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Hu K, Sun W, Chen H, Luo J, Song Z, An R, Komiyama M, Liang X. Formation of an instantaneous nick for highly efficient adenylation of oligonucleotides by ligase without subsequent jointing. Chem Commun (Camb) 2024; 60:2942-2945. [PMID: 38374791 DOI: 10.1039/d4cc00590b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
By forming a nick at the adenylation site instantaneously, nucleic acids are efficiently adenylated by T4 DNA ligase. The subsequent ligation is successfully suppressed in terms of rapid conversion of the instantaneous nick to a more stable gap. It is helpful to understand enzymatic ligation dynamics, and the adenylated products can be used for various practical applications.
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Affiliation(s)
- Kunling Hu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Wenhua Sun
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Hui Chen
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Jian Luo
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Ziting Song
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Ran An
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao, P. R. China
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Xingguo Liang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao, P. R. China
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2
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Li B, Wang C. Endonuclease IV and T4 ligase enhanced detection of mutations in low abundance. Analyst 2024; 149:1050-1054. [PMID: 38231135 DOI: 10.1039/d3an02083e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
We propose a mutant detection approach based on endonuclease IV and DNA ligase in combination with qPCR. The enzymes functioned cooperatively to facilitate PCR for low abundance DNA detection. We demonstrate that our approach can distinguish mutations as low as 0.01%, indicating the potential application of this strategy in early cancer diagnosis.
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Affiliation(s)
- Bo Li
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China.
| | - Chunyan Wang
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China.
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3
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Gao L, Zhou Y, Cao L, Hu Z, Mao X, Zhang H, Zhang M, Yin H, Ai S. NAD + mediated photoelectrochemical biosensor for histone deacetylase Sirt1 detection based on CuO-BiVO 4-AgNCs heterojunction and hybridization chain reaction amplification. Anal Chim Acta 2023; 1284:341989. [PMID: 37996156 DOI: 10.1016/j.aca.2023.341989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Histone deacetylate Sirt1 has been involved in many important biological processes and is closely related to the occurrence and development of many diseases. Therefore, the accurate detection of Sirt1 is of great significance for the diagnosis and treatment of diseases caused by Sirt1 and the development of related drugs. RESULTS In this work, a photoelectrochemical biosensor was developed for Sirt1 detection based on the NAD + mediated Sirt1 recognition and E. Coli DNA ligase activity. CuO-BiVO4p-n heterojunction was employed as the photoactive material, rolling circle amplification (RCA), hybridization chain reaction (HCR) and AgNCs were used as triple signal amplifications. As a bifunctional cofactor, NAD+ played a crucial role for Sirt1 detection, where the peptide deacetylation catalyzed by Sirt1 consumed NAD+, and the decreased amount of NAD + inhibited the activity of E. Coli DNA ligase, leading to the failure on RCA reaction, and improving the HCR reaction. Finally, AgNCs were generated using C-rich DNA as carrier. The surface plasmon effect of AgNCs and its heterojunction with CuO and BiVO4 accelerated the transfer rate of photogenerated carriers and improved the photocurrent signal. When the detection range was 0.001-200 nM, the detection limit of the biosensor was 0.76 pM (S/N = 3). SIGNIFICANCE The applicability of the method was evaluated by studying the effects of known inhibitors nicotinamide and environmental pollutant halogenated carbazole on Sirt1 enzyme activity. The results showed that this method can be used as a new platform for screening Sirt1 enzyme inhibitors, and also provided a new biomarker for evaluating the ecotoxicological effects of environmental pollutants.
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Affiliation(s)
- Lanlan Gao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China.
| | - Lulu Cao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Zhenyong Hu
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Xinyue Mao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Haowei Zhang
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Miao Zhang
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Huanshun Yin
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China.
| | - Shiyun Ai
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
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4
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Song YL, He XL, Li Y, Wang M, Jiang M, Xu L, Yu X. Homogeneous detection of viral nucleic acid via selective recognition proximity ligation and signal amplification with T7 transcription and CRISPR/Cas12a system. Anal Chim Acta 2023; 1280:341881. [PMID: 37858564 DOI: 10.1016/j.aca.2023.341881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/23/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
The synthetic biology has employed the synthetic gene networks through engineering to construct various functions in biological systems. However, the use of gene circuits to create sensors for detecting low-abundance targets has been limited due to the lack of signal amplification strategies beyond direct output of detection signals. To address this issue, we introduce a novel method utilizing Selective Recognition Proximity Ligation and signal amplification with T7 Transcription and CRISPR/Cas12a system (SRPL-TraCs), which permits the incorporation of cell-free gene circuits with signal amplification and enables the construction of high-order cascade signal amplification strategy to detect biomarkers in homogeneous systems. Specifically, the SRPL-TraCs utilizes selective recognition proximity ligation with high-fidelity T4 DNA ligase and generates a unique crRNA via T7 transcription, along with target-activated Cas12a/crRNA system to achieve excellent specificity for HIV-1 DNA. With this straightforward synthetic biology-based method, the proposed SRPL-TraCs has the potential to detect numerous other interesting targets beyond the nucleic acids.
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Affiliation(s)
- Yong-Li Song
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiang-Lan He
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yong Li
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ming Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Xu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
| | - Xu Yu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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5
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Fernandes A, Williamson A, Matias PM, Moe E. Structure/function studies of the NAD +-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding. Extremophiles 2023; 27:26. [PMID: 37712998 PMCID: PMC10504179 DOI: 10.1007/s00792-023-01309-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023]
Abstract
Bacterial NAD+-dependent DNA ligases (LigAs) are enzymes involved in replication, recombination, and DNA-repair processes by catalyzing the formation of phosphodiester bonds in the backbone of DNA. These multidomain proteins exhibit four modular domains, that are highly conserved across species, with the BRCT (breast cancer type 1 C-terminus) domain on the C-terminus of the enzyme. In this study, we expressed and purified both recombinant full-length and a C-terminally truncated LigA from Deinococcus radiodurans (DrLigA and DrLigA∆BRCT) and characterized them using biochemical and X-ray crystallography techniques. Using seeds of DrLigA spherulites, we obtained ≤ 100 µm plate crystals of DrLigA∆BRCT. The crystal structure of the truncated protein was obtained at 3.4 Å resolution, revealing DrLigA∆BRCT in a non-adenylated state. Using molecular beacon-based activity assays, we demonstrated that DNA ligation via nick sealing remains unaffected in the truncated DrLigA∆BRCT. However, DNA-binding assays revealed a reduction in the affinity of DrLigA∆BRCT for dsDNA. Thus, we conclude that the flexible BRCT domain, while not critical for DNA nick-joining, plays a role in the DNA binding process, which may be a conserved function of the BRCT domain in LigA-type DNA ligases.
