness of the T4 DNA ligase's ability to maintain excellent ligation yields for the matched system at elevated temperatures. Although our observations are consistent with previous mechanistic work on T4 DNA ligase, by mapping out the temperature dependence for different ligase concentrations and probe modifications, we identify simple strategies for introducing greater selectivity into SNP discrimination based on ligation yields.
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Affiliation(s)
- Eiman A Osman
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Sarah C Hales
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gunwant K Matharu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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20
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Kim J, Ahn JK, Kim JS, Choi BR, Cho J, Lee H. Highly selective detection of single nucleotide polymorphism (SNP) using a dumbbell DNA probe with a gap-filling approach. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2020.03.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Yamamoto Y, Terai T, Kumachi S, Nemoto N. In Vitro Construction of Large-scale DNA Libraries from Fragments Containing Random Regions using Deoxyinosine-containing Oligonucleotides and Endonuclease V. ACS COMBINATORIAL SCIENCE 2020; 22:165-171. [PMID: 32212679 DOI: 10.1021/acscombsci.9b00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient and precise construction of DNA libraries is a fundamental starting point for directed evolution of polypeptides. Recently, several in vitro selection methods have been reported that do not rely on cells for protein expression, where peptide libraries in the order of 1013 species are used for in vitro affinity selection. To maximize their potential, simple yet versatile construction of DNA libraries from several fragments containing random regions without bacterial transformation is essential. To address this issue, we herein propose a novel DNA construction methodology based on the use of polymerase chain reaction (PCR) primers containing a single deoxyinosine (I) residue near their 5' end. Treatment of the PCR products with endonuclease V generates 3' overhangs with customized lengths and sequences, which can be ligated accurately and efficiently with other fragments having exactly complementary overhangs. As a proof of concept, we constructed an artificial gene library of single-domain antibodies from four DNA fragments.
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Affiliation(s)
- Yasuhide Yamamoto
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama City, 338-8570, Japan
| | - Takuya Terai
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama City, 338-8570, Japan
| | - Shigefumi Kumachi
- Epsilon Molecular Engineering, Inc., 255 Shimo-okubo, Sakura-ku, Saitama City 338-8570, Saitama, Japan
| | - Naoto Nemoto
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama City, 338-8570, Japan
- Epsilon Molecular Engineering, Inc., 255 Shimo-okubo, Sakura-ku, Saitama City 338-8570, Saitama, Japan
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22
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Wang J, Zhu J, Wang C, Zhou G, Yu X, Fan H, An R, Komiyama M, Liang X. Thermus thermophilus DNA Ligase Connects Two Fragments Having Exceptionally Short Complementary Termini at High Temperatures. Biochemistry 2020; 59:400-406. [PMID: 31887028 DOI: 10.1021/acs.biochem.9b00866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thermus thermophilus DNA ligase (Tth DNA ligase) is widely employed for cloning, enzymatic synthesis, and molecular diagnostics at high temperatures (e.g., 65 °C). It has been long believed that the complementary ends must be very long (e.g., >30 bp) to place two DNA fragments nearby for the ligation. In the current study, the length of the complementary portion was systematically varied, and the ligation efficiency was evaluated using the high resolution melting (HRM) method. Unexpectedly, very short oligonucleotides (7-10 nt) were successfully ligated on the complementary overhang attached to a dsDNA at 70 °C. Furthermore, sticky ends with the overhang of only 4 nt long, available after scission with many restriction enzymes, were also efficiently ligated at 45-70 °C. The ligation yield for the 6-nt-long sticky ends was as high as 80%. It was concluded that Tth DNA ligase can be used as a unique tool for DNA manipulation that cannot be otherwise easily accomplished.
