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Novgorodtseva AI, Lomzov AA, Vasilyeva SV. Synthesis and Properties of α-Phosphate-Modified Nucleoside Triphosphates. Molecules 2024; 29:4121. [PMID: 39274969 PMCID: PMC11397104 DOI: 10.3390/molecules29174121] [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: 07/18/2024] [Revised: 08/25/2024] [Accepted: 08/28/2024] [Indexed: 09/16/2024] Open
Abstract
This review article is focused on the progress made in the synthesis of 5'-α-P-modified nucleoside triphosphates (α-phosphate mimetics). A variety of α-P-modified nucleoside triphosphates (NTPαXYs, Y = O, S; X = S, Se, BH3, alkyl, amine, N-alkyl, imido, or others) have been developed. There is a unique class of nucleoside triphosphate analogs with different properties. The main chemical approaches to the synthesis of NTPαXYs are analyzed and systematized here. Using the data presented here on the diversity of NTPαXYs and their synthesis protocols, it is possible to select an appropriate method for obtaining a desired α-phosphate mimetic. Triphosphates' substrate properties toward nucleic acid metabolism enzymes are highlighted too. We reviewed some of the most prominent applications of NTPαXYs including the use of modified dNTPs in studies on mechanisms of action of polymerases or in systematic evolution of ligands by exponential enrichment (SELEX). The presence of heteroatoms such as sulfur, selenium, or boron in α-phosphate makes modified triphosphates nuclease resistant. The most distinctive feature of NTPαXYs is that they can be recognized by polymerases. As a result, S-, Se-, or BH3-modified phosphate residues can be incorporated into DNA or RNA. This property has made NTPαXYs a multifunctional tool in molecular biology. This review will be of interest to synthetic chemists, biochemists, biotechnologists, or biologists engaged in basic or applied research.
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Affiliation(s)
- Alina I Novgorodtseva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Svetlana V Vasilyeva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
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2
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Liu J, Li W, Jin X, Lin F, Han J, Zhang Y. Optimal tagging strategies for illuminating expression profiles of genes with different abundance in zebrafish. Commun Biol 2023; 6:1300. [PMID: 38129658 PMCID: PMC10739737 DOI: 10.1038/s42003-023-05686-1] [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: 01/18/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
CRISPR-mediated knock-in (KI) technology opens a new era of fluorescent-protein labeling in zebrafish, a preferred model organism for in vivo imaging. We described here an optimized zebrafish gene-tagging strategy, which enables easy and high-efficiency KI, ensures high odds of obtaining seamless KI germlines and is suitable for wide applications. Plasmid donors for 3'-labeling were optimized by shortening the microhomologous arms and by reducing the number and reversing the sequence of the consensus Cas9/sgRNA binding sites. To allow for scar-less KI across the genome, linearized dsDNA donors with 5'-chemical modifications were generated and successfully incorporated into our method. To refine the germline screen workflow and expedite the screen process, we combined fluorescence enrichment and caudal-fin junction-PCR. Furthermore, to trace proteins expressed at a low abundance, we developed a fluorescent signal amplifier using the transcriptional activation strategy. Together, our strategies enable efficient gene-tagging and sensitive expression detection for almost every gene in zebrafish.
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Affiliation(s)
- Jiannan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Wenyuan Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Xuepu Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Fanjia Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
- Laboratory Animal Center, Xiamen University, 361102, Xiamen, Fujian, China.
- Research Unit of Cellular Stress of CAMS, Cancer Research Center of Xiamen University, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, 361102, Xiamen, Fujian, China.
| | - Yingying Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
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3
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Wade Wolfe MM, Pluth MD. Understanding Reactive Sulfur Species through P/S Synergy. Inorg Chem 2023; 62:10.1021/acs.inorgchem.3c01976. [PMID: 37615644 PMCID: PMC11131337 DOI: 10.1021/acs.inorgchem.3c01976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
We investigated the differential oxidative and nucleophilic chemistry of reactive sulfur and oxygen anions (SSNO-, SNO-, NO2-, S42-, and HS-) using the simple reducing electrophile PPh2Cl. In the case of SSNO- reacting with PPh2Cl, a complex mixture of mono and diphosphorus products is formed exclusively in the P(V) oxidation state. We found that the phosphine stoichiometry dictates selectivity for oxidation to P=S/P=O products or transformation to P2 species. Interestingly, only chalcogen atoms are incorporated into the phosphorus products and, instead, nitrogen is released in the form of NO gas. Finally, we demonstrate that more reducing anions (S42- and HS-) also react with PPh2Cl with P=S bond formation as a key reaction driving force.
