1
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Liu Y, Chen B, He M, Hu B. Detection of terminal deoxynucleotidyl transferase activity based on self-mediated nucleic acid elongation and elemental labeling inductively coupled plasma-mass spectrometry. Talanta 2024; 274:125979. [PMID: 38537358 DOI: 10.1016/j.talanta.2024.125979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/29/2024] [Accepted: 03/20/2024] [Indexed: 05/04/2024]
Abstract
Terminal deoxynucleotidyl transferase (TdT), a specialized DNA polymerase, is recognized as a promising biomarker for acute leukemia. Herein, taking the advantage of the self-mediated strand elongation property of TdT, a simple and sensitive method for TdT activity assay was developed based on gold nanoparticles (AuNPs) labeling inductively coupled plasma mass spectrometry (ICP-MS). In the presence of TdT, the primer DNA on magnetic beads is elongated with an adenine-rich single stranded long chain that can label poly-thymine modified AuNPs. After acid elution, the labeled AuNPs were detected by ICP-MS, and the signal intensity of 197Au reflected the TdT activity. Under the optimal conditions, the limit of detection for TdT activity is down to 0.054 U mL-1, along with good selectivity and strong tolerance to other interfering proteins. Furthermore, it achieves a straightforward and accurate detection of TdT activity in acute lymphoblastic leukemia cells without sample pre-processing and tool enzyme addition. Therefore, the proposed method shows great promise as a valuable tool for TdT-related biological research and leukemia therapeutics.
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Affiliation(s)
- Yuwei Liu
- Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Beibei Chen
- Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Man He
- Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Bin Hu
- Department of Chemistry, Wuhan University, Wuhan, 430072, China.
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2
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Ohtsubo Y, Kawahara S, Nagata Y. Clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis by Taq polymerase involves nick-translation. Sci Rep 2024; 14:2030. [PMID: 38263346 PMCID: PMC10805873 DOI: 10.1038/s41598-024-52095-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/13/2024] [Indexed: 01/25/2024] Open
Abstract
The development and characterization of a new enzyme reaction contribute to advancements in modern biotechnology. Here, we report a novel CIS (clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis) reaction catalyzed by Taq polymerase. In the reaction, a single-stranded DNA (ssDNA) with 3' Cs is attached with a preformed 3' G-tail of double-stranded DNA (dsDNA); DNA syntheses starting from both 3' ends result in the incorporation of ssDNA. A 3' G-tail length of 3 nucleotides adequately supports this reaction, indicating that Taq polymerase can clump short Watson-Crick base pairs as short as three pairs and use them to initiate DNA polymerization. The reverse transcriptase from Molony murine leukemia virus catalyzes strand displacement synthesis and produces flapped-end DNA, whereas the reaction by Taq polymerase involves the nick translation. These new reaction properties may be beneficial for the development of new molecular tools applicable in various fields. Apart from its CIS reaction activity, we also report that Taq polymerase has the undesirable characteristic of removing 5' fluorescent labels from dsDNA. This characteristic may have compromised various experiments involving the preparation of fluorescently-labeled dsDNA by PCR for a long time.
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Grants
- 19H02865 Ministry of Education, Culture, Sports, Science and Technology,Japan
- 22H02233 Ministry of Education, Culture, Sports, Science and Technology,Japan
- 22K19124 Ministry of Education, Culture, Sports, Science and Technology,Japan
- K-2016-004 Institute for Fermentation, Osaka,Japan
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Affiliation(s)
- Yoshiyuki Ohtsubo
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan.
| | - Syoutaro Kawahara
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Yuji Nagata
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
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3
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Yang H, Zhu L, Wang X, Song Y, Dong Y, Xu W. Extension characteristics of TdT and its application in biosensors. Crit Rev Biotechnol 2023:1-15. [PMID: 37880088 DOI: 10.1080/07388551.2023.2270772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023]
Abstract
The advantages of rapid amplification of nucleic acid without a template based on terminal deoxyribonucleotidyl transferase (TdT) have been widely used in the field of biosensors. However, the catalytic efficiency of TdT is affected by extension conditions. The sensitivity of TdT- mediated biosensors can be improved only under appropriate conditions. Therefore, in this review, we provide a comprehensive overview of TdT extension characteristics and its applications in biosensors. We focus on the relationship between TdT extension conditions and extension efficiency. Furthermore, the construction strategy of TdT-mediated biosensors according to five different recognition types and their applications in targets are discussed and, finally, several current challenges and prospects in the field are taken into consideration.
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Affiliation(s)
- He Yang
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Longjiao Zhu
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Xinxin Wang
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Yuhan Song
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Food Science and Nutritional Engineering, Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), China Agricultural University, Beijing, China
| | - Yulan Dong
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wentao Xu
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Food Science and Nutritional Engineering, Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), China Agricultural University, Beijing, China
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4
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Ren Y, Jin L, Zeng H, Busquets R, He G, Deng S, He Q, Khan MR, Deng R, Chi Y. Primer-Engineered Transferase Enzyme for One-Pot and Amplified Detection of Cobalt Pollution and Peptide Remover Screening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:877-883. [PMID: 36563311 DOI: 10.1021/acs.jafc.2c07223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Extensive consumption of cobalt in the chemical field such as for battery materials, alloy, pigments, and dyes has aggravated the pollution of cobalt both in food and the environment, and assays for its on-site monitoring are urgently demanded. Herein, we utilized enzyme dependence on metal cofactors to develop terminal transferase (TdT) as a recognition element, achieving a one-pot sensitive and specific assay for detecting cobalt pollution. We engineered a 3'-OH terminus primer to improve the discrimination capacity of TdT for Co2+ from other bivalent cations. The TdT extension reaction amplified the recognition of Co2+ and yielded a limit of detection of 0.99 μM for Co2+ detection. Then, the TdT-based assay was designed to precisely detect cobalt in food and agricultural soil samples. By end-measurement of fluorescence using a microplate reader, the multiplexing assay enabled the rapid screening of the peptide remover for cobalt pollution. The TdT-based assay can be a promising tool for cobalt pollution monitoring and control.
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Affiliation(s)
- Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Lulu Jin
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Hongling Zeng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Rosa Busquets
- School of Life Sciences, Pharmacy and Chemistry, Kingston University London, Penrhyn Road, KT1 2EE Kingston Upon Thames, United Kingdom
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Yuanlong Chi
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
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5
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Li CC, Liu WX, Jiang S, Liu M, Luo X, Zhang CY. Construction of Bioluminescent Sensors for Label-Free, Template-Free, Separation-Free, and Sequence-Independent Detection of both Clustered and Isolated Damage in Genomic DNA. Anal Chem 2022; 94:14716-14724. [PMID: 36223141 DOI: 10.1021/acs.analchem.2c03134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA damage induced by endogenous/exogenous factors may cause various diseases, and the genomic DNA damage has become an important biomarker for clinical diagnosis and risk assessment, but it remains a great challenge to accurately quantify both clustered and isolated damage because of their random locations, large diversity, and low abundance. Herein, we demonstrate the development of bioluminescent sensors for label-free, template-free, separation-free, and sequence-independent detection of both clustered and isolated damage in genomic DNA based on the base-excision repair (BER) pathway and terminal transferase (TdT)-initiated template-free isothermal cyclic amplification. The damaged bases are cleaved by DNA glycosylase to generate a new 3'-OH terminus, and subsequently, TdT catalyzes the repeated incorporation of dTTPs into the 3'-OH terminus to produce poly-T structures which can hybridize with the signal probe to form a poly-T sequence/signal probe duplex. Under the lambda exonuclease hydrolysis, a large number of adenosine monophosphate (AMP) molecules are produced to generate a high bioluminescence signal through the cyclic interconversion of AMP-adenosine triphosphate (ATP)-AMP in the presence of luciferin and firefly luciferase. Moreover, the introduction of APE1-induced cyclic cleavage signal amplification can greatly improve the detection sensitivity. The proposed strategy can detect both clustered and isolated damage in genomic DNA with extremely high sensitivity and excellent specificity, and it can even distinguish 0.001% DNA damage in the mixture. Importantly, it can detect the cellular DNA damage with a detection limit of 0.011 ng and further extend to measure various DNA damage with the integration of appropriate DNA repair enzymes.