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Affiliation(s)
- Jing Wang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,CAS Key laboratory of Marine Ecology and Environmental Sciences , Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 , China
| | - Jianming Zhu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Chenru Wang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Guangqing Zhou
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xin Yu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Huijun Fan
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003 , China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003 , China
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23
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Zhu J, Wang J, Cheng K, Chen H, An R, Zhang Y, Komiyama M, Liang X. Effective Characterization of DNA Ligation Kinetics by High-Resolution Melting Analysis. Chembiochem 2019; 21:785-788. [PMID: 31592561 DOI: 10.1002/cbic.201900489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/07/2019] [Indexed: 12/31/2022]
Abstract
High-resolution melting (HRM) analysis has been improved and applied for the first time to quantitative analysis of enzymatic reactions. By using the relative ratios of peak intensities of substrates and products, the quantitativity of conventional HRM analysis has been improved to allow detailed kinetic analysis. As an example, the ligation of sticky ends through the action of T4 DNA ligase has been kinetically analyzed, with comprehensive data on substrate specificity and other properties having been obtained. For the first time, the kinetic parameters (kobs and apparent Km ) of sticky-end ligation were obtained for both fully matched and mismatched sticky ends. The effect of ATP concentration on sticky-end ligation was also investigated. The improved HRM method should also be applicable to versatile DNA-transforming enzymes, because the only requirement is that the products have Tm values different enough from the substrates.
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Affiliation(s)
- Jianming Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Jing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Kai Cheng
- 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
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, 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, 266003, P. R. China
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24
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Potapov V, Ong JL, Langhorst BW, Bilotti K, Cahoon D, Canton B, Knight TF, Evans TC, Lohman GJS. A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining. Nucleic Acids Res 2019; 46:e79. [PMID: 29741723 PMCID: PMC6061786 DOI: 10.1093/nar/gky303] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 12/14/2022] Open
Abstract
DNA ligases are key enzymes in molecular and synthetic biology that catalyze the joining of breaks in duplex DNA and the end-joining of DNA fragments. Ligation fidelity (discrimination against the ligation of substrates containing mismatched base pairs) and bias (preferential ligation of particular sequences over others) have been well-studied in the context of nick ligation. However, almost no data exist for fidelity and bias in end-joining ligation contexts. In this study, we applied Pacific Biosciences Single-Molecule Real-Time sequencing technology to directly sequence the products of a highly multiplexed ligation reaction. This method has been used to profile the ligation of all three-base 5′-overhangs by T4 DNA ligase under typical ligation conditions in a single experiment. We report the relative frequency of all ligation products with or without mismatches, the position-dependent frequency of each mismatch, and the surprising observation that 5′-TNA overhangs ligate extremely inefficiently compared to all other Watson–Crick pairings. The method can easily be extended to profile other ligases, end-types (e.g. blunt ends and overhangs of different lengths), and the effect of adjacent sequence on the ligation results. Further, the method has the potential to provide new insights into the thermodynamics of annealing and the kinetics of end-joining reactions.
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Affiliation(s)
- Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Jennifer L Ong
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Bradley W Langhorst
- Applications and Product Development, New England Biolabs, Ipswich, MA 01938, USA
| | | | | | | | | | - Thomas C Evans
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
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25
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Cozens C, Pinheiro VB. Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis. Nucleic Acids Res 2019; 46:e51. [PMID: 29409059 PMCID: PMC5934624 DOI: 10.1093/nar/gky067] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/24/2018] [Indexed: 12/15/2022] Open
Abstract
Engineering proteins for designer functions and biotechnological applications almost invariably requires (or at least benefits from) multiple mutations to non-contiguous residues. Several methods for multiple site-directed mutagenesis exist, but there remains a need for fast and simple methods to efficiently introduce such mutations – particularly for generating large, high quality libraries for directed evolution. Here, we present Darwin Assembly, which can deliver high quality libraries of >108 transformants, targeting multiple (>10) distal sites with minimal wild-type contamination (<0.25% of total population) and which takes a single working day from purified plasmid to library transformation. We demonstrate its efficacy with whole gene codon reassignment of chloramphenicol acetyl transferase, mutating 19 codons in a single reaction in KOD DNA polymerase and generating high quality, multiple-site libraries in T7 RNA polymerase and Tgo DNA polymerase. Darwin Assembly uses commercially available enzymes, can be readily automated, and offers a cost-effective route to highly complex and customizable library generation.