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Affiliation(s)
- Michael M Wade Wolfe
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impart, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-1253, United States
| | - Michael D Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impart, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-1253, United States
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4
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Huang D, Shen P, Xu C, Xu Z, Cheng D, Zhu X, Fang M, Wang Z, Xu Z. Dual nucleases-assisted cyclic amplification using polydopamine nanospheres-based biosensors for one-pot detection of microRNAs. Biosens Bioelectron 2023; 222:114957. [PMID: 36463653 DOI: 10.1016/j.bios.2022.114957] [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: 09/20/2022] [Revised: 10/27/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
The accurate detection of microRNAs (miRNAs) is essential in the early diagnosis and treatment of cancers. Existing miRNA detection methods represented by nucleic acid amplification (NAA) techniques, such as qRT-PCR, suffer from the small size of miRNAs and lead to limited practicability. CRISPR Cas13a system, another valuable toolbox for nucleic acid detection, relies heavily on the behaviors of accompanying isothermal NAA techniques, which prompts similar deficiencies in miRNA detection. In this study, a dual nucleases-assisted cyclic amplification (DUNCAN) strategy has been established to replace NAA techniques for one-pot detection of miRNAs. The DUNCAN strategy contained an initial reaction based on CRISPR Cas13a for target recognition, and an accompanied cyclic reaction using DNA probes protected by polydopamine nanospheres (PDANSs) for signal amplification and result readout. Exemplified by miR-19b, which has been confirmed to be related to several tumors, the quantitative detection through the DUNCAN strategy was achieved in the dynamic range of 10-106 fM, with a calculated detection limit of 1.27 fM. Besides, the DUNCAN strategy presented well selectivity and anti-interference performance for accurate detection of miR-19b in complex miRNA mixtures, different cell lines and clinical samples compared with qRT-PCR. All these performances demonstrated the promising potential of the DUNCAN strategy in clinical miRNA detection and diagnosis.
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Affiliation(s)
- Di Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Peijie Shen
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Chutian Xu
- Department of Biomedical Engineering, School of Engineering, Tufts University, Medford, MA, 02155, USA
| | - Zhipeng Xu
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310027, China
| | - Dongyuan Cheng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, 410000, China
| | - Mengjun Fang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Ziyi Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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5
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Son H, Park J, Hwang I, Jung Y, Bae S, Lee S. Mg 2+-dependent conformational rearrangements of CRISPR-Cas12a R-loop complex are mandatory for complete double-stranded DNA cleavage. Proc Natl Acad Sci U S A 2021; 118:e2113747118. [PMID: 34853172 PMCID: PMC8670479 DOI: 10.1073/pnas.2113747118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas12a, an RNA-guided DNA targeting endonuclease, has been widely used for genome editing and nucleic acid detection. As part of the essential processes for both of these applications, the two strands of double-stranded DNA are sequentially cleaved by a single catalytic site of Cas12a, but the mechanistic details that govern the generation of complete breaks in double-stranded DNA remain to be elucidated. Here, using single-molecule fluorescence resonance energy transfer assay, we identified two conformational intermediates that form consecutively following the initial cleavage of the nontarget strand. Specifically, these two intermediates are the result of further unwinding of the target DNA in the protospacer-adjacent motif (PAM)-distal region and the subsequent binding of the target strand to the catalytic site. Notably, the PAM-distal DNA unwound conformation was stabilized by Mg2+ ions, thereby significantly promoting the binding and cleavage of the target strand. These findings enabled us to propose a Mg2+-dependent kinetic model for the mechanism whereby Cas12a achieves cleavage of the target DNA, highlighting the presence of conformational rearrangements for the complete cleavage of the double-stranded DNA target.
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Affiliation(s)
- Heyjin Son
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jaeil Park
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Injoo Hwang
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Youngri Jung
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea;
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6
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Mochizuki S, Miyamoto N, Sakurai K. Oligonucleotide delivery to antigen presenting cells by using schizophyllan. Drug Metab Pharmacokinet 2021; 42:100434. [PMID: 34896749 DOI: 10.1016/j.dmpk.2021.100434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
Schizophyllan (SPG), a member of the β-glucan family, can form novel complexes with homo-polynucleotides such as poly(dA) through hydrogen bonding between two main chain glucoses and the one nucleotide base. Dectin-1, one of the major receptors for β-glucans, is known to be expressed on antigen presenting cells (APCs) such as macrophages and dendritic cells. This suggests that the above-mentioned complexes could deliver bound functional oligonucleotides (ODNs) including antisense (AS)-ODNs, small interfering RNA, and CpG-ODNs to the APCs. Analysis using a quartz crystal microbalance revealed that a complex consisting of SPG and dA60 with a phosphorothioate backbone was recognized by recombinant Dectin-1 protein. Treatment with this complex containing an AS-ODN for tumor necrosis factor alpha protected mice against lipopolysaccharide-induced hepatitis at a very low AS-ODN dose. Moreover, immunization with CpG-ODN/SPG complex and antigenic proteins induced potent antigen specific immune responses. The present review also represents peptide delivery by conjugation with dA60 and the preparation of a nanogel using DNA-DNA hybridization. These findings indicate that the delivery of a specific ODN using β-glucans could be used for treating various diseases caused by APCs and for activating antigen specific immune responses.