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Affiliation(s)
- Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Wan-Xin Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,Zichuan Experimental Middle School, Zibo 255100, China
| | - Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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6
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Han H, Cui J, Zhou D, Hua D, Peng W, Lin M, Zhang Y, Li F, Gong X, Zhang J. Single-stranded RNA as primers of terminal deoxynucleotidyl transferase for template-independent DNA polymerization. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Wang X, Xu J, Qin P, Yan C, Liu G, Chen W. Self-assembly of a polythymine embedded activatable molecular beacon for one-step quantification of terminal deoxynucleotidyl transferase activity. Anal Chim Acta 2020; 1141:127-135. [PMID: 33248645 DOI: 10.1016/j.aca.2020.10.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 02/07/2023]
Abstract
We describe an isothermal, single-reaction, and one-step method for signal-on quantification of terminal deoxynucleotidyl transferase (TdT) activity based on the periodic elongation and assembly of polythymine embedded activatable molecular beacon (PTA-MB) into DNA nanostructures. PTA-MB is easily designed according to the rule of the conventional molecular beacon (MB) but engineered with a polyT composed loop. Upon exposure to the specific target TdT, the MB is first elongated with an adenine-rich (A-rich) long chain so that it can then act as the anchoring substrate to capture many original PTA-MBs along its strand. Their unfolding contributes to preliminary fluorescence emission. Significantly, the assembled PTA-MBs can also be elongated and hybridized with residual free PTA-MBs for the second round of signal amplification. Accordingly, multiple rounds of elongation, assembly, and activation of initial PTA-MBs can lead to the formation of DNA nanostructures and induce a dramatically enhanced fluorescence signal for qualitative and quantitative evaluation of TdT activity. The final assay indicated a limit of detection (LOD) of 0.042 U mL-1 TdT and showed excellent selectivity for TdT versus other common enzymes. Moreover, the practical applicability was validated by direct/absolute quantification of TdT in real biological specimens and accurate monitoring of the activity of TdT pretreated by low/high temperature and heavy metal ions. These findings demonstrated that this functional PTA-MB and its unique assembly behavior is most likely to promote the study of oligonucleotide probe-based DNA assembly, providing a reliable, convenient, and universal platform for precise and point-of-care monitoring of various biomolecules.
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Affiliation(s)
- Xinxin Wang
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Panzhu Qin
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Chao Yan
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China; Research Center for Biomedical and Health Science, School of Life and Health, Anhui Science & Technology University, Fengyang, 233100, China
| | - Guodong Liu
- Research Center for Biomedical and Health Science, School of Life and Health, Anhui Science & Technology University, Fengyang, 233100, China
| | - Wei Chen
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
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8
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Huang Z, Lin Q, Ye X, Yang B, Zhang R, Chen H, Weng W, Kong J. Terminal deoxynucleotidyl transferase based signal amplification for enzyme-linked aptamer-sorbent assay of colorectal cancer exosomes. Talanta 2020; 218:121089. [PMID: 32797865 DOI: 10.1016/j.talanta.2020.121089] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022]
Abstract
Exosomes have received increasingly significant attention and have shown great clinical value as biomarkers for a number of diseases. However, there is still a lack of a highly sensitive and visualized method for the detection of exosomes in numerous samples simultaneously. Here, we developed a high-throughput, colorimetric and simple method to detect colorectal cancer (CRC) exosomes based on terminal deoxynucleotidyl transferase (TdT)-aided ultraviolet signal amplification. Anti-A33, a CRC exosomal protein marker, was selected as a capture probe, and a facility-prepared EpCAM (CRC exosomal protein) aptamer-Au-primer complex was used as a signal probe. After the CRC exosomes were captured onto the surface of 96-well plates, the primer was extended to the poly(biotin-adenine) chains with the help of TdT, resulting in an increase in the binding amount of avidin-modified horseradish peroxidase (Av-HRP) for H2O2-mediated oxidation of 3,3',5,5'-tetramethyl benzidine (TMB) in enzyme-linked aptamer-sorbent assay (ELASA). The results showed that the incorporation of ploy(biotin-A) enabled approximately 10.4-fold signal amplification. This approach achieved a linear range of 9.75 × 103-1.95 × 106 particles/μL for CRC cell-derived exosomes. The feasibility of the developed assay was evaluated using clinical serum samples. CRC patients (n = 16) could be clearly and successfully distinguished from healthy individuals (n = 9). Furthermore, this proposed platform holds considerable potential for the detection of different targets, simply by changing the aptamer and antibody.
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Affiliation(s)
- Zhipeng Huang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Xin Ye
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Bin Yang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Ren Zhang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai, 200438, China.
| | - Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China.
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai, 200438, China.
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9
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Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3' Terminal Structures for Enzymatic De Novo DNA Synthesis. Genes (Basel) 2020; 11:genes11010102. [PMID: 31963235 PMCID: PMC7016565 DOI: 10.3390/genes11010102] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 01/13/2023] Open
Abstract
Enzymatic oligonucleotide synthesis methods based on the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) promise to enable the de novo synthesis of long oligonucleotides under mild, aqueous conditions. Intermediates with a 3′ terminal structure (hairpins) will inevitably arise during synthesis, but TdT has poor activity on these structured substrates, limiting its usefulness for oligonucleotide synthesis. Here, we described two parallel efforts to improve the activity of TdT on hairpins: (1) optimization of the concentrations of the divalent cation cofactors and (2) engineering TdT for enhanced thermostability, enabling reactions at elevated temperatures. By combining both of these improvements, we obtained a ~10-fold increase in the elongation rate of a guanine-cytosine hairpin.
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10
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Li XY, Cui YX, Du YC, Tang AN, Kong DM. Isothermal cross-boosting extension–nicking reaction mediated exponential signal amplification for ultrasensitive detection of polynucleotide kinase. Analyst 2020; 145:3742-3748. [DOI: 10.1039/c9an02569c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel nucleic acid-based isothermal signal amplification strategy, named cross-boosting extension–nicking reaction (CBENR) is developed and successfully used for rapid and ultrasensitive detection of polynucleotide kinase (PNK) activity.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
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11
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Hu Q, Gan S, Bao Y, Zhang Y, Han D, Niu L. Controlled/“living” radical polymerization-based signal amplification strategies for biosensing. J Mater Chem B 2020; 8:3327-3340. [DOI: 10.1039/c9tb02419k] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Controlled/“living” radical polymerization-based signal amplification strategies and their applications in highly sensitive biosensing of clinically relevant biomolecules are reviewed.
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Affiliation(s)
- Qiong Hu
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Shiyu Gan
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Yu Bao
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Yuwei Zhang
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Dongxue Han
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Li Niu
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
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12
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Visual Detection of Cucumber Green Mottle Mosaic Virus Based on Terminal Deoxynucleotidyl Transferase Coupled with DNAzymes Amplification. SENSORS 2019; 19:s19061298. [PMID: 30875853 PMCID: PMC6471243 DOI: 10.3390/s19061298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/03/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
A simple, rapid, and sensitive visual detection method for observing cucumber green mottle mosaic virus was reported based on the template-independent polymerization activity of terminal deoxynucleotidyl transferase (TdT), coupled with the cascade amplification of Mg2+-dependent DNAzyme and hemin/G-quadruplex DNAzyme. Briefly, the hybridized dsDNA of T1/P1 was cut into two parts at its position of 5′-AA↓CG↑TT-3′ by the restricted enzyme AcII. The longer, newborn fragment originating from P1 was tailed at its 3’-end by oligo dG, and an intact enzymatic sequence of Mg2+-dependent DNAzyme was generated. The substrate sequence in the loop segment of the hairpin probe (HP) hybridized with the newborn enzymatic sequence and was cleaved into two parts in the presence of Mg2+. The locked G-quadruplex sequence in the stem segment of the HP was released, which catalyzed the oxidation of ABTS2- in the presence of H2O2, and the resulting solution turned green. A correlation between the absorbance and concentration of T1 was obtained in a range from 0.1 pM to 2 nM, with a detection limit of 0.1 pM. In addition to promoting a lower detection limit and shorter monitoring time, this method also demonstrated an excellent selectivity to single or double nucleotide changes. Therefore, the designed strategy provided a rapid and efficient platform for viral inspection and plant protection.