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Affiliation(s)
| | - Vitor B Pinheiro
- University College London, Gower Street, London WC1E 6BT, UK.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street WC1E 7HX, UK
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26
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Haines MC, Storch M, Oyarzún DA, Stan GB, Baldwin GS. Riboswitch identification using Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR). Synth Biol (Oxf) 2019; 4:ysz019. [PMID: 32995542 PMCID: PMC7445825 DOI: 10.1093/synbio/ysz019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022] Open
Abstract
In vitro selection of ligand-responsive ribozymes can identify rare, functional sequences from large libraries. While powerful, key caveats of this approach include lengthy and demanding experimental workflows; unpredictable experimental outcomes and unknown functionality of enriched sequences in vivo. To address the first of these limitations, we developed Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR). LigASERR is scalable, amenable to automation and requires less time to implement compared to alternative methods. To improve the predictability of experiments, we modeled the underlying selection process, predicting experimental outcomes based on sequence and population parameters. We applied this new methodology and model to the enrichment of a known, in vitro-selected sequence from a bespoke library. Prior to implementing selection, conditions were optimized and target sequence dynamics accurately predicted for the majority of the experiment. In addition to enriching the target sequence, we identified two new, theophylline-activated ribozymes. Notably, all three sequences yielded riboswitches functional in Escherichia coli, suggesting LigASERR and similar in vitro selection methods can be utilized for generating functional riboswitches in this organism.
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Affiliation(s)
- Matthew C Haines
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Marko Storch
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,London BioFoundry, Imperial College Translation & Innovation Hub, London, UK
| | - Diego A Oyarzún
- School of Informatics, University of Edinburgh, Edinburgh, UK.,School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Geoff S Baldwin
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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27
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Kaplan E, Ilkit M, de Hoog GS. Comparison of the rolling circle amplification and ligase-dependent reaction methods for the identification of opportunistic Exophiala species. Med Mycol 2018; 56:759-769. [PMID: 29087521 DOI: 10.1093/mmy/myx095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 09/06/2017] [Indexed: 01/08/2023] Open
Abstract
We developed two ligase-dependent probe amplification assays based on rolling circle amplification (RCA) and the ligase-dependent reaction (LDR) to differentiate species of Exophiala targeting the rDNA internal transcribed spacer region. We focused on Exophiala dermatitidis and E. phaeomuriformis, two opportunistic inhabitants of indoor wet cells, and further detected E. heteromorpha, E. xenobiotica, and E. crusticola; 57 reference isolates representing the five species were tested. Depending on the RCA probes used, the sensitivity was 100%, and the specificity ranged from 3.7% to 88.6% (median: 46.1%). In contrast, the sensitivity and specificity of the LDR probes targeting the same isolates were 88.6-100% (median: 95.8%) and 95.4-100% (median: 97.7%), respectively. We analyzed 198 additional environmental isolates representing the same Exophiala species. Overall, the sensitivity and specificity of LDR ranged from 89.7% to 100% (median: 94.1%) and from 93.9% to 100% (median: 96.9%), respectively. The assessment of performance and validation of LDR probes using SYBR Green quantitative polymerase chain reaction revealed high reproducibility and an acceptable range limit, in line with the guidelines of the European Network of GMO Laboratories. In conclusion, the LDR assay was more reliable and less expensive than RCA for species-level identification of Exophiala isolates.
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Affiliation(s)
- Engin Kaplan
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - G Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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28
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Gong J, Li Y, Lin T, Feng X, Chu L. Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations. RSC Adv 2018; 8:27375-27381. [PMID: 35540013 PMCID: PMC9083282 DOI: 10.1039/c8ra05259j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/23/2018] [Indexed: 12/01/2022] Open
Abstract
With the continuous development and application of targeted drugs, it is particularly desirable to find a non-invasive diagnostic approach to screen patients for precision treatment. Specifically, detection of multiple cancer-related mutations is very important for targeted therapy and prediction of drug resistance. Although numerous advanced PCR methods have been developed to discriminate single nucleotide polymorphisms, their drawbacks significantly limit their application, such as low sensitivity and throughput, complicated operations, and expensive costs. In order to overcome these challenges, in this study, we developed a method combining multiplex and sensitive real-time PCR assay with rolling circle amplification. This allows specific and sensitive discrimination of the single nucleotide mutation and provides convenient multiplex detection by real-time PCR assay. The clinical potential of the MPRP assay was further demonstrated by comparing samples from 8 patients with a digital PCR assay. The coincident results between these two methods indicated that the MPRP assay can provide a specific, sensitive, and convenient method for multiplex detection of cancer-related mutations.