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Affiliation(s)
- Andreia Fernandes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Adele Williamson
- Department of Chemistry, UiT-The Arctic University of Norway, Tromsø, Norway
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Institute of Experimental and Technological Biology (IBET), Oeiras, Portugal
| | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal.
- Department of Chemistry, UiT-The Arctic University of Norway, Tromsø, Norway.
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Lokhande KB, Shrivastava A, Singh A. In silico
discovery of potent inhibitors against monkeypox's major structural proteins. J Biomol Struct Dyn 2023; 41:14259-14274. [PMID: 36841550 DOI: 10.1080/07391102.2023.2183342] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/07/2023] [Indexed: 02/27/2023]
Abstract
Monkeypox virus (MPXV) outbreak in non-endemic countries is a worldwide public health emergency. An enveloped double-stranded DNA virus belongs to the genus Orth poxvirus. A viral zoonotic infection known as monkeypox has been a serious risk to public health, especially in Africa. However, it has recently spread to other continents, so it might soon become a worldwide problem. There is an increased risk of transmission of the virus because there is a lack of effective treatment that cures the disease. To stop the multi-country outbreak from spreading, it is important to discover effective medications urgently. The objective of the current study is to swiftly find new treatments for the monkeypox virus using advanced computational approaches. By investigating five potential MPXV targets (DNA ligase, Palmytilated Extracellular Enveloped Virus (EEV) membrane protein, Scaffold protein D13, Thymidylate Kinase, and Viral core cysteine proteinase), this research was carried out using cutting-edge computational techniques against human monkeypox virus infection. Here we present the accurate 3D structures and their binding cavities of the selected targets with higher confidence using AlphaFold 2 and SiteMap analysis. Molecular docking and MD simulation analysis revealed the top five potential lead compounds with higher binding affinity and stability toward selected targets. Binding free energy calculations and other essential dynamics analysis supports the finding. The selected lead compounds utilizing virtual screening and drug repurposing approach reported in this study are beneficial for medical scientists and experimental biologists in drug development for the treatment of human MPXV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kiran Bharat Lokhande
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Ashutosh Singh
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
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8
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Liao L, Yao J, Yuan R, Xiang Y, Jiang B. Lighting-up aptamer transcriptional amplification for highly sensitive and label-free FEN1 detection. Spectrochim Acta A Mol Biomol Spectrosc 2023; 284:121760. [PMID: 36030671 DOI: 10.1016/j.saa.2022.121760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Specific and sensitive detection of flap endonuclease 1 (FEN1), an enzyme biomarker involved in DNA replications and several metabolic pathways, is of high values for the diagnosis of various cancers. In this work, a fluorescence strategy based on transcriptional amplification of lighting-up aptamers for label-free, low background and sensitive monitoring of FEN1 is developed. FEN1 cleaves the 5' flap of the DNA complex probe with double flaps to form a notched dsDNA, which is ligated by T4 DNA ligase to yield fully complementary dsDNA. Subsequently, T7 RNA polymerase binds the promoter region to initiate cyclic transcriptional generation of many RNA aptamers that associate with the malachite green dye to yield highly amplified fluorescence for detecting FEN1 with detection limit as low as 0.22 pM in a selective way. In addition, the method can achieve diluted serum monitoring of low concentrations of FEN1, exhibiting its potential for the diagnosis of early-stage cancers.
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Affiliation(s)
- Lei Liao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Jianglong Yao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Williams JS, Tumbale PP, Arana ME, Rana JA, Williams RS, Kunkel TA. High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication. Nat Commun 2021; 12:482. [PMID: 33473124 PMCID: PMC7817679 DOI: 10.1038/s41467-020-20800-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
DNA ligase 1 (LIG1, Cdc9 in yeast) finalizes eukaryotic nuclear DNA replication by sealing Okazaki fragments using DNA end-joining reactions that strongly discriminate against incorrectly paired DNA substrates. Whether intrinsic ligation fidelity contributes to the accuracy of replication of the nuclear genome is unknown. Here, we show that an engineered low-fidelity LIG1Cdc9 variant confers a novel mutator phenotype in yeast typified by the accumulation of single base insertion mutations in homonucleotide runs. The rate at which these additions are generated increases upon concomitant inactivation of DNA mismatch repair, or by inactivation of the Fen1Rad27 Okazaki fragment maturation (OFM) nuclease. Biochemical and structural data establish that LIG1Cdc9 normally avoids erroneous ligation of DNA polymerase slippage products, and this protection is compromised by mutation of a LIG1Cdc9 high-fidelity metal binding site. Collectively, our data indicate that high-fidelity DNA ligation is required to prevent insertion mutations, and that this may be particularly critical following strand displacement synthesis during the completion of OFM.
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Affiliation(s)
- Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Percy P Tumbale
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Mercedes E Arana
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Julian A Rana
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.
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11
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Li D, Zheng C, Zhou J, Chen B, Xu R, Yuan W, Zheng E, Liang W, Yang Y, He L, Shi J, Yan C, Wang X, Chen J. pGP-B2E, a Recombinant Compatible TA/TB-Ligation Vector for Rapid and Inexpensive Gene Cloning. Mol Biotechnol 2019; 62:56-66. [PMID: 31749084 DOI: 10.1007/s12033-019-00226-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA cloning is the basic step for different fields of life science, and many efforts have been made to simplify this procedure. In this study, we report two general purpose plasmids (pGP), pGP-XB2E and pGP-B2E, for rapid and cost-effective construct of basic clones. The BciVI and XcmI cleavage sites are designed in pGP-XB2E to test plasmid linearization efficiency. The plasmid has better linearization efficiency by using BciVI which could almost completely digest 2 μg plasmid in 10 min with only one-tenth the recommended enzyme concentration. In order to further optimize the pGP-XB2E, a new plasmid, pGP-B2E, which removed XcmI cleavage site was designed. This vector is highly efficient for cloning PCR products up to 1812 bp, and the number of colonies was about five times that of pGP-XB2E. In addition to TA cloning, blunt-end PCR products with T ended in the primer could be positively linked to the T-vector pGP-B2E without A-tailing treatment (TB cloning). Moreover, as an entry vector, pGP-B2E was also compatible for gateway recombination reaction without frameshift mutations. In general, this vector provides a universal, quick, and cost-efficient method for basic molecular cloning.