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Affiliation(s)
- Shinichi Mochizuki
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka, 808-0135, Japan.
| | - Noriko Miyamoto
- Department of Applied Chemistry, Aichi Institute of Technology, 1247, Yachigusa, Yakusacho, Toyota, Aichi, 470-0392, Japan
| | - Kazuo Sakurai
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka, 808-0135, Japan
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7
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Gong J, Kan L, Zhang X, He Y, Pan J, Zhao L, Li Q, Liu M, Tian J, Lin S, Lu Z, Xue L, Wang C, Tang G. An enhanced method for nucleic acid detection with CRISPR-Cas12a using phosphorothioate modified primers and optimized gold-nanopaticle strip. Bioact Mater 2021; 6:4580-4590. [PMID: 34095617 PMCID: PMC8141609 DOI: 10.1016/j.bioactmat.2021.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 12/13/2022] Open
Abstract
CRISPR-Cas12a system has been shown promising for nucleic acid diagnostics due to its rapid, portable and accurate features. However, cleavage of the amplicons and primers by the cis- and trans-activity of Cas12a hinders the attempts to integrate the amplification and detection into a single reaction. Through phosphorothioate modification of primers, we realized onepot detection with high sensitivity using plasmids of SARS-CoV-2, HPV16 and HPV18. We also identified the activated Cas12a has a much higher affinity to C nucleotide-rich reporter than others. By applying such reporters, the reaction time required for a lateral-flow readout was significantly reduced. Furthermore, to improve the specificity of the strip-based assay, we created a novel reporter and, when combined with a customized gold-nanopaticle strip, the readout was greatly enhanced owing to the elimination of the nonspecific signal. This established system, termed Targeting DNA by Cas12a-based Eye Sight Testing in an Onepot Reaction (TESTOR), was validated using clinical cervical scrape samples for human papillomaviruses (HPVs) detection. Our system represents a general approach to integrating the nucleic acid amplification and detection into a single reaction in CRISPR-Cas systems, highlighting its potential as a rapid, portable and accurate detection platform of nucleic acids.
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Affiliation(s)
- Jiaojiao Gong
- Yaneng Biotech, Co., Ltd, Fosun Pharma, Shenzhen 518100, China
| | - Lijuan Kan
- Department of Laboratory Medicine, Luohu District People's Hospital, Shenzhen 518001, China
| | - Xiuming Zhang
- Department of Laboratory Medicine, Luohu District People's Hospital, Shenzhen 518001, China
| | - Ying He
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Jiaqiang Pan
- Yaneng Biotech, Co., Ltd, Fosun Pharma, Shenzhen 518100, China
| | - Liping Zhao
- Department of Laboratory Medicine, Nanning First People's Hospital, Nanning 530022, China
| | - Qianyun Li
- Department of Neurology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo 315010, China
| | - Menghao Liu
- Nanobiological Medicine Center, Key Lab of Fuel Cell Technology of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, China
| | - Jie Tian
- Yaneng Biotech, Co., Ltd, Fosun Pharma, Shenzhen 518100, China
| | - Sili Lin
- Yaneng Biotech, Co., Ltd, Fosun Pharma, Shenzhen 518100, China
| | - Zhouyu Lu
- Yaneng Biotech, Co., Ltd, Fosun Pharma, Shenzhen 518100, China
| | - Liang Xue
- Yaneng Biotech, Co., Ltd, Fosun Pharma, Shenzhen 518100, China
| | - Chaojun Wang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Guanghui Tang
- Yaneng Biotech, Co., Ltd, Fosun Pharma, Shenzhen 518100, China
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8
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Mei M, Mu L, Liang S, Wang Y, She G, Shi W. A general configurational strategy to quencher-free aptasensors. Biosens Bioelectron 2021; 178:113025. [PMID: 33529860 DOI: 10.1016/j.bios.2021.113025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022]
Abstract
The aptasensor, developed from the aptamer, has aroused wide concern in recent years owing to its high sensitivity and specificity. However, the quenching unit involved in the most of the aptasensors is indispensable to the fabrication of an aptasensor, which would undoubtedly increase the complexity of the device. In this study, a facile strategy was developed for construction of the quencher-free aptasensors, in which the quenching units can be omitted, and only an aptamer strand and a fluorophore are necessary. Distinguishable from the configuration of the traditional ones, the aptasensors developed in this work rationally employed the intrinsic quenching abilities of the analytes to directly regulate the fluorescence of the fluorophore. Furthermore, the aptamer strand as a discriminatory unit efficiently captured the corresponding analytes to around the fluorophores. As a result, the fluorescence of the aptasensor can be significantly sensitive to the analytes. The generality of the current design is evidenced by the successful fabrication of seven quencher-free aptasensors for Cu2+, Ag+, Hg2+, ATP and dopamine through 6-FAM labeling aptamers of Cu2+, Ag+, Hg2+, ATP, dopamine, 5-TAMRA and ROX labeling aptamers of Cu2+. Present strategy endows an aptasensor with a simple structure, high selectivity and fine sensitivity. The configuration of the quencher-free aptasensors fabricated in this work can be readily utilized for more aptasensors.