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Affiliation(s)
- Jian Gong
- Hebei Medical University Hebei 050017 China
| | - Yishuai Li
- Department of Thoracic Surgery, Hebei Chest Hospital Hebei 050000 China
| | - Ting Lin
- Apexbio Biotech Co., LTD Beijing 100176 China
| | | | - Li Chu
- Hebei Medical University Hebei 050017 China
- Department of Pharmacology, Hebei University of Chinese Medicine Hebei 050200 China
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29
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Azuara-Liceaga E, Betanzos A, Cardona-Felix CS, Castañeda-Ortiz EJ, Cárdenas H, Cárdenas-Guerra RE, Pastor-Palacios G, García-Rivera G, Hernández-Álvarez D, Trasviña-Arenas CH, Diaz-Quezada C, Orozco E, Brieba LG. The Sole DNA Ligase in Entamoeba histolytica Is a High-Fidelity DNA Ligase Involved in DNA Damage Repair. Front Cell Infect Microbiol 2018; 8:214. [PMID: 30050869 PMCID: PMC6052137 DOI: 10.3389/fcimb.2018.00214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/07/2018] [Indexed: 01/03/2023] Open
Abstract
The protozoan parasite Entamoeba histolytica is exposed to reactive oxygen and nitric oxide species that have the potential to damage its genome. E. histolytica harbors enzymes involved in DNA repair pathways like Base and Nucleotide Excision Repair. The majority of DNA repairs pathways converge in their final step in which a DNA ligase seals the DNA nicks. In contrast to other eukaryotes, the genome of E. histolytica encodes only one DNA ligase (EhDNAligI), suggesting that this ligase is involved in both DNA replication and DNA repair. Therefore, the aim of this work was to characterize EhDNAligI, its ligation fidelity and its ability to ligate opposite DNA mismatches and oxidative DNA lesions, and to study its expression changes and localization during and after recovery from UV and H2O2 treatment. We found that EhDNAligI is a high-fidelity DNA ligase on canonical substrates and is able to discriminate erroneous base-pairing opposite DNA lesions. EhDNAligI expression decreases after DNA damage induced by UV and H2O2 treatments, but it was upregulated during recovery time. Upon oxidative DNA damage, EhDNAligI relocates into the nucleus where it co-localizes with EhPCNA and the 8-oxoG adduct. The appearance and disappearance of 8-oxoG during and after both treatments suggest that DNA damaged was efficiently repaired because the mainly NER and BER components are expressed in this parasite and some of them were modulated after DNA insults. All these data disclose the relevance of EhDNAligI as a specialized and unique ligase in E. histolytica that may be involved in DNA repair of the 8-oxoG lesions.
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Affiliation(s)
- Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico,*Correspondence: Elisa Azuara-Liceaga
| | - Abigail Betanzos
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico,Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Cesar S. Cardona-Felix
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | | | - Helios Cárdenas
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Rosa E. Cárdenas-Guerra
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Guillermo Pastor-Palacios
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - David Hernández-Álvarez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Carlos H. Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico,Luis G. Brieba
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Rodda AE, Parker BJ, Spencer A, Corrie SR. Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges. ACS Sens 2018; 3:540-560. [PMID: 29441780 DOI: 10.1021/acssensors.7b00953] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.
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Affiliation(s)
| | | | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne, Victoria 3004, Australia
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31
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Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Engineering of a DNA Polymerase for Direct m 6 A Sequencing. Angew Chem Int Ed Engl 2018; 57:417-421. [PMID: 29115744 PMCID: PMC5768020 DOI: 10.1002/anie.201710209] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 12/16/2022]
Abstract
Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6 -methyladenosine (m6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6 A-containing RNA prior to sequencing, since m6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m6 A sites directly from the sequencing data of untreated RNA samples.