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13
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Hermanová M, Havranová‐Vidláková P, Ondráčková A, Kumar SS, Bowater R, Fojta M. Label‐free Voltammetric Detection of Products of Terminal Deoxynucleotidyl Transferase Tailing Reaction. ELECTROANAL 2019. [DOI: 10.1002/elan.201800452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Monika Hermanová
- Institute of Biophysics Czech Academy of Sciences Kralovopolska 135 612 65 Brno Czech Republic
| | | | - Anna Ondráčková
- Institute of Biophysics Czech Academy of Sciences Kralovopolska 135 612 65 Brno Czech Republic
| | - Swathi Senthil Kumar
- School of Biological Sciences University of East Anglia Norwich Norwich Research Park NR4 7TJ United Kingdom
| | - Richard Bowater
- School of Biological Sciences University of East Anglia Norwich Norwich Research Park NR4 7TJ United Kingdom
| | - Miroslav Fojta
- Institute of Biophysics Czech Academy of Sciences Kralovopolska 135 612 65 Brno Czech Republic
- Central European Institute of Technology Masaryk University Kamenice 753/5 CZ-625 00 Brno Czech Republic
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14
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Sasagawa Y, Hayashi T, Nikaido I. Strategies for Converting RNA to Amplifiable cDNA for Single-Cell RNA Sequencing Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:1-17. [PMID: 30968357 DOI: 10.1007/978-981-13-6037-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This review describes the features of molecular biology techniques for single-cell RNA sequencing (scRNA-seq), including methods developed in our laboratory. Existing scRNA-seq methods require the conversion of first-strand cDNA to amplifiable cDNA followed by whole-transcript amplification. There are three primary strategies for this conversion: poly-A tagging, template switching, and RNase H-DNA polymerase I-mediated second-strand cDNA synthesis for in vitro transcription. We discuss the merits and limitations of these strategies and describe our Reverse Transcription with Random Displacement Amplification technology that allows for direct first-strand cDNA amplification from RNA without the need for conversion to an amplifiable cDNA. We believe that this review provides all users of single-cell transcriptome technologies with an understanding of the relationship between the quantitative performance of various methods and their molecular features.
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Affiliation(s)
- Yohei Sasagawa
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan.
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15
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A versatile method for the UVA-induced cross-linking of acetophenone- or benzophenone-functionalized DNA. Sci Rep 2018; 8:16484. [PMID: 30405165 PMCID: PMC6220319 DOI: 10.1038/s41598-018-34892-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/25/2018] [Indexed: 11/08/2022] Open
Abstract
Bioconjugation, biosensing, bioimaging, bionanomaterials, etc., are only a few examples of application of functionalized DNA. Since base-modified nucleic acids contribute not only to a broad range of biotechnological fields but also to the understanding of various cellular processes, it is crucial to design novel modifications with unique properties. Here, we demonstrate the utilization of N4-cytidine modified oligonucleotides, which contain reactive acetophenone (AP) or benzophenone (BP) groups, for the UV-induced cross-linking. We find that terminal deoxynucleotidyl transferase-mediated 3'-tailing using AP/BP-containing modified nucleotides generates photoactive DNA, suitable for a straightforward covalent cross-linking with both interacting proteins and a variety of well-known solid polymeric supports. Moreover, we show that AP/BP-functionalization of nucleic acid molecules induces an efficient cross-linking upon exposure to UVA light. Our findings reveal that 3'-tailed single-stranded DNA bearing AP/BP-moieties is easily photoimmobilized onto untreated polystyrene, polypropylene, polylactate, polydimethylsiloxane, sol-gel and borosilicate glass substrates. Furthermore, we demonstrate that such immobilized DNA probes can be further used for successful hybridization of complementary DNA targets. Our results establish novel N4-cytosine nucleobase modifications as photoreactive labels and suggest an effortless approach for photoimmobilization of nucleic acids.
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16
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Wang LJ, Ren M, Liang L, Zhang CY. Controllable fabrication of bio-bar codes for dendritically amplified sensing of human T-lymphotropic viruses. Chem Sci 2018; 9:4942-4949. [PMID: 29938021 PMCID: PMC5994793 DOI: 10.1039/c8sc01641k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
We demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA.
Human T-lymphotropic virus type II (HTLV-II) is an important type-C retrovirus, closely related to a variety of human diseases. Here, we demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA by the integration of terminal deoxynucleotidyl transferase (TdT)-catalyzed template-free polymerization extension with bio-bar-code amplification (BCA). HTLV-II DNA hybridizes with magnetic microparticle (MMP)-modified capture probe 1, forming a stable DNA duplex with a protruding 3′-hydroxylated sequence which may function as a primer to initiate the TdT-catalyzed first-step polymerization extension for the generation of a poly-thymidine (T) sequence. The resultant poly-T products may hybridize with poly-adenine (A) capture probe 2, inducing the self-assembly of multiple capture probe 2-/reporter probe-functionalized Au nanoparticles (AuNPs) onto the MMP. Subsequently, the reporter probes may act as the primers to initiate the TdT-catalyzed second-step polymerization extension, producing large numbers of G-rich DNAzymes for the generation of an enhanced chemiluminescence signal. Taking advantage of the efficient polymerization extension reaction catalyzed by TdT, the high amplification efficiency of BCA, and the intrinsically high sensitivity of G-rich DNAzyme-driven chemiluminescence, this method exhibits ultrahigh sensitivity with a limit of detection of as low as 0.50 aM and a large dynamic range of 9 orders of magnitude from 1 aM to 1 nM. Moreover, this method can be applied for the discrimination of a single-base mismatch and the measurement of HTLV-II DNA in both human serum and human T-lymphocytic leukemia cells, holding great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Ming Ren
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Li Liang
- Department of Tumor Chemotherapy and Radiation Sickness , Peking University Third Hospital , Beijing 100191 , China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
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17
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Zhang Y, Li QN, Li CC, Zhang CY. Label-free and high-throughput bioluminescence detection of uracil-DNA glycosylase in cancer cells through tricyclic cascade signal amplification. Chem Commun (Camb) 2018; 54:6991-6994. [DOI: 10.1039/c8cc03769h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We develop a label-free and high-throughput bioluminescence method for the sensitive detection of uracil DNA glycosylase through tricyclic cascade signal amplification.
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Affiliation(s)
- Yan Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Qing-nan Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chen-chen Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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18
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Havranová-Vidláková P, Špaček J, Vítová L, Hermanová M, Dadová J, Raindlová V, Hocek M, Fojta M, Havran L. Butylacrylate-nucleobase Conjugates as Targets for Two-step Redox Labeling of DNA with an Osmium Tetroxide Complex. ELECTROANAL 2017. [DOI: 10.1002/elan.201700702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Jan Špaček
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
| | - Lada Vítová
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
| | - Monika Hermanová
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
| | - Jitka Dadová
- The Czech Academy of Sciences; Institute of Organic Chemistry and Biochemistry; Flemingovo namesti 2 16610 Prague 6 Czech Republic
| | - Veronika Raindlová
- The Czech Academy of Sciences; Institute of Organic Chemistry and Biochemistry; Flemingovo namesti 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- The Czech Academy of Sciences; Institute of Organic Chemistry and Biochemistry; Flemingovo namesti 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science; Charles University in Prague; Hlavova 8, Prague- 2 12843 Czech Republic
| | - Miroslav Fojta
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
- Central European Institute of Technology; Masaryk University; Kamenice 753/5 625 00 Brno Czech Republic
| | - Luděk Havran
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
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19
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Telomerase activity is required for the telomere G-overhang structure in Trypanosoma brucei. Sci Rep 2017; 7:15983. [PMID: 29167542 PMCID: PMC5700094 DOI: 10.1038/s41598-017-16182-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/08/2017] [Indexed: 01/24/2023] Open
Abstract
Trypanosoma brucei causes fatal human African trypanosomiasis and evades the host immune response by regularly switching its major surface antigen, VSG, which is expressed exclusively from subtelomeric loci. Telomere length and telomere proteins play important roles in regulating VSG silencing and switching. T. brucei telomerase plays a key role in maintaining telomere length, and T. brucei telomeres terminate in a single-stranded 3′ G-rich overhang. Understanding the detailed structure of the telomere G-overhang and its maintenance will contribute greatly to better understanding telomere maintenance mechanisms. Using an optimized adaptor ligation assay, we found that most T. brucei telomere G-overhangs end in 5′ TTAGGG 3′, while a small portion of G-overhangs end in 5′ TAGGGT 3′. Additionally, the protein and the RNA components of the telomerase (TbTERT and TbTR) and TbKu are required for telomere G-overhangs that end in 5′ TTAGGG 3′ but do not significantly affect the 5′ TAGGGT 3′-ending overhangs, indicating that telomerase-mediated telomere synthesis is important for the telomere G-overhang structure. Furthermore, using telomere oligo ligation-mediated PCR, we showed for the first time that the T. brucei telomere 5′ end sequence – an important feature of the telomere terminal structure – is not random but preferentially 5′ CCTAAC 3′.