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Affiliation(s)
- Dongyue Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, People's Republic of China
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Chao Zheng
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, 712100, People's Republic of China
| | - Jie Zhou
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Bin Chen
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Rumeng Xu
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Wenxia Yuan
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Ersong Zheng
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Weifang Liang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, People's Republic of China
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Yong Yang
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Lijuan He
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Jianghua Shi
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Chengqi Yan
- Institute of Biotechnology, Ningbo Academy of Agricultural Sciences, Ningbo, 315101, People's Republic of China
| | - Xuming Wang
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.
| | - Jianping Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, People's Republic of China.
- State Key Laboratory of Breeding Base for Zhejiang Agricultural Products Quality and Safety, MOA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.
- Institute of Plant Virology, Ningbo University, Ningbo, People's Republic of China.
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12
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Abstract
DNA double-strand breaks (DSBs) are harmful lesions leading to genomic instability or diversity. Non-homologous end-joining (NHEJ) is a prominent DSB repair pathway, which has long been considered to be error-prone. However, recent data have pointed to the intrinsic precision of NHEJ. Three reasons can account for the apparent fallibility of NHEJ: 1) the existence of a highly error-prone alternative end-joining process; 2) the adaptability of canonical C-NHEJ (Ku- and Xrcc4/ligase IV-dependent) to imperfect complementary ends; and 3) the requirement to first process chemically incompatible DNA ends that cannot be ligated directly. Thus, C-NHEJ is conservative but adaptable, and the accuracy of the repair is dictated by the structure of the DNA ends rather than by the C-NHEJ machinery. We present data from different organisms that describe the conservative/versatile properties of C-NHEJ. The advantages of the adaptability/versatility of C-NHEJ are discussed for the development of the immune repertoire and the resistance to ionizing radiation, especially at low doses, and for targeted genome manipulation.
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Affiliation(s)
- Mireille Bétermier
- CNRS, Centre de Génétique Moléculaire, UPR3404, Gif-sur-Yvette, France
- CNRS, Centre de Recherches de Gif-sur-Yvette, FRC3115, Gif-sur-Yvette, France
- Université Paris-Sud, Département de Biologie, Orsay, France
| | - Pascale Bertrand
- CEA, DSV, Institut de Radiobiologie Moléculaire et Cellulaire, Laboratoire Réparation et Vieillissement, Fontenay-aux-Roses, France
- UMR 8200 CNRS, Villejuif, France
| | - Bernard S. Lopez
- Université Paris-Sud, Département de Biologie, Orsay, France
- UMR 8200 CNRS, Villejuif, France
- Institut de Cancérologie, Gustave Roussy, Villejuif, France
- * E-mail:
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13
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Reyon D, Maeder ML, Khayter C, Tsai SQ, Foley JE, Sander JD, Joung JK. Engineering customized TALE nucleases (TALENs) and TALE transcription factors by fast ligation-based automatable solid-phase high-throughput (FLASH) assembly. Curr Protoc Mol Biol 2013; Chapter 12:Unit 12.16. [PMID: 23821439 PMCID: PMC3767754 DOI: 10.1002/0471142727.mb1216s103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Customized DNA-binding domains made using transcription activator-like effector (TALE) repeats are rapidly growing in importance as widely applicable research tools. TALE nucleases (TALENs), composed of an engineered array of TALE repeats fused to the FokI nuclease domain, have been used successfully for directed genome editing in various organisms and cell types. TALE transcription factors (TALE-TFs), consisting of engineered TALE repeat arrays linked to a transcriptional regulatory domain, have been used to up- or downregulate expression of endogenous genes in human cells and plants. This unit describes a detailed protocol for the recently described fast ligation-based automatable solid-phase high-throughput (FLASH) assembly method. FLASH enables automated high-throughput construction of engineered TALE repeats using an automated liquid handling robot or manually using a multichannel pipet. Using the automated approach, a single researcher can construct up to 96 DNA fragments encoding TALE repeat arrays of various lengths in a single day, and then clone these to construct sequence-verified TALEN or TALE-TF expression plasmids in a week or less. Plasmids required for FLASH are available by request from the Joung lab (http://eGenome.org). This unit also describes improvements to the Zinc Finger and TALE Targeter (ZiFiT Targeter) web server (http://ZiFiT.partners.org) that facilitate the design and construction of FLASH TALE repeat arrays in high throughput.
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Affiliation(s)
- Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Morgan L. Maeder
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115 USA
| | - Cyd Khayter
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
| | - Shengdar Q. Tsai
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Jonathan E. Foley
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
| | - Jeffry D. Sander
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
- Correspondence to: or
| | - J. Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115 USA
- Correspondence to: or
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14
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Gao F, Zhou H, Li W, Zhang X. Detection of ligation products of DNA linkers with 5'-OH ends by denaturing PAGE silver stain. PLoS One 2012; 7:e39251. [PMID: 22761747 PMCID: PMC3384673 DOI: 10.1371/journal.pone.0039251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
To explore if DNA linkers with 5′-hydroxyl (OH) ends could be joined by commercial T4 and E. coli DNA ligase, these linkers were synthesized by using the solid-phase phosphoramidite method and joined by using commercial T4 and E. coli DNA ligases. The ligation products were detected by using denaturing PAGE silver stain and PCR method. About 0.5–1% of linkers A–B and E–F, and 0.13–0.5% of linkers C–D could be joined by T4 DNA ligases. About 0.25–0.77% of linkers A–B and E–F, and 0.06–0.39% of linkers C–D could be joined by E. coli DNA ligases. A 1-base deletion (-G) and a 5-base deletion (-GGAGC) could be found at the ligation junctions of the linkers. But about 80% of the ligation products purified with a PCR product purification kit did not contain these base deletions, meaning that some linkers had been correctly joined by T4 and E. coli DNA ligases. In addition, about 0.025–0.1% of oligo 11 could be phosphorylated by commercial T4 DNA ligase. The phosphorylation products could be increased when the phosphorylation reaction was extended from 1 hr to 2 hrs. We speculated that perhaps the linkers with 5′-OH ends could be joined by T4 or E. coli DNA ligase in 2 different manners: (i) about 0.025–0.1% of linkers could be phosphorylated by commercial T4 DNA ligase, and then these phosphorylated linkers could be joined to the 3′-OH ends of other linkers; and (ii) the linkers could delete one or more nucleotide(s) at their 5′-ends and thereby generated some 5′-phosphate ends, and then these 5′-phosphate ends could be joined to the 3′-OH ends of other linkers at a low efficiency. Our findings may probably indicate that some DNA nicks with 5′-OH ends can be joined by commercial T4 or E. coli DNA ligase even in the absence of PNK.