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Affiliation(s)
- Joos Aschenbrenner
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Stephan Werner
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, IMoPA, UMR7365 CNRS-ULBiopôle de L'Université de Lorraine9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Martina Adam
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, IMoPA, UMR7365 CNRS-ULBiopôle de L'Université de Lorraine9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
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32
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Cui Y, Han X, An R, Zhou G, Komiyama M, Liang X. Cyclization of secondarily structured oligonucleotides to single-stranded rings by using Taq DNA ligase at high temperatures. RSC Adv 2018; 8:18972-18979. [PMID: 35539641 PMCID: PMC9080623 DOI: 10.1039/c8ra02804d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 05/10/2018] [Indexed: 11/21/2022] Open
Abstract
Single-stranded DNA rings play important roles in nanoarchitectures, molecular machines, DNA detection, etc. Although T4 DNA ligase has been widely employed to cyclize single-stranded oligonucleotides into rings, the cyclization efficiency is very low when the oligonucleotides (l-DNAs) take complicated secondary structures at ambient temperatures. In the present study, this problem has been solved by using Thermus aquaticus DNA ligase (Taq DNA ligase) at higher temperatures (65 and 70 °C) where the secondary structures are less stable or completely destroyed. This method is based on our new finding that this ligase successfully functions even when the splint strand is short and forms no stable duplex with l-DNA (at least in the absence of the enzyme). In order to increase the efficiency of cyclization, various operation factors (lengths and sequences of splint, as well as the size of the DNA ring) have been investigated. Based on these results, DNA rings have been successfully synthesized from secondarily structured oligonucleotides in high yields and high selectivity. The present methodology is applicable to the preparation of versatile DNA rings involving complicated secondary structures, which should show novel properties and greatly widen the scope of DNA-based nanotechnology. We have achieved the efficient preparation of single-stranded DNA rings from secondarily structured oligonucleotides.![]()
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Affiliation(s)
- Yixiao Cui
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Xutiange Han
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Ran An
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
| | - Guangqing Zhou
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Makoto Komiyama
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- National Institute for Materials Science (NIMS)
| | - Xingguo Liang
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
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33
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Bauer RJ, Zhelkovsky A, Bilotti K, Crowell LE, Evans TC, McReynolds LA, Lohman GJS. Comparative analysis of the end-joining activity of several DNA ligases. PLoS One 2017; 12:e0190062. [PMID: 29284038 PMCID: PMC5746248 DOI: 10.1371/journal.pone.0190062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/07/2017] [Indexed: 11/29/2022] Open
Abstract
DNA ligases catalyze the repair of phosphate backbone breaks in DNA, acting with highest activity on breaks in one strand of duplex DNA. Some DNA ligases have also been observed to ligate two DNA fragments with short complementary overhangs or blunt-ended termini. In this study, several wild-type DNA ligases (phage T3, T4, and T7 DNA ligases, Paramecium bursaria chlorella virus 1 (PBCV1) DNA ligase, human DNA ligase 3, and Escherichia coli DNA ligase) were tested for their ability to ligate DNA fragments with several difficult to ligate end structures (blunt-ended termini, 3′- and 5′- single base overhangs, and 5′-two base overhangs). This analysis revealed that T4 DNA ligase, the most common enzyme utilized for in vitro ligation, had its greatest activity on blunt- and 2-base overhangs, and poorest on 5′-single base overhangs. Other ligases had different substrate specificity: T3 DNA ligase ligated only blunt ends well; PBCV1 DNA ligase joined 3′-single base overhangs and 2-base overhangs effectively with little blunt or 5′- single base overhang activity; and human ligase 3 had highest activity on blunt ends and 5′-single base overhangs. There is no correlation of activity among ligases on blunt DNA ends with their activity on single base overhangs. In addition, DNA binding domains (Sso7d, hLig3 zinc finger, and T4 DNA ligase N-terminal domain) were fused to PBCV1 DNA ligase to explore whether modified binding to DNA would lead to greater activity on these difficult to ligate substrates. These engineered ligases showed both an increased binding affinity for DNA and increased activity, but did not alter the relative substrate preferences of PBCV1 DNA ligase, indicating active site structure plays a role in determining substrate preference.