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20
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Design of reactive-end DNA oligomers via incorporation of oxanine into oligonucleotides using terminal deoxynucleotidyl transferase. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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Winz ML, Cahová H, Nübel G, Frindert J, Höfer K, Jäschke A. Capture and sequencing of NAD-capped RNA sequences with NAD captureSeq. Nat Protoc 2016; 12:122-149. [PMID: 27977022 DOI: 10.1038/nprot.2016.163] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here we describe a protocol for NAD captureSeq that allows for the identification of nicotinamide-adenine dinucleotide (NAD)-capped RNA sequences in total RNA samples from different organisms. NAD-capped RNA is first chemo-enzymatically biotinylated with high efficiency, permitting selective capture on streptavidin beads. Then, a highly efficient library preparation protocol tailored to immobilized, 5'-modified RNA is applied, with adaptor ligation to the RNA's 3' terminus and reverse transcription (RT) performed on-bead. Then, cDNA is released into solution, tailed, ligated to a second adaptor and PCR-amplified. After next-generation sequencing (NGS) of the DNA library, enriched sequences are identified by comparison with a control sample in which the first step of chemo-enzymatic biotinylation is omitted. Because the downstream protocol does not necessarily rely on NAD-modified but on 'clickable' or biotin-modified RNA, it can be applied to other RNA modifications or RNA-biomolecule interactions. The central part of this protocol can be completed in ∼7 d, excluding preparatory steps, sequencing and bioinformatic analysis.
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Affiliation(s)
- Marie-Luise Winz
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Hana Cahová
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Gabriele Nübel
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Jens Frindert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Katharina Höfer
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
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22
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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23
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Winz ML, Linder EC, André T, Becker J, Jäschke A. Nucleotidyl transferase assisted DNA labeling with different click chemistries. Nucleic Acids Res 2015; 43:e110. [PMID: 26013812 PMCID: PMC4787804 DOI: 10.1093/nar/gkv544] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/12/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we present a simple, modular and efficient strategy that allows the 3′-terminal labeling of DNA, regardless of whether it has been chemically or enzymatically synthesized or isolated from natural sources. We first incorporate a range of modified nucleotides at the 3′-terminus, using terminal deoxynucleotidyl transferase. In the second step, we convert the incorporated nucleotides, using either of four highly efficient click chemistry-type reactions, namely copper-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, Staudinger ligation or Diels-Alder reaction with inverse electron demand. Moreover, we create internal modifications, making use of either ligation or primer extension, after the nucleotidyl transferase step, prior to the click reaction. We further study the influence of linker variants on the reactivity of azides in different click reactions. We find that different click reactions exhibit distinct substrate preferences, a fact that is often overlooked, but should be considered when labeling oligonucleotides or other biomolecules with click chemistry. Finally, our findings allowed us to extend our previously published RNA labeling strategy to the use of a different copper-free click chemistry, namely the Staudinger ligation.
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Affiliation(s)
- Marie-Luise Winz
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Eva Christina Linder
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Timon André
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Juliane Becker
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Andres Jäschke
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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24
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Tokunaga S, Stegeman JJ. Elimination of nonspecific bands in non-radioactive electrophoretic mobility shift assays using the digoxigenin system. Anal Biochem 2014; 465:70-2. [PMID: 25004462 DOI: 10.1016/j.ab.2014.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 11/26/2022]
Abstract
In the course of detecting nuclear transcription factors by electrophoretic mobility shift assay using digoxigenin (DIG)-labeled probes, we encountered a problem with a considerable nonspecific shift band in negative control lanes from which protein extracts were omitted. This nonspecific shift band can interfere with the detection of the desired target protein. Purification of the DIG-labeled probes by removing unincorporated DIG-labeled nucleotides did not resolve the problem. However, the introduction of an additional step of heating at 95 °C for 5 min and subsequent reannealing after DIG-labeled probe synthesis eliminated these nonspecific shift bands and allowed accurate analysis of the target protein.
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Affiliation(s)
- Saimi Tokunaga
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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25
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Structure of the herpes simplex virus 1 genome: manipulation of nicks and gaps can abrogate infectivity and alter the cellular DNA damage response. J Virol 2014; 88:10146-56. [PMID: 24965466 DOI: 10.1128/jvi.01723-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED The herpes simplex virus 1 (HSV-1) virion DNA contains nicks and gaps, and in this study a novel assay for estimating the size and number of gaps in virion DNA was developed. Consistent with previous reports, we estimate that there are approximately 15 gaps per genome, and we calculate the average gap length to be approximately 30 bases. Virion DNA was isolated and treated with DNA-modifying enzymes in order to fill in the gaps and modify the ends. Interestingly, filling in gaps, blunting the ends, or adding random sequences to the 3' ends of DNA, producing 3' flaps, did not impair the infectivity of treated DNA following transfection of Vero cells. On the other hand, the formation of 5' flaps in the DNA following treatment resulted in a dramatic reduction (95 to 100%) in infectivity. Virion DNA stimulated DNA-PKcs activity in transfected cells, and DNA with 5' flaps stimulated a higher level of DNA-PKcs activity than that observed in cells transfected with untreated virion DNA. The infectivity of 5'-flapped DNA was restored in cells that do not express DNA-PKcs and in cells cotransfected with the immediate early protein ICP0, which degrades DNA-PKcs. These results are consistent with previous reports that DNA-dependent protein kinase (DNA-PK) and the nonhomologous end joining (NHEJ) repair pathway are intrinsically antiviral and that ICP0 can counteract this effect. We suggest that HSV-1 DNA with 5' flaps may induce an antiviral state due to the induction of a DNA damage response, primarily mediated by NHEJ, that renders the HSV-1 genome less efficient for lytic infection. IMPORTANCE For productive lytic infection to occur, HSV-1 must counteract a variety of cellular intrinsic antiviral mechanisms, including the DNA damage response (DDR). DDR pathways have been associated with silencing of gene expression, cell cycle arrest, and induction of apoptosis. In addition, the fate of viral genomes is likely to play a role in whether viral genomes adopt a configuration suitable for lytic DNA replication. This study demonstrates that virion DNA activates the cellular DDR kinase, DNA-PK, and that this response is inhibitory to viral infection. Furthermore, we show that HSV-1 ubiquitin ligase, ICP0, plays an important role in counteracting the negative effects of DNA-PK activation. These findings support the notion that DNA-PK is antiviral and suggest that the fate of incoming viral DNA has important consequences for the progression of lytic infection. This study underscores the complex evolutionary relationships between HSV and its host.
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26
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Winz ML, Samanta A, Benzinger D, Jäschke A. Site-specific terminal and internal labeling of RNA by poly(A) polymerase tailing and copper-catalyzed or copper-free strain-promoted click chemistry. Nucleic Acids Res 2012; 40:e78. [PMID: 22344697 PMCID: PMC3378897 DOI: 10.1093/nar/gks062] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The modification of RNA with fluorophores, affinity tags and reactive moieties is of enormous utility for studying RNA localization, structure and dynamics as well as diverse biological phenomena involving RNA as an interacting partner. Here we report a labeling approach in which the RNA of interest—of either synthetic or biological origin—is modified at its 3′-end by a poly(A) polymerase with an azido-derivatized nucleotide. The azide is later on conjugated via copper-catalyzed or strain-promoted azide–alkyne click reaction. Under optimized conditions, a single modified nucleotide of choice (A, C, G, U) containing an azide at the 2′-position can be incorporated site-specifically. We have identified ligases that tolerate the presence of a 2′-azido group at the ligation site. This azide is subsequently reacted with a fluorophore alkyne. With this stepwise approach, we are able to achieve site-specific, internal backbone-labeling of de novo synthesized RNA molecules.