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Affiliation(s)
- Feng Gao
- Department of Anal and Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Huafu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Li
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
- * E-mail:
| | - Xuerong Zhang
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
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15
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Li Y, Tang J, Pan Z, Xiao P, Zhou D, Jin L, Pan M, Lu Z. Single nucleotide polymorphism genotyping and point mutation detection by ligation on microarrays. J Nanosci Nanotechnol 2011; 11:994-1003. [PMID: 21456129 DOI: 10.1166/jnn.2011.3056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Based on the principle of sequencing by ligation, a novel method referred to as "Minisequencing by ligation" for detecting known single nucleotide variant in high-throughput assay formats is reported in this article. By designing a sequencing primer and fluorescently labeled probes each with a "discriminating" base according to the single base variation, this method can be used to analyze single nucleotide polymorphism (SNP) or point mutation in a number of samples in parallel. In our current study, three known nucleotides at a given position of three DNA templates with different CG contents are firstly genotyped on aldehyde-modified slide to testify the feasibility and optimize the reaction conditions. Then, by performing ligation reaction between phosphorylated 5' end of the sequencing primer and hydroxylated 3' end of the labeled probe or phosphorylated 5' end of the labeled probe and hydroxylated 3' end of the sequencing primer, a SNP locus (rs1800497 (C/T)) and a point mutation (Mt1555 (A/G)) have been accurately detected on aldehyde-modified microarray and Sepharose beads in acrylamide gel, respectively. It has demonstrated that "minisequencing by ligation," as a promising methodology, can perform point mutation and SNP analysis in a simple, cost-effective, robust and high-throughput way.
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Affiliation(s)
- Yanqiang Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
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16
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Abstract
We established a novel method, Gene Expression Profiling via Multigene Concatemers (MgC-GEP), to study multigene expression patterns simultaneously. This method consists of the following steps: (1) cDNA was obtained using specific reverse primers containing an adaptor. (2) During the initial 1-3 cycles of polymerase chain reaction (PCR), the products containing universal adaptors with digestion sites at both termini were amplified using specific forward and reverse primers containing the adaptors. (3) In the subsequent 4-28 cycles, the universal adaptors were used as primers to yield products. (4) The products were digested and ligated to produce concatemers. (5) The concatemers were cloned into the vector and sequenced. Then, the occurrence of each gene tag was determined. To validate MgC-GEP, we analyzed 20 genes in Saccharomyces cerevisiae induced by weak acid using MgC-GEP combined with real-time reverse transcription (RT)-PCR. Compared with the results of real-time RT-PCR and the previous reports of microarray analysis, MgC-GEP can precisely determine the transcript levels of multigenes simultaneously. Importantly, MgC-GEP is a cost effective strategy that can be widely used in most laboratories without specific equipment. MgC-GEP is a potentially powerful tool for multigene expression profiling, particularly for moderate-throughput analysis.
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Affiliation(s)
- Kai Jin
- Genetic Engineering Research Center, School of Bioengineering, Chongqing University, Chongqing, People's Republic of China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, People's Republic of China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, People's Republic of China
| | - Xiaoli Zheng
- Genetic Engineering Research Center, School of Bioengineering, Chongqing University, Chongqing, People's Republic of China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, People's Republic of China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, People's Republic of China
| | - Yuxian Xia
- Genetic Engineering Research Center, School of Bioengineering, Chongqing University, Chongqing, People's Republic of China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, People's Republic of China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, People's Republic of China
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17
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Pal S, Polyak SJ, Bano N, Qiu WC, Carithers RL, Shuhart M, Gretch DR, Das A. Hepatitis C virus induces oxidative stress, DNA damage and modulates the DNA repair enzyme NEIL1. J Gastroenterol Hepatol 2010; 25:627-34. [PMID: 20074151 PMCID: PMC3565844 DOI: 10.1111/j.1440-1746.2009.06128.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Hepatitis C virus (HCV)-induced chronic inflammation may induce oxidative stress which could compromise the repair of damaged DNA, rendering cells more susceptible to spontaneous or mutagen-induced alterations, the underlying cause of liver cirrhosis and hepatocellular carcinoma. In the current study we examined the induction of reactive oxygen species (ROS) resulting from HCV infection and evaluated its effect on the host DNA damage and repair machinery. METHODS HCV infected human hepatoma cells were analyzed to determine (i) ROS, (ii) 8-oxoG and (iii) DNA glycosylases NEIL1, NEIL2, OGG1. Liver biopsies were analyzed for NEIL1. RESULTS Human hepatoma cells infected with HCV JFH-1 showed 30-60-fold increases in ROS levels compared to uninfected cells. Levels of the oxidatively modified guanosine base 8-oxoguanine (8-oxoG) were significantly increased sixfold in the HCV-infected cells. Because DNA glycosylases are the enzymes that remove oxidized nucleotides, their expression in HCV-infected cells was analyzed. NEIL1 but not OGG1 or NEIL2 gene expression was impaired in HCV-infected cells. In accordance, we found reduced glycosylase (NEIL1-specific) activity in HCV-infected cells. The antioxidant N-acetyl cystein (NAC) efficiently reversed the NEIL1 repression by inhibiting ROS induction by HCV. NEIL1 expression was also partly restored when virus-infected cells were treated with interferon (IFN). HCV core and to a lesser extent NS3-4a and NS5A induced ROS, and downregulated NEIL1 expression. Liver biopsy specimens showed significant impairment of NEIL1 levels in HCV-infected patients with advanced liver disease compared to patients with no disease. CONCLUSION Collectively, the data indicate that HCV induction of ROS and perturbation of NEIL1 expression may be mechanistically involved in progression of liver disease and suggest that antioxidant and antiviral therapies can reverse these deleterious effects of HCV in part by restoring function of the DNA repair enzyme/s.
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Affiliation(s)
- Sampa Pal
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195-7110 USA.