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Affiliation(s)
- Robert J. Bauer
- Research Division, New England Biolabs, Inc., Ipswich, MA, United States of America
| | - Alexander Zhelkovsky
- Research Division, New England Biolabs, Inc., Ipswich, MA, United States of America
| | - Katharina Bilotti
- Research Division, New England Biolabs, Inc., Ipswich, MA, United States of America
| | - Laura E. Crowell
- Research Division, New England Biolabs, Inc., Ipswich, MA, United States of America
| | - Thomas C. Evans
- Research Division, New England Biolabs, Inc., Ipswich, MA, United States of America
| | - Larry A. McReynolds
- Research Division, New England Biolabs, Inc., Ipswich, MA, United States of America
| | - Gregory J. S. Lohman
- Research Division, New England Biolabs, Inc., Ipswich, MA, United States of America
- * E-mail:
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34
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Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Entwicklung einer DNA-Polymerase für die direkte m6A-Sequenzierung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joos Aschenbrenner
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Stephan Werner
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudingerweg 5 55128 Mainz Deutschland
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie, Articulaire, IMoPA, UMR7365 CNRS-UL; Biopôle de L'Université de Lorraine; 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Martina Adam
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie, Articulaire, IMoPA, UMR7365 CNRS-UL; Biopôle de L'Université de Lorraine; 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Mark Helm
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudingerweg 5 55128 Mainz Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Konstanz Research School Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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35
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Song Y, Kilburn D, Song JH, Cheng Y, Saeui CT, Cheung DG, Croce CM, Yarema KJ, Meltzer SJ, Liu KJ, Wang TH. Determination of absolute expression profiles using multiplexed miRNA analysis. PLoS One 2017; 12:e0180988. [PMID: 28704432 PMCID: PMC5509254 DOI: 10.1371/journal.pone.0180988] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/23/2017] [Indexed: 12/19/2022] Open
Abstract
Accurate measurement of miRNA expression is critical to understanding their role in gene expression as well as their application as disease biomarkers. Correct identification of changes in miRNA expression rests on reliable normalization to account for biological and technological variance between samples. Ligo-miR is a multiplex assay designed to rapidly measure absolute miRNA copy numbers, thus reducing dependence on biological controls. It uses a simple 2-step ligation process to generate length coded products that can be quantified using a variety of DNA sizing methods. We demonstrate Ligo-miR's ability to quantify miRNA expression down to 20 copies per cell sensitivity, accurately discriminate between closely related miRNA, and reliably measure differential changes as small as 1.2-fold. Then, benchmarking studies were performed to show the high correlation between Ligo-miR, microarray, and TaqMan qRT-PCR. Finally, Ligo-miR was used to determine copy number profiles in a number of breast, esophageal, and pancreatic cell lines and to demonstrate the utility of copy number analysis for providing layered insight into expression profile changes.
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Affiliation(s)
- Yunke Song
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Duncan Kilburn
- Circulomics Inc, Baltimore, Maryland, United States of America
- * E-mail: (DK); (TW)
| | - Jee Hoon Song
- Department of Medicine (GI Division) and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yulan Cheng
- Department of Medicine (GI Division) and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christopher T. Saeui
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Douglas G. Cheung
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Kevin J. Yarema
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Stephen J. Meltzer
- Department of Medicine (GI Division) and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kelvin J. Liu
- Circulomics Inc, Baltimore, Maryland, United States of America
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, United States of America
- Center of Cancer Nanotechnology Excellence, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DK); (TW)
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36
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Wang X, Chen F, Zhang D, Zhao Y, Wei J, Wang L, Song S, Fan C, Zhao Y. Single copy-sensitive electrochemical assay for circulating methylated DNA in clinical samples with ultrahigh specificity based on a sequential discrimination-amplification strategy. Chem Sci 2017; 8:4764-4770. [PMID: 28959399 PMCID: PMC5603958 DOI: 10.1039/c7sc01035d] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/15/2017] [Indexed: 12/18/2022] Open
Abstract
Tumor-related circulating methylated DNA represents only a small fraction of the total DNA in clinical samples (e.g. plasma), challenging the accurate analysis of specific DNA methylation patterns. Yet conventional assays based on the real-time quantitative methylation-specific PCR (qMSP) are generally limited in detection sensitivity and specificity due to its non-specific amplification interference including primer dimers and off-target amplification. Here we propose a single copy-sensitive electrochemical assay for circulating methylated DNA with ultrahigh specificity on the basis of a sequential discrimination-amplification strategy. Methylated DNA rather than unmethylated DNA in a bisulfite-modified sample is identified and amplified by the asymmetric MSP to generate abundant biotin-labeled single-stranded amplicons with reduced primer-dimer artifacts. Self-assembled tetrahedral DNA probes, which are readily decorated on an electrode surface as nanostructured probes with ordered orientation and well controlled spacing, enable the highly efficient hybridization of the specific single-stranded amplicons due to greatly increased target accessibility and significantly decreased noise. The interfacial hybridization event is quantitatively translated into electrochemical signals utilizing an enzymatic amplification. The proposed assay integrates dual sequence discrimination processes and cascade signal amplification processes, achieving the identification of as few as one methylated DNA molecule in the presence of a 1000-fold excess of unmethylated alleles. Furthermore, the excellent assay performance enables tumor related methylation detection in lung cancer patients with 200 microlitre plasma samples. The results are in good consistency with those of clinical diagnosis, whereas the conventional qMSP failed to detect the corresponding methylation pattern of these clinically confirmed positive patients in such trace amounts of samples.