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Affiliation(s)
- Mingliang Mei
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lixuan Mu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Sen Liang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangwei She
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wensheng Shi
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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Zhu S, Zheng T, Kong L, Li J, Cao B, DeMott MS, Sun Y, Chen Y, Deng Z, Dedon PC, You D. Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications. Biomolecules 2020; 10:biom10111491. [PMID: 33126637 PMCID: PMC7692671 DOI: 10.3390/biom10111491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023] Open
Abstract
DNA phosphorothioate (PT) modification is a novel modification that occurs on the DNA backbone, which refers to a non-bridging phosphate oxygen replaced by sulfur. This exclusive DNA modification widely distributes in bacteria but has not been found in eukaryotes to date. PT modification renders DNA nuclease tolerance and serves as a constitute element of bacterial restriction-modification (R-M) defensive system and more biological functions are awaiting exploration. Identification and quantification of the bacterial PT modifications are thus critical to better understanding their biological functions. This work describes three detailed methods derived from iodine-induced specific cleavage-an iodine-induced cleavage assay (ICA), a deep sequencing of iodine-induced cleavage at PT site (ICDS) and an iodine-induced cleavage PT sequencing (PT-IC-Seq)-for the investigation of PT modifications. Using these approaches, we have identified the presence of PT modifications and quantized the frequency of PT modifications in bacteria. These characterizations contributed to the high-resolution genomic mapping of PT modifications, in which the distribution of PT modification sites on the genome was marked accurately and the frequency of the specific modified sites was reliably obtained. Here, we provide time-saving and less labor-consuming methods for both of qualitative and quantitative analysis of genomic PT modifications. The application of these methodologies will offer great potential for better understanding the biology of the PT modifications and open the door to future further systematical study.
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Affiliation(s)
- Sucheng Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Tao Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Jinli Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Bo Cao
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China;
| | - Michael S. DeMott
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (M.S.D.); (P.C.D.)
| | - Yihua Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Ying Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (M.S.D.); (P.C.D.)
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
- Correspondence: ; Tel.: +86-21-62933765
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10
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Sasaki S, Izumi H, Morimoto Y, Sakurai K, Mochizuki S. Induction of potent cell growth inhibition by schizophyllan/K-ras antisense complex in combination with gemcitabine. Bioorg Med Chem 2020; 28:115668. [PMID: 32828430 DOI: 10.1016/j.bmc.2020.115668] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Antisense oligonucleotides (AS-ODNs) specifically hybridize with target mRNAs, resulting in interference with the splicing mechanism or the regulation of protein translation. In our previous reports, we demonstrated that β-glucan schizophyllan (SPG) can form a complex with AS-ODNs attached with oligo deoxyadenosine dA40 (AS-ODN-dA40/SPG), and that this complex can be recognized by β-glucan receptor Dectin-1 on antigen presenting cells and lung cancer cells. In many types of cancer cell, activating K-ras mutations related to malignancy are frequently observed. In this study, we first designed 78 AS-ODNs for K-ras to optimize the sequence for highly efficient gene suppression. The selected AS-ODN (K-AS07) having dA40 made a complex with SPG. The resultant complex (K-AS07-dA40/SPG) showed an effect of silencing the ras gene in the cells (PC9: human adenocarcinoma differentiated from lung tissue) expressing Dectin-1, leading to the suppression of cell growth. Furthermore, the cytotoxic effect was enhanced when used in combination with the anticancer drug gemcitabine. Gemcitabine, a derivative of cytidine, was shown to interact with dA40 in a sequence-dependent manner. This interaction did not appear to be so strong, with the gemcitabine being released from the complex after internalization into the cells. SPG and the dA40 part of K-AS07-dA40 play roles in carriers for K-AS07 and gemcitabine, respectively, resulting in a strong cytotoxic effect. This combination effect is a novel feature of the AS-ODN-dA40/SPG complexes. These results could facilitate the clinical application of these complexes for cancer treatment.