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18
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Wang KY, Zhao YH, Li WG. [DNA double-strand breaks repair and severe combined immunodeficiencies]. Sheng Li Ke Xue Jin Zhan 2008; 39:182-184. [PMID: 18664190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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19
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Abstract
This protocol describes a method for the one-tube preparative-scale assembly of a specific DNA molecule, the enzymatic ligation assisted by nucleases (ELAN) technique. DNA fragments in ligation reactions are capable of combining to produce numerous products. The ELAN method uses judicious choice of restriction enzyme sites coupled with simultaneous digestion and ligation reactions to create just one product, by converting off-pathway products back into substrate. The experimental parameters critical for a successful ELAN reaction are discussed, and the ordered, one-tube assembly of four DNA fragments in the presence of eight restriction enzymes is demonstrated. This technique will be useful to those performing gene construction, DNA computing, biophysics and even standard molecular cloning. Starting with reactant fragments, the protocol takes 4-16 h to produce nanogram to microgram yields, depending on the complexity of the reaction.
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Affiliation(s)
- Gregory J Cost
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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20
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Dai Q, Fong R, Saikia M, Stephenson D, Yu YT, Pan T, Piccirilli JA. Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res 2007; 35:6322-9. [PMID: 17881375 PMCID: PMC2094055 DOI: 10.1093/nar/gkm657] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Over 100 chemical types of RNA modifications have been identified in thousands of sites in all three domains of life. Recent data suggest that modifications function synergistically to mediate biological function, and that cells may coordinately modulate modification levels for regulatory purposes. However, this area of RNA biology remains largely unexplored due to the lack of robust, high-throughput methods to quantify the extent of modification at specific sites. Recently, we developed a facile enzymatic ligation-based method for detection and quantitation of methylated 2′-hydroxyl groups within RNA. Here we exploit the principles of molecular recognition and nucleic acid chemistry to establish the experimental parameters for ligation-based detection and quantitation of pseudouridine (Ψ) and N6-methyladenosine (m6A), two abundant modifications in eukaryotic rRNA/tRNA and mRNA, respectively. Detection of pseudouridylation at several sites in the large subunit rRNA derived from yeast demonstrates the feasibility of the approach for analysis of pseudouridylation in biological RNA samples.
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Affiliation(s)
- Qing Dai
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Robert Fong
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mridusmita Saikia
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - David Stephenson
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Yi-tao Yu
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joseph A. Piccirilli
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
- *To whom correspondence should be addressed. +1 773 702 9312+1 773 702 0271 Correspondence may also be addressed to Tao Pan. +1 773 702 4179+1 773 702 0439; E-mail:
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21
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Xiao SM, Li GQ, Zhou RQ, Li WH, Yang JW. Combined PCR-oligonucleotide ligation assay for detection of dairy cattle-derived Cyclospora sp. Vet Parasitol 2007; 149:185-90. [PMID: 17850971 DOI: 10.1016/j.vetpar.2007.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 07/22/2007] [Accepted: 08/01/2007] [Indexed: 11/22/2022]
Abstract
A rapid and sensitive assay for the detection of Cyclospora species in dairy cattle faecal specimens has been developed. The method utilizes a nested PCR to amplify a 168-bp DNA fragment of the 18S rRNA gene of cattle-derived Cyclospora sp. and an enzyme-linked immunosorbent assay (ELISA)-based oligonucleotide ligation assay (OLA) to detect the amplified product. In this study, the OLA technique was compared with conventional gel electrophoresis for the detection of amplified product. In evaluating the PCR-OLA for Cyclospora sp. and non-Cyclospora parasites, A(405) reading value for Cyclospora species was significantly higher than those for non-Cyclospora control. At known concentrations of purified amplicons from cattle-derived Cyclospora sp., the OLA was able to detect more than 0.5 ng of the amplified DNA. Of 168 clinical specimens collected from four dairy cattle farms, 6 were positive by both PCR-gel electrophoresis and the PCR-OLA procedure, and 2 were positive only by PCR-OLA, indicating the PCR-OLA procedure was more sensitive than the common way with gel electrophoresis. The results indicated that the PCR-OLA is simple, rapid and suitable in clinical detection of cattle-derived Cyclospora species.
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Affiliation(s)
- S M Xiao
- Department of Veterinary Parasitology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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22
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Kuhn H. A nonisotopic assay for unambiguous assignment of DNA glycosylase functionality. Anal Biochem 2007; 366:105-7. [PMID: 17499571 DOI: 10.1016/j.ab.2007.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Accepted: 04/04/2007] [Indexed: 11/17/2022]
Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington St., Boston, MA 02215, USA.
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23
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Abstract
Most eukaryotic mRNA precursors (pre-mRNAs) are interrupted by non-coding intervening sequences known as introns which must be precisely and efficiently removed to yield correct mature mRNAs. The process of intron excision, pre-mRNA splicing, takes place in a multicomponent ribonucleoprotein complexes which assemble in a stepwise pathway. Extensive studies, both genetic and biochemical, have revealed that numerous protein factors function to achieve fidelity in splicing, however the details of this process is poorly understood. We have developed a splicing assay system using the single molecule imaging technique to study the kinetics of the splicing reaction.
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Affiliation(s)
- Yo Ishihama
- Graduate School of Science and Engineering, Waseda University, Shinjyuku-ku, Tokyo 169-8555, Japan
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24
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Akhras MS, Thiyagarajan S, Villablanca AC, Davis RW, Nyrén P, Pourmand N. PathogenMip assay: a multiplex pathogen detection assay. PLoS One 2007; 2:e223. [PMID: 17311101 PMCID: PMC1794193 DOI: 10.1371/journal.pone.0000223] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 01/26/2007] [Indexed: 01/15/2023] Open
Abstract
The Molecular Inversion Probe (MIP) assay has been previously applied to a large-scale human SNP detection. Here we describe the PathogenMip Assay, a complete protocol for probe production and applied approaches to pathogen detection. We have demonstrated the utility of this assay with an initial set of 24 probes targeting the most clinically relevant HPV genotypes associated with cervical cancer progression. Probe construction was based on a novel, cost-effective, ligase-based protocol. The assay was validated by performing pyrosequencing and Microarray chip detection in parallel experiments. HPV plasmids were used to validate sensitivity and selectivity of the assay. In addition, 20 genomic DNA extracts from primary tumors were genotyped with the PathogenMip Assay results and were in 100% agreement with conventional sequencing using an L1-based HPV genotyping protocol. The PathogenMip Assay is a widely accessible protocol for producing and using highly discriminating probes, with experimentally validated results in pathogen genotyping, which could potentially be applied to the detection and characterization of any microbe.