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Affiliation(s)
- Marie-Luise Winz
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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27
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Link G, Bogorad L. Sizes, locations, and directions of transcription of two genes on a cloned maize chloroplast DNA sequence. Proc Natl Acad Sci U S A 2010; 77:1832-6. [PMID: 16592800 PMCID: PMC348602 DOI: 10.1073/pnas.77.4.1832] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
mRNA for the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxylase (dimerizing), EC 4.1.1.39] of Zea mays is complementary to an uninterrupted 1600-base-pair-long chloroplast DNA sequence that has been mapped precisely within the 4350-base-pair-long chloroplast DNA fragment Bam 9 to which it had been traced earlier [Bedbrook, J. R., Coen, D. M., Beaton, A. R., Bogorad, L. & Rich, A. (1979) J. Biol. Chem. 254, 905-910]. An additional 1400-base-pair-long uninterrupted region that is colinear with a chloroplast RNA has been detected on Bam 9. The transcript from this region is part of a 2200-nucleotide-long RNA. The remainder of the DNA sequence for the 2200-base-pair RNA maps outside Bam 9. The 1600-base-pair LS gene and the gene for the 2200-nucleotide transcript are close to one another. They are separated by an untranscribed intercistronic "gap" about 330 base pairs long. These two closely packed genes are inverted on the chromosome-i.e., their 3' termini are at opposite ends of the untranscribed gap and they map on opposite strands.
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Affiliation(s)
- G Link
- The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138
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28
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Deichelbohrer I, Messer W, Trautner TA. Genome of Bacillus subtilis Bacteriophage SPP1: Structure and Nucleotide Sequence of pac, the Origin of DNA Packaging. J Virol 2010; 42:83-90. [PMID: 16789222 PMCID: PMC256047 DOI: 10.1128/jvi.42.1.83-90.1982] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The DNA of Bacillus subtilis bacteriophage SPP1 is terminally redundant and partially circularly permuted. To explain these parameters, we followed the Streisinger-Botstein models of phage maturation and assumed that packaging of SPP1 DNA begins at a unique genomic site ("pac") and proceeds sequentially from there. We describe the sequence of about 1,000 nucleotides surrounding pac. This together with size determinations of small, pac-terminated restriction fragments has revealed heterogeneity of the natural pac ends of SPP1 DNA. Such ends fell in each DNA strand into a region of five to seven nucleotides. However, within this range more than 50% of all molecules terminated with defined cytosines on both strands, generating a 3' protruding terminus. The nucleotide sequence of the DNA segment surrounding pac did not reveal any features which would distinguish this region.
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Affiliation(s)
- I Deichelbohrer
- Max-Planck-Institut für Molekulare Genetik, Abteilung Trautner, D-1000 Berlin 33, Germany
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29
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Mizushina Y, Zhang J, Pugliese A, Kim SH, Lü J. Anti-cancer gallotannin penta-O-galloyl-beta-D-glucose is a nanomolar inhibitor of select mammalian DNA polymerases. Biochem Pharmacol 2010; 80:1125-32. [PMID: 20599777 DOI: 10.1016/j.bcp.2010.06.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 06/18/2010] [Accepted: 06/21/2010] [Indexed: 11/16/2022]
Abstract
Penta-1,2,3,4,6-O-galloyl-beta-D-glucose (PGG) has been shown by us and others to inhibit the in vivo growth of human prostate cancer (PCa) xenografts in athymic nude mice and mouse lung cancer allograft in syngenic mice without evident adverse effect on their body weight. We observed a rapid inhibition of DNA synthesis in S-phase cells in PGG-exposed cancer cells and in PGG-treated isolated nuclei. The purpose of the present study was to test the hypothesis that PGG inhibits DNA replicative synthesis through a direct inhibition of one or more DNA polymerases (pols). Using purified pols, we show that PGG exhibited a selective inhibition against the activities of B-family replicative pols (alpha, delta and epsilon) and Y-family (eta, iota and kappa) of bypass synthesis pols, and the inhibitory effect of PGG on pol alpha was the strongest with IC(50) value of 13 nM. PGG also inhibited pol beta, but the potency was an order of magnitude less than against pol alpha. PGG inhibition of pol alpha and kappa activity was non-competitive with respect to the DNA template-primer and the dNTP substrate; whereas it inhibited pol beta competitively. Docking simulation on pol beta, which is the only mammalian pol with solved crystal structure, suggests several favorable interactions with the catalytic pocket/binding site for the incoming dNTP. These results support PGG as a novel inhibitor of select families of mammalian pols by distinct mechanisms, and suggest that the potent pol inhibition may contribute to its anti-cancer efficacy.
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Affiliation(s)
- Yoshiyuki Mizushina
- Laboratory of Food & Nutritional Sciences, Department of Nutritional Science, Kobe-Gakuin University, Kobe, Japan.
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30
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Rittié L, Perbal B. Enzymes used in molecular biology: a useful guide. J Cell Commun Signal 2008; 2:25-45. [PMID: 18766469 DOI: 10.1007/s12079-008-0026-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 08/13/2008] [Indexed: 12/31/2022] Open
Abstract
Since molecular cloning has become routine laboratory technique, manufacturers offer countless sources of enzymes to generate and manipulate nucleic acids. Thus, selecting the appropriate enzyme for a specific task may seem difficult to the novice. This review aims at providing the readers with some cues for understanding the function and specificities of the different sources of polymerases, ligases, nucleases, phosphatases, methylases, and topoisomerases used for molecular cloning. We provide a description of the most commonly used enzymes of each group, and explain their properties and mechanism of action. By pointing out key requirements for each enzymatic activity and clarifying their limitations, we aim at guiding the reader in selecting appropriate enzymatic source and optimal experimental conditions for molecular cloning experiments.
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Affiliation(s)
- Laure Rittié
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA,
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DAWSON DEAN, STETLER DEBORAHJ, SWANTON MARSHALT, HERRICK GLENN. Tandemly Repeated Sequence Families in Micronuclear DNA of the CiliateStylonychia pustulata1. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1550-7408.1983.tb05334.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ishimaru C, Kuriyama I, Shimazaki N, Koiwai O, Sakaguchi K, Kato I, Yoshida H, Mizushina Y. Cholesterol hemisuccinate: a selective inhibitor of family X DNA polymerases. Biochem Biophys Res Commun 2007; 354:619-25. [PMID: 17241613 DOI: 10.1016/j.bbrc.2007.01.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 01/09/2007] [Indexed: 11/26/2022]
Abstract
Cholesterol hemisuccinate (compound 5), which consists of succinic acid esterified to the beta-hydroxyl group of cholesterol, selectively and strongly inhibited the activities of mammalian DNA polymerases (pols) such as pol beta, pol lambda, and terminal deoxynucleotidyltransferase (TdT), which are family X pols, in vitro, and the IC50 values were 2.9, 6.3, and 6.5 microM, respectively. The compound moderately suppressed the activities of other mammalian pols such as pol A (i.e., pol gamma), pol B (i.e., pols alpha, delta, and epsilon), and pol Y (i.e., pols iota, eta, and kappa) with 50% inhibition observed at concentrations of 131, 89.2-98.0, and 120-125 microM, respectively. The compound had no influence on the activities of plant pols alpha and beta, prokaryotic pols and other DNA metabolic enzymes tested. Since other cholesterol-related compounds such as cholesterol, cholesteryl chloride, cholesteryl bromide, cholesteryl acetate, and cholesteryl-5alpha, 6alpha-epoxide (compounds 1-4 and 6, respectively) did not influence the activities of any enzymes tested, the hemisuccinate group of compound 5 could be important for inhibition of the pol X family. Surface plasmon resonance analysis demonstrated that compound 5 bound selectively to the C-terminal 31 kDa domain of pol beta and pol lambda containing a pol beta-like region. On the basis of these results, the inhibitory mechanism of compound 5 on the pol X family was discussed.
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Affiliation(s)
- Chisato Ishimaru
- Laboratory of Food & Nutritional Sciences, Department of Nutritional Science, Kobe-Gakuin University, Kobe, Hyogo 651-2180, Japan
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Bollum FJ. Terminal deoxynucleotidyl transferase: biological studies. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 47:347-74. [PMID: 364939 DOI: 10.1002/9780470122921.ch6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Guerra CE. Analysis of oligonucleotide microarrays by 3' end labeling using fluorescent nucleotides and terminal transferase. Biotechniques 2006; 41:53-6. [PMID: 16869513 DOI: 10.2144/000112182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A simple enzymatic labeling procedure is described to determine spot quality in oligonucleotide microarrays. By using fluorescently labeled dideoxynucleotides or ribonucleotides as substrate for terminal deoxynucleotidyl transferase (TdT), a single fluorophore can be covalently attached at the 3' end of each oligonucleotide probe molecule in the spot. Fluorescein-12-ddUTP CyTM3-ddUTP Cy5-UTP, and Cy3-UTP were compared as TdT substrates for 3' end labeling an array of 1273 hexamer probes. Cy5-UTP was found to show minimal bias toward probe base composition and is therefore well suited for quantitative analysis of microarray spots where the oligonucleotide probes are coupled via a 5' end linkage to the solid phase.