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Affiliation(s)
- Shogo Sasaki
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Hiroto Izumi
- University of Occupational and Environmental Health, 1-1 Isegaoka, Yahatanishi-ku, Kitakyushu, Fukuoka 807-8555, Japan
| | - Yasuo Morimoto
- University of Occupational and Environmental Health, 1-1 Isegaoka, Yahatanishi-ku, Kitakyushu, Fukuoka 807-8555, Japan
| | - Kazuo Sakurai
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Shinichi Mochizuki
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan.
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11
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Xiong X, Wu G, Wei Y, Liu L, Zhang Y, Su R, Jiang X, Li M, Gao H, Tian X, Zhang Y, Hu L, Chen S, Tang Y, Jiang S, Huang R, Li Z, Wang Y, Deng Z, Wang J, Dedon PC, Chen S, Wang L. SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities. Nat Microbiol 2020; 5:917-928. [PMID: 32251370 DOI: 10.1038/s41564-020-0700-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 03/02/2020] [Indexed: 01/07/2023]
Abstract
Bacteria have evolved diverse mechanisms to fend off predation by bacteriophages. We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component. Here, we describe an unusual SspABCD-SspE PT system in Vibrio cyclitrophicus, Escherichia coli and Streptomyces yokosukanensis, which has distinct genetic organization, biochemical functions and phenotypic behaviour. SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase and possibly introducing nicks to facilitate sulfur incorporation. Strikingly, SspABCD coupled with SspE provides protection against phages in unusual ways: (1) SspE senses sequence-specific PTs by virtue of its PT-stimulated NTPase activity to exert its anti-phage activity, and (2) SspE inhibits phage propagation by introducing nicking damage to impair phage DNA replication. These results not only expand our knowledge about the diversity and functions of DNA PT modification but also enhance our understanding of the known arsenal of defence systems.
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Affiliation(s)
- Xiaolin Xiong
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Wei
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Liqiong Liu
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Yubing Zhang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Su
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xianyue Jiang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Mengxue Li
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Haiyan Gao
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Xihao Tian
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yizhou Zhang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Li Hu
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Si Chen
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - You Tang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Susu Jiang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Ruolin Huang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yunfu Wang
- Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zixin Deng
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shi Chen
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Lianrong Wang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China. .,Taihe Hospital, Hubei University of Medicine, Shiyan, China. .,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China.
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12
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Yasugi M, Motooka D, Nakamura S, Miyake M. Phosphorothioation of foreign DNA influences the transformation efficiency in Clostridium perfringens NCTC8239. Anaerobe 2019; 61:102085. [PMID: 31401257 DOI: 10.1016/j.anaerobe.2019.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 11/29/2022]
Abstract
Major advances in Clostridium perfringens genetics have been achieved through the development of electroporation-induced transformation; however, highly transformable strains are still limited. SM101 is the only useful strain for genetic manipulation via transformation in C. perfringens causing foodborne illness (FBI). We focused on the FBI strain NCTC8239, which is transformed at a low frequency, because it has a gene cassette that is predicted to encode enzymes involved in DNA phosphorothioation (PT). The oxidant-dependent degradation of NCTC8239 genomic DNA suggested that the genome is PT-modified. When foreign DNA was PT-modified using a plasmid expressing Salmonella enterica PT modification enzymes, the transformation efficiency of NCTC8239 was significantly higher than that using an unmodified plasmid. We then attempted to establish a highly transformable derivative of NCTC8239, and focused on DptFGH, which are predicted to be PT restriction enzymes. A dptG-null mutant exhibited significantly higher transformation efficiency with unmodified foreign DNA than did the wild-type strain. Furthermore, the mutant was transformed with the unmodified plasmid as efficiently as with a PT-modified plasmid, implying that DptG is involved in PT-dependent restriction. Thus, the present results revealed that PT modifications of foreign DNA influence the transformation frequency of NCTC8239 and suggest that PT is a factor contributing to transformation efficiency in NCTC8239.
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Affiliation(s)
- Mayo Yasugi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan.
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masami Miyake
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
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13
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Yao P, Liu Y, Wang C, Lan W, Wang C, Cao C. Investigating the interactions between DNA and DndE during DNA phosphorothioation. FEBS Lett 2019; 593:2790-2799. [PMID: 31276192 DOI: 10.1002/1873-3468.13529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 01/08/2023]
Abstract
The DNA phosphorothioate modification is a novel physiological variation in bacteria. DndE controls this modification by binding to dsDNA via a mechanism that remains unclear. Structural analysis of the wild-type DndE tetramer suggests that a positively charged region in its center is important for DNA binding. In the present study, we replaced residues G21 and G24 in this region with lysines, which increases the DNA binding affinity but does not affect the DNA degradation phenotype. Structural analysis of the mutant indicates that it forms a new tetrameric conformation and that DndE interacts with DNA as a monomer rather than as a tetramer. A structural model of the DndE-DNA complex, based on its structural homolog P22 Arc repressor, indicates that two flexible loops in DndE are determinants of DNA binding.