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Affiliation(s)
- Michael S. Akhras
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
- Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Sreedevi Thiyagarajan
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Andrea C. Villablanca
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Pål Nyrén
- Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Nader Pourmand
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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25
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de Jong RN, Daniëls MA, Kaptein R, Folkers GE. Enzyme free cloning for high throughput gene cloning and expression. ACTA ACUST UNITED AC 2007; 7:109-18. [PMID: 17295099 DOI: 10.1007/s10969-006-9014-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 12/14/2006] [Indexed: 10/23/2022]
Abstract
Structural and functional genomics initiatives significantly improved cloning methods over the past few years. Although recombinational cloning is highly efficient, its costs urged us to search for an alternative high throughput (HTP) cloning method. We implemented a modified Enzyme Free Cloning (EFC) procedure, a PCR-only method that eliminates all variables other than PCR efficiency by circumventing enzymatic treatments. We compared the cloning efficiency of EFC with that of Ligation Independent Cloning (LIC). Both methods are well suited for HTP cloning, but EFC yields three times more transformants and a cloning efficiency of 91%, comparable with recombinational cloning methods and significantly better than LIC (79%). EFC requires only nanogram amounts of both vector and insert, does not require highly competent cells and is, in contrast to LIC, largely insensitive to variations in PCR product concentration. Automated protein expression screening of expression strains directly transformed with EFC reactions showed, that the traditional preceding step via a cloning strain can be circumvented. EFC proves an efficient and robust HTP cloning method, that is compatible with existing Ligation Independent Cloning vectors, and highly suitable for automation.
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Affiliation(s)
- Rob N de Jong
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Abstract
High affinity target-binding aptamers are identified from random oligonucleotide libraries by an in vitro selection process called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Since the SELEX process includes a PCR amplification step the randomized region of the oligonucleotide libraries need to be flanked by two fixed primer binding sequences. These primer binding sites are often difficult to truncate because they may be necessary to maintain the structure of the aptamer or may even be part of the target binding motif. We designed a novel type of RNA library that carries fixed sequences which constrain the oligonucleotides into a partly double-stranded structure, thereby minimizing the risk that the primer binding sequences become part of the target-binding motif. Moreover, the specific design of the library including the use of tandem RNA Polymerase promoters allows the selection of oligonucleotides without any primer binding sequences. The library was used to select aptamers to the mirror-image peptide of ghrelin. Ghrelin is a potent stimulator of growth-hormone release and food intake. After selection, the identified aptamer sequences were directly synthesized in their mirror-image configuration. The final 44 nt-Spiegelmer, named NOX-B11-3, blocks ghrelin action in a cell culture assay displaying an IC50 of 4.5 nM at 37°C.
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Affiliation(s)
| | | | - Sven Klussmann
- To whom correspondence should be addressed. Tel: +49 30 726247 100; Fax: +49 30 726247 225;
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27
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Abstract
The proximity ligation assay (PLA) has previously been used for the sensitive and specific detection of single proteins. In order to adapt PLA methods for the detection of cell surfaces, we have generated multivalent peptide–oligonucleotide–phycoerythrin conjugates (‘burrs’) that can bind adjacent to one another on a cell surface and be ligated together to form unique amplicons. Real-time PCR detection of burr ligation events specifically identified as few as 100 Bacillus anthracis, 10 Bacillus subtilis and 1 Bacillus cereus spore. Burrs should prove to be generally useful for detecting and mapping interactions and distances between cell surface proteins.
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Affiliation(s)
| | - Andrew D. Ellington
- Institute for Cell and Molecular Biology, University of Texas at AustinAustin, TX 78712, USA
| | - Matthew Levy
- Institute for Cell and Molecular Biology, University of Texas at AustinAustin, TX 78712, USA
- To whom correspondence should be addressed. Tel: + 1 512 471 6445; Fax: +1 512 471 7014;
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28
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Douglas P, Gupta S, Morrice N, Meek K, Lees-Miller SP. DNA-PK-dependent phosphorylation of Ku70/80 is not required for non-homologous end joining. DNA Repair (Amst) 2005; 4:1006-18. [PMID: 15941674 DOI: 10.1016/j.dnarep.2005.05.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2005] [Revised: 05/03/2005] [Accepted: 05/05/2005] [Indexed: 11/30/2022]
Abstract
The Ku70/80 heterodimer is a major player in non-homologous end joining and the repair of DNA double-strand breaks. Studies suggest that once bound to a DNA double-strand break, Ku recruits the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) to form the DNA-dependent protein kinase holoenzyme complex (DNA-PK). We previously identified four DNA-PK phosphorylation sites on the Ku70/80 heterodimer: serine 6 of Ku70, serine 577 and 580 and threonine 715 of Ku80. This raised the interesting possibility that DNA-PK-dependent phosphorylation of Ku could provide a mechanism for the regulation of non-homologous end joining. Here, using mass spectrometry and phosphospecific antibodies we confirm that these sites are phosphorylated in vitro by purified DNA-PK. However, we show that neither DNA-PK nor the related protein kinase ataxia-telangiectasia mutated (ATM) is required for phosphorylation of Ku at these sites in vivo. Furthermore, Ku containing serine/threonine to alanine mutations at these sites was fully able to complement the radiation sensitivity of Ku negative mammalian cells indicating that phosphorylation at these sites is not required for non-homologous end joining. Interestingly, both Ku70 and Ku80 were phosphorylated in cells treated with the protein phosphatase inhibitor okadaic acid under conditions known to inactivate protein phosphatase 2A-like protein phosphatases. Moreover, okadaic acid-induced phosphorylation of Ku80 was inhibited by nanomolar concentrations of the protein kinase inhibitor staurosporine. These results suggest that the phosphorylation of Ku70 and Ku80 is regulated by a protein phosphatase 2A-like protein phosphatase and a staurosporine sensitive protein kinase in vivo, but that DNA-PK-mediated phosphorylation of Ku is not required for DNA double-strand break repair.