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Affiliation(s)
- Xuyao Wang
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Dexin Zhang
- Department of Respiratory Medicine , The Second Affiliated Hospital of Medical College , Xi'an Jiaotong University , Xiwu Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Lihua Wang
- Division of Physical Biology , Bioimaging Center , Shanghai Synchrotron Radiation Facility , CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , P. R. China
| | - Shiping Song
- Division of Physical Biology , Bioimaging Center , Shanghai Synchrotron Radiation Facility , CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , P. R. China
| | - Chunhai Fan
- Division of Physical Biology , Bioimaging Center , Shanghai Synchrotron Radiation Facility , CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
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37
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Bauer RJ, Jurkiw TJ, Evans TC, Lohman GJS. Rapid Time Scale Analysis of T4 DNA Ligase-DNA Binding. Biochemistry 2017; 56:1117-1129. [PMID: 28165732 DOI: 10.1021/acs.biochem.6b01261] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA ligases, essential to both in vivo genome integrity and in vitro molecular biology, catalyze phosphodiester bond formation between adjacent 3'-OH and 5'-phosphorylated termini in dsDNA. This reaction requires enzyme self-adenylylation, using ATP or NAD+ as a cofactor, and AMP release concomitant with phosphodiester bond formation. In this study, we present the first fast time scale binding kinetics of T4 DNA ligase to both nicked substrate DNA (nDNA) and product-equivalent non-nicked dsDNA, as well as binding and release kinetics of AMP. The described assays utilized a fluorescein-dT labeled DNA substrate as a reporter for ligase·DNA interactions via stopped-flow fluorescence spectroscopy. The analysis revealed that binding to nDNA by the active adenylylated ligase occurs in two steps, an initial rapid association equilibrium followed by a transition to a second bound state prior to catalysis. Furthermore, the ligase binds and dissociates from nicked and nonsubstrate dsDNA rapidly with initial association affinities on the order of 100 nM regardless of enzyme adenylylation state. DNA binding occurs through a two-step mechanism in all cases, confirming prior proposals of transient binding followed by a transition to a productive ligase·nDNA (Lig·nDNA) conformation but suggesting that weaker nonproductive "closed" complexes are formed as well. These observations demonstrate the mechanistic underpinnings of competitive inhibition by rapid binding of nonsubstrate DNA, and of substrate inhibition by blocking of the self-adenylylation reaction through nick binding by deadenylylated ligase. Our analysis further reveals that product release is not the rate-determining step in turnover.
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Affiliation(s)
- Robert J Bauer
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
| | - Thomas J Jurkiw
- University of Michigan Medical School , Ann Arbor, Michigan 48109-0600, United States
| | - Thomas C Evans
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
| | - Gregory J S Lohman
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
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38
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Pergolizzi G, Wagner GK, Bowater RP. Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. Biosci Rep 2016; 36:00391. [PMID: 27582505 PMCID: PMC5052709 DOI: 10.1042/bsr20160003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide ( β -NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD+ affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.