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Mizushina Y, Yagita E, Kuramochi K, Kuriyama I, Shimazaki N, Koiwai O, Uchiyama Y, Yomezawa Y, Sugawara F, Kobayashi S, Sakaguchi K, Yoshida H. 5-(Hydroxymethyl)-2-furfural: a selective inhibitor of DNA polymerase lambda and terminal deoxynucleotidyltransferase. Arch Biochem Biophys 2005; 446:69-76. [PMID: 16405901 DOI: 10.1016/j.abb.2005.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Revised: 11/24/2005] [Accepted: 11/29/2005] [Indexed: 11/23/2022]
Abstract
5-(Hydroxymethyl)-2-furfural (HMF), a pyrolysate of carbohydrate isolated from instant coffee (Coffea arabica L.), selectively inhibits the activities of mammalian DNA polymerase lambda (pol lambda) and terminal deoxynucleotidyltransferase (TdT) which are family X pols, in vitro. The compound influenced neither the activities of replicative DNA polymerases such as alpha, delta, and epsilon, nor even the activity of pol beta which is from the same family and thought to have a very similar three-dimensional structure to the pol beta-like region of pol lambda. Since parts of HMF such as furan, furfuryl alcohol, and 2-furaldehyde did not influence the activities of any enzymes tested, the substituted form of furan with a hyroxymethyl group and a formyl group might be important for the inhibition of pol lambda and TdT. The inhibitory effect of HMF on intact pol lambda (i.e., residues 1-575), a truncated pol lambda lacking the N-terminal BRCA1 C-terminus domain (133-575, del-1 pol lambda) and another truncated pol lambda lacking the N-terminal proline-rich region (245-575, del-2 pol lambda) was dose-dependent, and 50% inhibition was observed at a concentration of 26.1, 10.3, and 4.6 microM, respectively. The IC(50) value of HMF for TdT was the same as that for del-2 pol lambda (5.5 microM). The HMF-induced inhibition of both pol lambda and TdT activities was competitive with respect to both the DNA template-primer and the dNTP substrate. On the basis of these results, HMF was suggested to bind to the pol beta-like region of pol lambda and TdT.
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Affiliation(s)
- Yoshiyuki Mizushina
- Laboratory of Food and Nutritional Sciences, Department of Nutritional Science, Kobe-Gakuin University, Nishi-ku, Kobe, Hyogo 651-2180, Japan.
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Rother D, Orawski G, Bardischewsky F, Friedrich CG. SoxRS-mediated regulation of chemotrophic sulfur oxidation in Paracoccus pantotrophus. Microbiology (Reading) 2005; 151:1707-1716. [PMID: 15870478 DOI: 10.1099/mic.0.27724-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Paracoccus pantotrophus GB17 requires thiosulfate for induction of the sulfur-oxidizing (Sox) enzyme system. The soxRS genes are divergently oriented to the soxVWXYZA–H genes. soxR predicts a transcriptional regulator of the ArsR family and soxS a periplasmic thioredoxin. The homogenote mutant GBΩS carrying a disruption of soxS by the Ω-kanamycin-resistance-encoding interposon expressed a low thiosulfate-oxidizing activity under heterotrophic and mixotrophic growth conditions. This activity was repressed by complementation with soxR, suggesting that SoxR acts as a repressor and SoxS is essential for full expression. Sequence analysis uncovered operator characteristics in the intergenic regions soxS–soxV and soxW–soxX. In each region a transcription start site was identified by primer extension analysis. Both regions were cloned into the vector pRI1 and transferred to P. pantotrophus. Strains harbouring pRI1 with soxS–soxV or soxW–soxX expressed the sox genes under heterotrophic conditions at a low rate, indicating repressor titration. Sequence analysis of SoxR suggested a helix–turn–helix (HTH) motif at position 87–108 and uncovered an invariant Cys-80 and a cysteine residue at the C-terminus. SoxR was overproduced in Escherichia coli with an N-terminal His6-tag and purified to near homogeneity. Electrophoretic gel mobility shift assays with SoxR retarded the soxS–soxV region as a single band while the soxW–soxX region revealed at least two protein–DNA complexes. These data demonstrated binding of SoxR to the relevant DNA. This is believed to be the first report of regulation of chemotrophic sulfur oxidation at the molecular level.
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Affiliation(s)
- Dagmar Rother
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Universität Dortmund, Emil-Figge-Strasse 66, D-44221 Dortmund, Germany
| | - Grazyna Orawski
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Universität Dortmund, Emil-Figge-Strasse 66, D-44221 Dortmund, Germany
| | - Frank Bardischewsky
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Universität Dortmund, Emil-Figge-Strasse 66, D-44221 Dortmund, Germany
| | - Cornelius G Friedrich
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Universität Dortmund, Emil-Figge-Strasse 66, D-44221 Dortmund, Germany
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37
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Maga G, Ramadan K, Locatelli GA, Shevelev I, Spadari S, Hübscher U. DNA elongation by the human DNA polymerase lambda polymerase and terminal transferase activities are differentially coordinated by proliferating cell nuclear antigen and replication protein A. J Biol Chem 2004; 280:1971-81. [PMID: 15537631 DOI: 10.1074/jbc.m411650200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase lambda contains template-dependent (DNA polymerase) and template-independent (terminal transferase) activities. In this study we enzymologically characterized the terminal transferase activity of polymerase lambda (pol lambda-tdt). Pol lambda-tdt activity was strongly influenced by the nature of the 3'-terminal sequence of the DNA substrate, and it required a single-stranded (ss) DNA 3'-overhang of about 9-12 nucleotides for optimal activity. The strong preference observed for pyrimidine versus purine nucleotide incorporation was found to be due, at least partially, to a steric block imposed by the residue Tyr-505 in the active site of pol lambda. Pol lambda-tdt was found to be able to elongate a 3'-ssDNA end by two alternative mechanisms: first, a template-independent one resulting in addition of 1 or 2 nucleotides, and second, a template-dependent one where a homopolymeric tract as short as 3 nucleotides at the 3'-end could be used as a template to direct DNA polymerization by a looping back mechanism. Furthermore repetitive cycles of DNA synthesis resulted in the expansion of such a short homopolymeric terminal sequence. Most importantly we found that the proliferating cell nuclear antigen was able to selectively block the looping back mechanism while stimulating the single terminal nucleotide addition. Finally replication protein A completely suppressed the transferase activity of pol lambda while stimulating the polymerase activity, suggesting that proliferating cell nuclear antigen and replication protein A can coordinate the polymerase and the terminal transferase activities of pol lambda.
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Affiliation(s)
- Giovanni Maga
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, I-27100 Pavia, Italy.
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38
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Oldenburg DJ, Bendich AJ. Mitochondrial DNA from the liverwort Marchantia polymorpha: circularly permuted linear molecules, head-to-tail concatemers, and a 5' protein. J Mol Biol 2001; 310:549-62. [PMID: 11439023 DOI: 10.1006/jmbi.2001.4783] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mapping predicts that the mitochondrial genome of the liverwort Marchantia polymorpha exists as a circular molecule, although nearly all the mitochondrial DNA (mtDNA) is found as genome-sized and multigenomic molecules in linear and branched form. We used restriction enzymes with one recognition site per genome, end-specific exonucleases and pulsed-field gel electrophoresis (PFGE) to analyze the arrangement of genomic units and the terminal structure of the molecules. We find a head-to-tail arrangement in the concatemers and circular permutation in both the monomeric and multigenomic molecules. The termini contain covalently bound protein at the 5' end and an open (unblocked) 3' end. We find that the standard in-gel procedure used to prepare large DNA molecules for PFGE may introduce extraction artifacts leading to erroneous conclusions about the termini. These artifacts can be reduced by omitting high salt (high EDTA) and protease during mitochondrial lysis. Our results suggest that the mtDNA may use a T4 phage-like mechanism of replication and that the linear molecules may be due to strand breaks mediated by type II topoisomerase.