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Affiliation(s)
- Pauline Douglas
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alta., Canada T2N 4N1
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29
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Esposito D, Gillette WK, Miller DA, Taylor TE, Frank PH, Hu R, Bekisz J, Hernandez J, Cregg JM, Zoon KC, Hartley JL. Gateway cloning is compatible with protein secretion from Pichia pastoris. Protein Expr Purif 2005; 40:424-8. [PMID: 15766886 PMCID: PMC7130006 DOI: 10.1016/j.pep.2004.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Revised: 12/09/2004] [Indexed: 11/15/2022]
Abstract
Secretion of a recombinant protein from the yeast Pichia pastoris requires the presence of a signal peptide at the amino terminus. Maintaining the full amino acid sequence of the signal peptide is thought to be important for proper signal processing and protein secretion. We show that at least for one protein, a synthetic human interferon, the presence of a Gateway recombination site within the signal peptide is fully compatible with high levels of protein secretion. The amino termini of the secreted interferon proteins cloned with Gateway and cloned with restriction enzymes and ligase are identical, and the proteins were highly active in biological assays. Compatibility with Gateway cloning simplifies construction of plasmids directing secretion of recombinant proteins from P. pastoris.
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Affiliation(s)
- Dominic Esposito
- Protein Expression Laboratory, SAIC Frederick, Inc., National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA
| | - William K. Gillette
- Protein Expression Laboratory, SAIC Frederick, Inc., National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA
| | - David A. Miller
- Protein Expression Laboratory, SAIC Frederick, Inc., National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA
| | - Troy E. Taylor
- Protein Expression Laboratory, SAIC Frederick, Inc., National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA
| | - Peter H. Frank
- Protein Expression Laboratory, SAIC Frederick, Inc., National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA
| | - Renqui Hu
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg 10 Rm 4A30A, Bethesda, MD 20892, USA
| | - Joseph Bekisz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg 10 Rm 4A30A, Bethesda, MD 20892, USA
| | - Jessica Hernandez
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg 10 Rm 4A30A, Bethesda, MD 20892, USA
| | - James M. Cregg
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA
| | - Kathryn C. Zoon
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg 10 Rm 4A30A, Bethesda, MD 20892, USA
| | - James L. Hartley
- Protein Expression Laboratory, SAIC Frederick, Inc., National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA
- Corresponding author. Fax: +1 301 846 6631
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30
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Hianik T, Rybar P, Andreev SY, Oretskaya TS, Vadgama P. Detection of DNA hybridization on a liposome surface using ultrasound velocimetry and turbidimetry methods. Bioorg Med Chem Lett 2005; 14:3897-900. [PMID: 15225693 DOI: 10.1016/j.bmcl.2004.05.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Revised: 05/21/2004] [Accepted: 05/25/2004] [Indexed: 10/26/2022]
Abstract
19-mer oligonucleotides with oleylamine tethered at 3' and 5' terminal, respectively, were incorporated into unilamellar liposomes of dioleoylphosphatidylcholine (DOPC). Addition of complementary nucleotide resulted in hybridization with oligonucleotides located on different liposomes and caused liposome aggregation. Significant changes of sound velocimetry and turbidity were readily observed at 10 nM concentration of the complementary chain.
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Affiliation(s)
- Tibor Hianik
- Department of Biophysics and Chemical Physics, Comenius University, 842 48 Bratislava, Slovakia.
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31
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Abstract
Isolating the core functional elements of an RNA is normally performed during the characterization of a new RNA in order to simplify further biochemical analysis. The removal of extraneous sequence is challenging and can lead to biases that result from the incomplete sampling of deletion variants. An impartial solution to this problem is to construct a library containing a large number of deletion constructs and to select functional RNA isolates that are at least as efficient as their full-length progenitors. Here, we use nonhomologous recombination and selection to isolate the catalytic core of a pyrimidine nucleotide synthase ribozyme. A variable-length pool of approximately 10(8) recombinant molecules that included deletions, inversions, and translocations of a 271-nucleotide-long ribozyme isolate was constructed by digesting and randomly religating its DNA genome. In vitro selection for functional ribozymes was then performed in a size-dependent and a size-independent manner. The final pools had nearly equivalent catalytic rates even though their length distributions were completely different, indicating that a diverse range of deletion constructs were functionally active. Four short sequence islands, requiring as little as 81 nt of sequence, were found within all of the truncated ribozymes and could be folded into a secondary structure consisting of three helix-loops. Our findings suggest that nonhomologous recombination is a highly efficient way to isolate a ribozyme's core motif and could prove to be a useful method for evolving new ribozyme functions from pre-existing sequences in a manner that may have played an important role early in evolution.
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Affiliation(s)
- Qing S Wang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Dr., Burnaby, B.C., V5A 1S6, Canada
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32
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Komiyama M. [DNA manipulation using artificial restriction enzymes]. Tanpakushitsu Kakusan Koso 2005; 50:81-6. [PMID: 15651419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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33
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Deng JY, Zhang XE, Mang Y, Zhang ZP, Zhou YF, Liu Q, Lu HB, Fu ZJ. Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism. Biosens Bioelectron 2004; 19:1277-83. [PMID: 15046760 DOI: 10.1016/j.bios.2003.11.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2003] [Revised: 10/24/2003] [Accepted: 11/26/2003] [Indexed: 10/26/2022]
Abstract
An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates.
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Affiliation(s)
- Jiao-Yu Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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34
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35
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Affiliation(s)
- J Kratochvil
- Abbott Laboratories, Diagnostics Division, North Chicago, IL
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36
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Studnicka GM, Lei SP, Lin HC, Wilcox G. Subcloning for DNA sequencing. Methods Mol Biol 2003; 23:69-74. [PMID: 8220772 DOI: 10.1385/0-89603-248-5:69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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37
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Affiliation(s)
- G P Pfeifer
- Beckman Research Institute of City of Hope, Duarte, CA
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38
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Affiliation(s)
- G Murphy
- JI Center for Plant Science Research, Norwich, England
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39
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Yamaguchi H, Kubota K, Harada A. Preparation of DNA catenanes and observation of their topological structures by atomic force microscopy. Nucleic Acids Symp Ser 2003:229-30. [PMID: 12903352 DOI: 10.1093/nass/44.1.229] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
DNA catenanes have been prepared by the reaction of T4 DNA ligase with linear DNA in the presence of nicked DNA. Single molecular images of DNA catenanes and large circular DNAs have been clearly observed by AFM using a tapping mode at room temperature and in an ambient atmosphere.