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Affiliation(s)
- Penfei Yao
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yaping Liu
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chengkun Wang
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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14
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Li J, Chen Y, Zheng T, Kong L, Zhu S, Sun Y, Deng Z, Yang L, You D. Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency. PLoS Genet 2019; 15:e1008026. [PMID: 30933976 PMCID: PMC6459556 DOI: 10.1371/journal.pgen.1008026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/11/2019] [Accepted: 02/17/2019] [Indexed: 12/31/2022] Open
Abstract
Phosphorothioate (PT) modifications of the DNA backbone, widespread in prokaryotes, are first identified in bacterial enteropathogens Escherichia coli B7A more than a decade ago. However, methods for high resolution mapping of PT modification level are still lacking. Here, we developed the PT-IC-seq technique, based on iodine-induced selective cleavage at PT sites and high-throughput next generation sequencing, as a mean to quantitatively characterizing the genomic landscape of PT modifications. Using PT-IC-seq we foud that most PT sites are partially modified at a lower PT frequency (< 5%) in E. coli B7A and Salmonella enterica serovar Cerro 87, and both show a heterogeneity pattern of PT modification similar to those of the typical methylation modification. Combining the iodine-induced cleavage and absolute quantification by droplet digital PCR, we developed the PT-IC-ddPCR technique to further measure the PT modification level. Consistent with the PT-IC-seq measurements, PT-IC-ddPCR analysis confirmed the lower PT frequency in E. coli B7A. Our study has demonstrated the heterogeneity of PT modification in the bacterial population and we also established general tools for rigorous mapping and characterization of PT modification events at whole genome level. We describe to our knowledge the first genome-wide quantitative characterization of PT landscape and provides appropriate strategies for further functional studies of PT modification.
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Affiliation(s)
- Jinli Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Sucheng Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yihua Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Litao Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (LY); (DY)
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (LY); (DY)
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15
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Zhang X, Chen H, Ji Y, Jiang K, Chen H. Sulfur Transfer Versus Phenyl Ring Transfer in the Gas Phase: Sequential Loss of CH 3OH and CH 3O-P=O from Protonated Phosphorothioates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:459-467. [PMID: 30569428 DOI: 10.1007/s13361-018-2098-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 06/09/2023]
Abstract
Collisional activation fragmentation of protonated phosphorothioates leads to skeletal rearrangement and formation of aryl sulfenylium cation (R-PhS+) via successive eliminations of CH3OH and CH3O-P=O. To better understand this unusual fragmentation reaction, isotope-labeling experiments and density functional theory (DFT) calculations were carried out to investigate two mechanistic pathways. In route 1, a direct intramolecular transfer of the R-phenyl group occurs from the oxygen atom to the sulfur atom on thiophosphoryl to form methoxyl S-(3-methyl-4-methylsulfanyl-phenyl) phosphonium thiolate (a4), which subsequently dissociates to form the m/z 169 cation. In route 2, the sulfur atom of the thiophosphoryl group undergoes two stepwise transfer (1,4-migration to the ortho-carbon atom of the phenyl ring followed by 1,2-migration to the ipso-carbon atom) to form an intermediate isomer, which undergoes the subsequent dissociation to form the m/z 169 cation. DFT calculations suggested that route 2 was more favorable than route 1 from the point view of kinetics. Graphical Abstract.
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Affiliation(s)
- Xiaoping Zhang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang, 330013, People's Republic of China
| | - Honghan Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang, 330013, People's Republic of China
| | - Yin Ji
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang, 330013, People's Republic of China
| | - Kezhi Jiang
- Key Laboratory of Organosilicon Chemistry and Material Technology, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Huanwen Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang, 330013, People's Republic of China.
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16
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Swarts DC, Jinek M. Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a. Mol Cell 2019; 73:589-600.e4. [PMID: 30639240 PMCID: PMC6858279 DOI: 10.1016/j.molcel.2018.11.021] [Citation(s) in RCA: 286] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/14/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12a (Cpf1) is an RNA-guided DNA-cutting nuclease that has been repurposed for genome editing. Upon target DNA binding, Cas12a cleaves both the target DNA in cis and non-target single-stranded DNAs (ssDNAs) in trans. To elucidate the molecular basis for both DNase cleavage modes, we performed structural and biochemical studies on Francisella novicida Cas12a. We show that guide RNA-target strand DNA hybridization conformationally activates Cas12a, triggering its trans-acting, non-specific, single-stranded DNase activity. In turn, cis cleavage of double-stranded DNA targets is a result of protospacer adjacent motif (PAM)-dependent DNA duplex unwinding, electrostatic stabilization of the displaced non-target DNA strand, and ordered sequential cleavage of the non-target and target DNA strands. Cas12a releases the PAM-distal DNA cleavage product and remains bound to the PAM-proximal DNA cleavage product in a catalytically competent, trans-active state. Together, these results provide a revised model for the molecular mechanisms of both the cis- and the trans-acting DNase activities of Cas12a enzymes, enabling their further exploitation as genome editing tools.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Proteins/chemistry
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Enzyme Activation
- Francisella/enzymology
- Francisella/genetics
- Gene Editing/methods
- Models, Molecular
- Nucleic Acid Conformation
- Protein Conformation
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- Daan C Swarts
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
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17
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Bila H, Kurisinkal EE, Bastings MMC. Engineering a stable future for DNA-origami as a biomaterial. Biomater Sci 2019; 7:532-541. [DOI: 10.1039/c8bm01249k] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Reviewing the various methods and effectivity to stabilize DNA origami in biological environments.