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Affiliation(s)
- Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, N/A, United Kingdom
| | - Gerd K Wagner
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London, N/A, United Kingdom
| | - Richard Peter Bowater
- School of Biological Sciences, University of East Anglia, Norwich, N/A, NR4 7TJ, United Kingdom
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39
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The Inhibitory Effect of Non-Substrate and Substrate DNA on the Ligation and Self-Adenylylation Reactions Catalyzed by T4 DNA Ligase. PLoS One 2016; 11:e0150802. [PMID: 26954034 PMCID: PMC4782999 DOI: 10.1371/journal.pone.0150802] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/19/2016] [Indexed: 02/02/2023] Open
Abstract
DNA ligases are essential both to in vivo replication, repair and recombination processes, and in vitro molecular biology protocols. Prior characterization of DNA ligases through gel shift assays has shown the presence of a nick site to be essential for tight binding between the enzyme and its dsDNA substrate, with no interaction evident on dsDNA lacking a nick. In the current study, we observed a significant substrate inhibition effect, as well as the inhibition of both the self-adenylylation and nick-sealing steps of T4 DNA ligase by non-nicked, non-substrate dsDNA. Inhibition by non-substrate DNA was dependent only on the total DNA concentration rather than the structure; with 1 μg/mL of 40-mers, 75-mers, or circular plasmid DNA all inhibiting ligation equally. A >15-fold reduction in T4 DNA ligase self-adenylylation rate when in the presence of high non-nicked dsDNA concentrations was observed. Finally, EMSAs were utilized to demonstrate that non-substrate dsDNA can compete with nicked dsDNA substrates for enzyme binding. Based upon these data, we hypothesize the inhibition of T4 DNA ligase by non-nicked dsDNA is direct evidence for a two-step nick-binding mechanism, with an initial, nick-independent, transient dsDNA-binding event preceding a transition to a stable binding complex in the presence of a nick site.
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Chauleau M, Shuman S. Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD+-dependent DNA ligase (LigA). Nucleic Acids Res 2016; 44:2298-309. [PMID: 26857547 PMCID: PMC4797296 DOI: 10.1093/nar/gkw049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 01/18/2016] [Indexed: 11/15/2022] Open
Abstract
Escherichia coli DNA ligase (EcoLigA) repairs 3′-OH/5′-PO4 nicks in duplex DNA via reaction of LigA with NAD+ to form a covalent LigA-(lysyl-Nζ)–AMP intermediate (step 1); transfer of AMP to the nick 5′-PO4 to form an AppDNA intermediate (step 2); and attack of the nick 3′-OH on AppDNA to form a 3′-5′ phosphodiester (step 3). A distinctive feature of EcoLigA is its stimulation by ammonium ion. Here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealing by EcoLigA–AMP. For substrates with correctly base-paired 3′-OH/5′-PO4 nicks, kstep2 was fast (6.8–27 s−1) and similar to kstep3 (8.3–42 s−1). Absent ammonium, kstep2 and kstep3 were 48-fold and 16-fold slower, respectively. EcoLigA was exquisitely sensitive to 3′-OH base mispairs and 3′ N:abasic lesions, which elicited 1000- to >20000-fold decrements in kstep2. The exception was the non-canonical 3′ A:oxoG configuration, which EcoLigA accepted as correctly paired for rapid sealing. These results underscore: (i) how EcoLigA requires proper positioning of the nick 3′ nucleoside for catalysis of 5′ adenylylation; and (ii) EcoLigA's potential to embed mutations during the repair of oxidative damage. EcoLigA was relatively tolerant of 5′-phosphate base mispairs and 5′ N:abasic lesions.
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Affiliation(s)
- Mathieu Chauleau
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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Greenough L, Schermerhorn KM, Mazzola L, Bybee J, Rivizzigno D, Cantin E, Slatko BE, Gardner AF. Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes. Nucleic Acids Res 2015; 44:e15. [PMID: 26365239 PMCID: PMC4737176 DOI: 10.1093/nar/gkv899] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/28/2015] [Indexed: 01/26/2023] Open
Abstract
Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid, high-throughput fluorescence capillary gel electrophoresis method as an alternative to traditional polyacrylamide gel electrophoresis to characterize nucleic acid metabolic enzymes. The principles of assay design described here can be applied to nearly any enzyme system that acts on a fluorescently labeled oligonucleotide substrate. Herein, we describe several assays using this core capillary gel electrophoresis methodology to accelerate study of nucleic acid enzymes. First, assays were designed to examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement synthesis and 3′-5′ exonuclease activity. Next, DNA repair activities of DNA ligase, flap endonuclease and RNase H2 were monitored. In addition, a multicolor assay that uses four different fluorescently labeled substrates in a single reaction was implemented to characterize GAN nuclease specificity. Finally, a dual-color fluorescence assay to monitor coupled enzyme reactions during Okazaki fragment maturation is described. These assays serve as a template to guide further technical development for enzyme characterization or nucleoside and non-nucleoside inhibitor screening in a high-throughput manner.
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Affiliation(s)
| | | | | | - Joanna Bybee
- From New England Biolabs, Inc., Ipswich, MA 01938, USA
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