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Affiliation(s)
- H Yamaguchi
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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40
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Affiliation(s)
- Jonas Jarvius
- Rudbeck Laboratory, Unit of Molecular Medicine, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
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41
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Okazaki T. [Days devoted to elucidating the mechanism of discontinuous DNA replication]. Tanpakushitsu Kakusan Koso 2003; 48:718-26. [PMID: 12816006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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42
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Zhang Y, Crothers DM. High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proc Natl Acad Sci U S A 2003; 100:3161-6. [PMID: 12629220 PMCID: PMC152263 DOI: 10.1073/pnas.0530189100] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2003] [Indexed: 11/18/2022] Open
Abstract
We have developed a high-throughput approach to the labor-intensive problems of DNA cyclization, which we use to characterize DNA curvature and mechanical properties. The method includes a combinatorial approach to make the DNA constructs needed and automated real-time measurement of the kinetics using fluorescence. We validated the approach and investigated the flexibility of two kinds of nicked DNA and AT dinucleotide repeats. We found that, although the nicks hardly alter the bending flexibility, they significantly increase the torsional flexibility, and that the AT repeat has 28% (+/-12%) lower bending rigidity than a generic DNA sequence.
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Affiliation(s)
- Yongli Zhang
- Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06511, USA
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43
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Abstract
Although DNA clearly outclasses any silicon-based computer when it comes to information storage and processing speed, a DNA-based PC is still a long way off
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44
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Affiliation(s)
- Philip K Liu
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
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45
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Nilsson M, Landegren U, Antson DO. Single-nucleotide sequence discrimination in situ using padlock probes. Curr Protoc Hum Genet 2002; Chapter 4:Unit 4.11. [PMID: 18428329 DOI: 10.1002/0471142905.hg0411s34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA ligases are very sensitive to mismatches at the DNA ends to be joined through ligation. This mechanism has been exploited to distinguish DNA sequence variants in situ using so-called padlock probes. Padlock probes are linear oligonucleotides with target-complementary sequences at both ends, and an on-target-complementary segment in between. The end sequences are brought next to each other upon hybridization to the target DNA sequence, and if the ends are perfectly matched to the target sequence, they can be joined by a DNA ligase. Padlock probes detect target sequences with very high specificity, because both probe segments must hybridize to the target for circularization to occur. This unit presents a protocol for discrimination between closely similar DNA sequences in situ using padlock probes. A discussion of methods for greatly amplifying the signal from circularized probes is also included.DNA ligases are very sensitive to mismatches at the DNA ends to be joined through ligation.
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46
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Abstract
Oxidation reactions that involve several oxygen and nitrogen reactive species together with nucleobase radical cations give rise among various classes of lesions to modified bases. About 70 of oxidized nucleosides that include diastereomeric forms have been characterized in mechanistic studies involving isolated DNA and related model compounds. However, only eight modified bases have been accurately measured within cellular DNA upon exposure to either gamma or UVA radiations. Emphasis is placed in this survey on recent developments of HPLC associated with tandem mass spectrometry (MS/MS) operating in the mild electrospray ionization mode. Interestingly, the HPLC-MS/MS assay in the multiple reaction monitoring mode appears to be the more sensitive and accurate method currently available for singling out several oxidized nucleosides including 8-oxo-7,8-dihydro-2'-deoxyguanosine, 8-oxo-7,8-dihydro-2'-deoxyadenosine, 5-formyl-2'-deoxyuridine, 5-(hydroxymethyl-2'-deoxyuridine, 5-hydroxy-2'-deoxyuridine, and the four diastereomers of 5,6-dihydroxy-5,6-dihydrothymidine within isolated and cellular DNA. However, one limitation of the assay that also applied to all chromatographic methods is the slight side-oxidation of normal bases during DNA extraction and subsequent work-up. This explains why the combined use of DNA repair glycosylases with either the comet assay or the alkaline elution technique is a better alternative to monitor the formation of low levels of oxidized bases within cellular DNA.
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Affiliation(s)
- Jean Cadet
- Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, Grenoble, France.
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47
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Abstract
A new approach is presented for the sensitive and selective scanning for unknown DNA mutations, based on ligation-mediated PCR and the use of the glycosylases TDG and MutY. These two highly selective enzymes together can detect about 70% of commonly observed polymorphisms and mutations in human tumors. DNA is cross-hybridized to form mismatches at the positions of point mutations, de-phosphorylated to eliminate any pre-existing phosphorylated DNA ends, and then exposed to enzymatic treatment to remove mismatched thymidine (TDG) or adenine (MutY). The resulting apurinic/apyrimidinic sites at the position of the mismatches are heat-converted to 5'-phosphate-containing strand breaks, the DNA is denatured, and an oligonucleotide is ligated at the position of the newly created 5'-phosphate-containing DNA ends. The ligated oligonucleotide then participates in a PCR reaction that amplifies exponentially only the mutation-containing fragments. Using this method, A-->G mutations in a p53 (TP53)-containing system, T-->G, G-->A, and C-->A, mutations in the Ku gene (XRCC5), and ATM, gene for a number of patient-derived genomic DNA samples have been successfully screened. This PCR-based assay is capable of detecting one mutated allele in 100 normal alleles and requires 5 to 100 ng of genomic DNA as starting material. The assay allows final visualization of the mutated fragments on a common ethidium gel or biotinylation and use in a capture format, potentially allowing the isolation of diverse mutated DNA fragments simultaneously. This versatile new approach should allow high throughput detection of DNA alterations and application in diverse areas of human mutation research.
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Affiliation(s)
- Yuzhi Zhang
- Department of Radiation Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
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48
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Gilpin CM, Dawson DJ, O'Kane G, Armstrong JG, Coulter C. Failure of commercial ligase chain reaction to detect Mycobacterium tuberculosis DNA in sputum samples from a patient with smear-positive pulmonary tuberculosis due to a deletion of the target region. J Clin Microbiol 2002; 40:2305-7. [PMID: 12037118 PMCID: PMC130798 DOI: 10.1128/jcm.40.6.2305-2307.2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report on a strain of Mycobacterium tuberculosis with a deletion in the protein antigen B gene overlapping the probe binding sites for the Abbott Diagnostics LCx M. tuberculosis (LCx-MTB) probe assay. A false-negative result with the LCx-MTB assay delayed a laboratory diagnosis of tuberculosis.
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Affiliation(s)
- Christopher M Gilpin
- Mycobacterium Reference Laboratory, Division of Microbiology, The Prince Charles Hospital, Chermside 4032, Australia.
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49
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Okazaki T. [The mechanism of discontinuous replication: how it was established]. Tanpakushitsu Kakusan Koso 2002; 47:249-60. [PMID: 11889802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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50
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Okazaki T. [Okazaki furaguments and discontinuous replication]. Seikagaku 2002; 74:103-17. [PMID: 11925936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Tuneko Okazaki
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192
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