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MESH Headings
- Artifacts
- DNA Replication
- DNA Restriction Enzymes/metabolism
- DNA Topoisomerases, Type II/metabolism
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA-Binding Proteins/metabolism
- Edetic Acid/pharmacology
- Electrophoresis, Gel, Pulsed-Field
- Endopeptidase K/metabolism
- Exodeoxyribonucleases/metabolism
- Genome
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Models, Genetic
- Nucleic Acid Conformation
- Plant Cells
- Plant Proteins/metabolism
- Plants/genetics
- Salts/pharmacology
- Viral Proteins
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Affiliation(s)
- D J Oldenburg
- Department of Botany, University of Washington, Seattle, WA 98195-5325, USA
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39
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Thiry M. Ultrastructural methods for nucleic acid detection by immunocytology. PROGRESS IN HISTOCHEMISTRY AND CYTOCHEMISTRY 1999; 34:87-159. [PMID: 10546283 DOI: 10.1016/s0079-6336(99)80008-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the present review are summarized recent developments in immunocytochemical detection of nucleic acids in biological materials at the ultrastructural level. Not only the approaches using antibodies to natural nucleic acids are described but also the techniques involving the use of antibodies raised against various nucleotide analogs incorporated beforehand into nucleic acids. Special emphasis is placed on each method's potential and limitations. These methods, combined or not with molecular biotechnology, are powerful tools for studying the structure and function of nucleic acids. They can be used to investigate the distribution and topological organization of DNA and RNA molecules or of specialized within these molecules in the cells.
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Affiliation(s)
- M Thiry
- Laboratory of Cell and Tissue Biology, Institute of Histology, University of Liège, Belgium.
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40
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Mundle SD, Ali A, Cartlidge JD, Reza S, Alvi S, Showel MM, Mativi BY, Shetty VT, Venugopal P, Gregory SA, Raza A. Evidence for involvement of tumor necrosis factor-alpha in apoptotic death of bone marrow cells in myelodysplastic syndromes. Am J Hematol 1999; 60:36-47. [PMID: 9883804 DOI: 10.1002/(sici)1096-8652(199901)60:1<36::aid-ajh7>3.0.co;2-#] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We previously reported excessive apoptosis and high levels of tumor necrosis factor-alpha (TNF-alpha) in the bone marrows of patients with myelodysplastic syndromes (MDS), using histochemical techniques. The present studies provide further circumstantial evidence for the involvement of TNF-alpha in apoptotic death of the marrow cells in MDS. Using our newly developed in situ double-labeling technique that sequentially employs DNA polymerase (DNA Pol) followed by terminal deoxynucleotidyl transferase (TdT) to label cells undergoing apoptosis, we have characterized DNA fragmentation patterns during spontaneous apoptosis in MDS bone marrow and in HL60 cells treated with TNF-alpha or etoposide (VP16). Clear DNA laddering detected by gel electrophoresis in MDS samples confirmed the unique length of apoptotic DNA fragments (180-200 bp). Surprisingly, however, phenotypically heterogeneous population of MDS cells as well as the homogenous population of HL60 cells showed three distinct labeling patterns after double labeling--only DNA-Pol reaction, only TdT reaction, and a combined DNA Pol + TdT reaction, albeit in different cohorts of cells. Each labeling pattern was found at all morphological stages of apoptosis. MDS mononuclear cells, during spontaneous apoptosis in 4 hr cultures, showed highest increase in double-labeled cells (DNA Pol + TdT reaction). Interestingly, this was paralleled by TNF-alpha-induced apoptosis in HL60 cells. In contrast, VP16 treatment of HL60 cells led to increased apoptosis in cells showing only TdT reaction. The double-labeling technique was applied to normal bone marrow and peripheral blood mononuclear cells after treatment with known endonucleases that specifically cause 3' recessed (BamHI), 5' recessed (PstI), or blunt ended (DraI) double-stranded DNA breaks. It was found that the DNA-Pol reaction in MDS and HL60 cells corresponds to 3' recessed DNA fragments, the TdT reaction to 5' recessed and/or blunt ended fragments, and a combined "DNA Pol + TdT reaction" corresponds to a copresence of 3' recessed with 5' recessed and/or blunt ended fragments. Clearly, therefore, apoptotic DNA fragments, in spite of a unique length, may have differently staggered ends that could be cell (or tissue) specific and be selectively triggered by different inducers of apoptosis. The presence of TNF-alpha-inducible apoptotic DNA fragmentation pattern in MDS supports its involvement in these disorders and suggests that anti-TNF-alpha (or anticytokine) therapy may be of special benefit to MDS patients, where no definitive treatment is yet available.
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Affiliation(s)
- S D Mundle
- Rush Cancer Institute, Rush-Presbyterian-St. Luke's Medical Center, Chicago, Illinois 60612, USA.
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41
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Abstract
Enzymatic labeling of nucleic acids is a fundamental tool in molecular biology with virtually every aspect of nucleic acid hybridization technique involving the use of labeled probes. Different methods for enzymatic labeling of DNA, RNA and oligonucleotide probes are available today. In this review, we will describe both radioactive and nonradioactive labeling methods, yet the choice of system for labeling the probe depends on the application under study.
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42
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Schmidt WM, Mueller MW. Controlled ribonucleotide tailing of cDNA ends (CRTC) by terminal deoxynucleotidyl transferase: a new approach in PCR-mediated analysis of mRNA sequences. Nucleic Acids Res 1996; 24:1789-91. [PMID: 8650002 PMCID: PMC145852 DOI: 10.1093/nar/24.9.1789] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Controlled ribonucleotide tailing of cDNA ends (CRTC) by terminal deoxynucleotidyl transferase is a polymerase chain reaction (PCR)-mediated technique that was developed to facilitate cloning and direct sequence analysis of complete 5'-terminal unknown coding regions of rare RNA molecules. In contrast with standard tailing protocols using dNTPs as the substrate, ribo-tailing of cDNA ends is easily controllable, self-limited (from two to four rNMP incorporations) and highly efficient (>98%). By virtue of the homopolymeric ribo-tail, the modified cDNA is anchored to the 3' overhang of a double-stranded DNA-adaptor in a T4 DNA ligase-dependent ligation. PCR amplification, mediated by two sequence-specific primers, yields the desired unique product suitable for cloning and dideoxy-sequencing.
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Affiliation(s)
- W M Schmidt
- Vienna Biocenter, Institute of Microbiology and Genetics, Austria
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43
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Bøe R, Gjertsen BT, Døskeland SO, Vintermyr OK. 8-Chloro-cAMP induces apoptotic cell death in a human mammary carcinoma cell (MCF-7) line. Br J Cancer 1995; 72:1151-9. [PMID: 7577461 PMCID: PMC2033955 DOI: 10.1038/bjc.1995.479] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
8-Cl-cAMP and 8-NH2-cAMP induced MCF-7 cell death. The type(s) of cell death were studied in more detail and compared with the cell death type (apoptosis) induced by okadaic acid, an inhibitor of serine/threonine phosphatases. By morphological criteria dying cells showed loss of cell-cell interactions and microvilli, condensation of nuclear chromatin and segregation of cytoplasmic organelles. By in situ nick end-labelling, using digoxigenin-conjugated dUTP as probe, a large fraction of 8-Cl-cAMP, 8-NH2-cAMP and 8-Cl-adenosine-exposed cells stained positively in the advanced stages of death. In the early phase of chromatin condensation the cells stained negatively. Specific (internucleosomal) DNA fragmentation was not observed. The MCF-7 cell death induced by 8-Cl-cAMP and 8-NH2-cAMP was not mediated by activation of the cAMP kinase since more stable cAMP analogues (8-CPT-cAMP and N6-benzoyl-cAMP) or forskolin failed to induce death. Furthermore, 8-Cl-cAMP action was counteracted by adenosine deaminase and 3-isobutyl-1-methylxanthine, and mimicked by 8-Cl-adenosine, a major metabolite of 8-Cl-cAMP. It is concluded that 8-Cl- and 8-NH2-cAMP can induce morphological and biochemical effects resembling apoptotic cell death in MCF-7 cells through their conversion into potent cytotoxic metabolite(s).