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Affiliation(s)
- Hale Bila
- Programmable Biomaterials Laboratory (PBL)
- Institute of Materials (IMX)/Interfaculty Bioengineering Institute (IBI)
- School of Engineering (STI)
- École Polytechnique Federale de Lausanne (EPFL)
- Lausanne
| | - Eva E. Kurisinkal
- Programmable Biomaterials Laboratory (PBL)
- Institute of Materials (IMX)/Interfaculty Bioengineering Institute (IBI)
- School of Engineering (STI)
- École Polytechnique Federale de Lausanne (EPFL)
- Lausanne
| | - Maartje M. C. Bastings
- Programmable Biomaterials Laboratory (PBL)
- Institute of Materials (IMX)/Interfaculty Bioengineering Institute (IBI)
- School of Engineering (STI)
- École Polytechnique Federale de Lausanne (EPFL)
- Lausanne
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18
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Osborn MF, Khvorova A. Improving siRNA Delivery In Vivo Through Lipid Conjugation. Nucleic Acid Ther 2018; 28:128-136. [PMID: 29746209 DOI: 10.1089/nat.2018.0725] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA interference (RNAi)-based therapeutics are approaching clinical approval for genetically defined diseases. Current clinical success is a result of significant innovations in the development of chemical architectures that support sustained, multi-month efficacy in vivo following a single administration. Conjugate-mediated delivery has established itself as the most promising platform for safe and targeted small interfering RNA (siRNA) delivery. Lipophilic conjugates represent a major class of modifications that improve siRNA pharmacokinetics and enable efficacy in a broad range of tissues. Here, we review current literature and define key features and limitations of this approach for in vivo modulation of gene expression.
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Affiliation(s)
- Maire F Osborn
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Anastasia Khvorova
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
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19
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Schwede F, Genieser HG, Rentsch A. The Chemistry of the Noncanonical Cyclic Dinucleotide 2'3'-cGAMP and Its Analogs. Handb Exp Pharmacol 2017; 238:359-384. [PMID: 27392950 DOI: 10.1007/164_2015_43] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The cyclic dinucleotides (CDNs) cyclic diguanosine monophosphate (c-diGMP) and cyclic diadenosine monophosphate (c-diAMP) with two canonical 3'→5' internucleotide linkages are ubiquitous second messenger molecules in bacteria, regulating a multitude of physiological processes. Recently the noncanonical CDN cyclic guanosine monophosphate-adenosine monophosphate (2'3'-cGAMP) featuring a mixed linkage, which consists of a 2'→5' and a 3'→5' internucleotide bond, has been identified as a signaling molecule in metazoan species in late 2012. 2'3'-cGAMP formation is biocatalyzed by cGAMP synthase (cGAS) upon sensing of cytosolic double-stranded DNA (dsDNA) and functions as an endogenous inducer of innate immunity by directly binding to and activating the adaptor protein stimulator of interferon genes (STING). Thereby 2'3'-cGAMP can stimulate interferon-β (INF-β) secretion, a major signaling pathway of host defense, which is independent of toll-like receptor (TLR) activation. Medicinal chemistry of 2'3'-cGAMP and development of corresponding analogs are still in their infancy, and only a handful of structurally related compounds are available to the scientific community. The aim of this chapter is to summarize synthetic approaches to prepare canonical and noncanonical endogenous CDNs including 2'3'-cGAMP. Furthermore, we will describe syntheses of 2'3'-cGAMP analogs bearing modifications, which will facilitate further studies of the emerging biological functions of 2'3'-cGAMP and to identify additional receptor proteins. Finally, we will review latest developments concerning 2'3'-cGAMP analogs with improved hydrolytic stability in cell cultures and in tissues, putatively qualifying for new therapeutic options on the basis of 2'3'-cGAMP signaling.