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Affiliation(s)
- R Bøe
- Department of Anatomy and Cell Biology, University of Bergen, Norway
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44
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Conrad F, Hanne A, Gaur RK, Krupp G. Enzymatic synthesis of 2'-modified nucleic acids: identification of important phosphate and ribose moieties in RNase P substrates. Nucleic Acids Res 1995; 23:1845-53. [PMID: 7541130 PMCID: PMC306953 DOI: 10.1093/nar/23.11.1845] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
For the first time mosaic nucleic acids composed of 50% RNA and 50% DNA can be obtained as transcripts with T7 RNA polymerase. Two NTPs could be replaced simultaneously in a transcription reaction. This means more than 40 deoxynucleotides were inserted in one transcript. Previously, a maximum of two deoxynucleotides could be incorporated and 2'-O-methyl-NTPs were not substrates at all. We obtained reasonable transcript yields with a maximal level of 99% 2'-O-methyl-NTPs, and the products contained up to 58% 2'-O-methylnucleotides at more than 20 positions. Sequence-specific nucleotide incorporation was monitored by sequence ladders (partial alkali or iodine cleavage). No base misincorporations were detected with 100% dGTP, dCTP and dTTP, and with partial incorporation of dATP alpha S, 2'-O-methyl-GTP alpha S and 2'-O-methyl-CTP alpha S, whereas they were found with dATP, 2'-O-methyl-ATP alpha S and 2'-O-methyl-UTP alpha S. Quantitative data allow predetermined modification levels of partially modified transcripts. Highly modified transcripts can be used for structural and functional studies, in modification interference approaches and for in vitro evolution procedures. Modification interference studies revealed a small number of important phosphate and ribose moieties in RNase P substrates. The conversion of T7 RNA polymerase to a DNA polymerase extends the observation that there is no absolute distinction between RNA and DNA polymerases. Accordingly, an adapted concept of a primordial RNA world is presented.
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Affiliation(s)
- F Conrad
- Institut für Allgemeine Mikrobiologie der Christian-Albrechts-Universität, Kiel, Germany
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45
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Thiry M. Nucleic acid compartmentalization within the cell nucleus by in situ transferase-immunogold techniques. Microsc Res Tech 1995; 31:4-21. [PMID: 7542939 DOI: 10.1002/jemt.1070310103] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In the present review, we report on recent results obtained by in situ transferase-immunogold techniques as to the ultrastructural distribution of DNA and RNA within the cell nucleus. Special emphasis is placed on the various nucleolar components and the various enigmatic structures of the extranucleolar region: interchromatin granules, coiled bodies, and simple nuclear bodies. These data are discussed in the light of our current understanding of the functional organization of the cell nucleus.
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Affiliation(s)
- M Thiry
- Laboratory of Cellular and Tissular Biology, University of Liège, Belgium
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46
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Tilly JL, Hsueh AJ. Microscale autoradiographic method for the qualitative and quantitative analysis of apoptotic DNA fragmentation. J Cell Physiol 1993; 154:519-26. [PMID: 8436601 DOI: 10.1002/jcp.1041540310] [Citation(s) in RCA: 226] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A method combining the advantages of electrophoretic DNA fractionation and autoradiography is described for the qualitative and quantitative analysis of internucleosomal DNA fragmentation that occurs during apoptosis, or "programmed cell death." This procedure utilizes terminal transferase enzyme to uniformly add one molecule of [alpha 32P]-dideoxynucleotide to the 3'-end of DNA fragments. Following gel electrophoresis and autoradiographic analysis, the total amount of radiolabel incorporated into the low molecular weight DNA fraction can be quantitated and used to estimate the degree of apoptotic DNA fragmentation in any given sample. This method requires as little as 15 ng of total cellular DNA and increases the sensitivity of apoptotic DNA detection by at least 100-fold over the widely used ethidium bromide staining method. The procedure should prove valuable for the analysis of apoptosis in minute quantities of tissues and cultured cells.
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Affiliation(s)
- J L Tilly
- Department of Gynecology and Obstetrics, Stanford University School of Medicine, California 94305-5317
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47
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Frohman MA. Rapid amplification of complementary DNA ends for generation of full-length complementary DNAs: thermal RACE. Methods Enzymol 1993; 218:340-56. [PMID: 7685466 DOI: 10.1016/0076-6879(93)18026-9] [Citation(s) in RCA: 394] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- M A Frohman
- Department of Pharmacological Sciences, State University of New York, Stony Brook 11794
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48
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Thiry M. Ultrastructural detection of DNA within the nucleolus by sensitive molecular immunocytochemistry. Exp Cell Res 1992; 200:135-44. [PMID: 1563481 DOI: 10.1016/s0014-4827(05)80081-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This paper describes a new technique for locating DNA on semithin or ultrathin sections of aldehyde-fixed and plastic-embedded cells or tissues. Sections were incubated in a medium containing bromodeoxyuridine (BUdR) triphosphate and terminal deoxynucleotidyltransferase. The labeled nucleotides bound at the surface of the sections were subsequently detected with an anti-BUdR antibody and immunoglobulin-gold complex. On semithin sections, labeled nucleotide detection was achieved by an amplification step with silver enhancement. This technique was applied to a wide variety of biological materials allowing a sensitive detection of DNA-containing structures, even where these are present in very low amounts. Examples of high resolution and sensitive detection include the DNA present in mitochondria, chloroplasts, mycoplasmas, and DNA viruses. Special attention focused on the location of DNA inside the nucleolus. In Ehrlich tumor cell nucleoli, DNA was detected in the fibrillar centers and not in the dense fibrillar component. Identical results were found in the nucleoli of other cell types. These results contradict earlier data but conform with other recent immunocytochemical observations concerning the correlation between structure and function in the nucleolus. This method provides a useful tool for investigations requiring highly precise correlations between a molecular function and a given ultrastructural morphology.
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Affiliation(s)
- M Thiry
- Laboratory of Cell and Tissue Biology, University of Liège, Belgium
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Strasser P, Zhang YP, Rohozinski J, Van Etten JL. The termini of the chlorella virus PBCV-1 genome are identical 2.2-kbp inverted repeats. Virology 1991; 180:763-9. [PMID: 1989390 DOI: 10.1016/0042-6822(91)90089-t] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Chlorella virus PBCV-1 genome is a linear nonpermuted 333-kbp dsDNA molecule with covalently closed hairpin termini. The termini (minus the hairpin) are identical inverted repeats of at least 2185 bases after which the sequence diverges. The inverted repeats contain two small potential open reading frames and several direct repeats. However, neither the open reading frames nor the remainder of the inverted repeats are transcribed during PBCV-1 replication. Twenty-nine other Chlorella virus DNAs, of 36 tested, hybridized to the PBCV-1 terminal fragments.
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Affiliation(s)
- P Strasser
- Department of Plant Pathology, University of Nebraska, Lincoln 68583-0722
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Lai TS, Chiang JY. Cloning and characterization of two major 3-methylcholanthrene inducible hamster liver cytochrome P450s. Arch Biochem Biophys 1990; 283:429-39. [PMID: 2275554 DOI: 10.1016/0003-9861(90)90664-k] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have studied the immunochemical properties of two major 3-methylcholanthrene inducible hamster liver cytochrome P450 isozymes, P450 MC1 and P450 MC4. Immunoblots using specific antibodies against P450 MC1 and P450 MC4 demonstrated that these two P450s were present in very low levels in control hamster livers and were greatly induced by 3-methylcholanthrene treatment. P450 MC1 was immunochemically different from P450 MC4, rat P450c and P450d, and rabbit LM4. The immunorelated polypeptide to P450 MC1 was not present in the control or the 3-methylcholanthrene-treated rat liver microsomes, whereas it was present in two human liver microsomal preparations. On the other hand, P450 MC4 was immunochemically related to rat P450d and rabbit LM4. The immunorelated polypeptide to P450 MC4 was present in the human and 3-methylcholanthrene-treated rat liver microsomes. We also isolated full-length cDNA clones encoding P450 MC1 and P450 MC4 mRNAs from a 3-methylcholanthrene-induced hamster liver cDNA library. The full-length cDNA clones of P450 MC1 and P450 MC4 contained 1771 and 1868 base pairs, which encoded polypeptides of 494 and 513 amino acids, respectively. RNA blot analysis revealed that the mRNAs for P450 MC1 and P450 MC4 were 2100 and 2600 bases in length, respectively. 3-Methylcholanthrene pretreatment increased the P450 MC1 mRNA level by 16-fold and the P450 MC4 mRNA level by 11-fold in the hamster livers. A comparison of the deduced amino acid sequences with other cytochrome P450s revealed that P450 MC1 was most similar to the mouse P450(15) alpha with 75% sequence identity, whereas P450 MC4 shared 87% identity with the rat P450d or mouse P3(450). These results indicated that P450 MC1 was a unique member (CYP2A8) in the P450IIA subfamily, whereas P450 MC4 was the hamster P450IA2.
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Affiliation(s)
- T S Lai
- Department of Biochemistry and Molecular Pathology, Northeastern Ohio Universities College of Medicine, Rootstown 44272
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