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Affiliation(s)
- Frank Schwede
- BIOLOG Life Science Institute, Forschungslabor und Biochemica-Vertrieb GmbH, Flughafendamm 9a, 28199, Bremen, Germany.
| | - Hans-Gottfried Genieser
- BIOLOG Life Science Institute, Forschungslabor und Biochemica-Vertrieb GmbH, Flughafendamm 9a, 28199, Bremen, Germany
| | - Andreas Rentsch
- BIOLOG Life Science Institute, Forschungslabor und Biochemica-Vertrieb GmbH, Flughafendamm 9a, 28199, Bremen, Germany
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20
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Iribe H, Miyamoto K, Takahashi T, Kobayashi Y, Leo J, Aida M, Ui-Tei K. Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets. ACS OMEGA 2017; 2:2055-2064. [PMID: 29450406 PMCID: PMC5808362 DOI: 10.1021/acsomega.7b00291] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 05/05/2017] [Indexed: 05/12/2023]
Abstract
Chemical modifications of 2'-O-methyl (2'-OMe) and locked nucleic acid (LNA) of the nucleotides in the seed region (positions 2-8) of the small interfering RNA (siRNA) guide strand significantly reduced seed-matched (SM) off-target effects. The siRNA with 2'-OMe modifications inhibited the expression of a completely-matched (CM) target gene, whereas that with LNA modifications did not inhibit the expression of the CM target. By computational predictions of conformational changes of siRNA by these modifications, we revealed that both modifications in the siRNA seed region reduce SM off-target effects by steric hindrance to base-pairing with target transcripts but LNA modifications also disturb the association of the siRNA guide strand with the Argonaute (AGO) protein by altering RNA conformation. Thus, chemical modifications of the siRNA guide strand, which alter steric conformation to disturb base-pairing with target transcripts but do not disturb the association with the AGO protein, may successfully suppress off-target effects without substantial loss of RNA silencing activity.
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Affiliation(s)
- Hanna Iribe
- Department
of Computational Biology and Medical Science, Graduate School of Frontier
Sciences, The University of Tokyo, Chiba 277-8581, Japan
| | - Kengo Miyamoto
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Tomoko Takahashi
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshiaki Kobayashi
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Jastina Leo
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Faculty
of Microbiology, Immunology and Molecular Genetics, University of California, Los
Angeles, California 90095, United States
| | - Misako Aida
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kumiko Ui-Tei
- Department
of Computational Biology and Medical Science, Graduate School of Frontier
Sciences, The University of Tokyo, Chiba 277-8581, Japan
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- E-mail:
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21
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Houlihan G, Arangundy-Franklin S, Holliger P. Exploring the Chemistry of Genetic Information Storage and Propagation through Polymerase Engineering. Acc Chem Res 2017; 50:1079-1087. [PMID: 28383245 PMCID: PMC5406124 DOI: 10.1021/acs.accounts.7b00056] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Nucleic
acids are a distinct form of sequence-defined biopolymer.
What sets them apart from other biopolymers such as polypeptides or
polysaccharides is their unique capacity to encode, store, and propagate
genetic information (molecular heredity). In nature, just two closely
related nucleic acids, DNA and RNA, function as repositories and carriers
of genetic information. They therefore are the molecular embodiment
of biological information. This naturally leads to questions regarding
the degree of variation from this seemingly ideal “Goldilocks”
chemistry that would still be compatible with the fundamental property
of molecular heredity. To address this question, chemists have
created a panoply of synthetic
nucleic acids comprising unnatural sugar ring congeners, backbone
linkages, and nucleobases in order to establish the molecular parameters
for encoding genetic information and its emergence at the origin of
life. A deeper analysis of the potential of these synthetic genetic
polymers for molecular heredity requires a means of replication and
a determination of the fidelity of information transfer. While non-enzymatic
synthesis is an increasingly powerful method, it currently remains
restricted to short polymers. Here we discuss efforts toward establishing
enzymatic synthesis, replication, and evolution of synthetic genetic
polymers through the engineering of polymerase enzymes found in nature. To endow natural polymerases with the ability to efficiently utilize
non-cognate nucleotide substrates, novel strategies for the screening
and directed evolution of polymerase function have been realized.
High throughput plate-based screens, phage display, and water-in-oil
emulsion technology based methods have yielded a number of engineered
polymerases, some of which can synthesize and reverse transcribe synthetic
genetic polymers with good efficiency and fidelity. The inception
of such polymerases demonstrates that, at a basic
level at least, molecular heredity is not restricted to the natural
nucleic acids DNA and RNA, but may be found in a large (if finite)
number of synthetic genetic polymers. And it has opened up these novel
sequence spaces for investigation. Although largely unexplored, first
tentative forays have yielded ligands (aptamers) against a range of
targets and several catalysts elaborated in a range of different chemistries.
Finally, taking the lead from established DNA designs, simple polyhedron
nanostructures have been described. We anticipate that further
progress in this area will expand the
range of synthetic genetic polymers that can be synthesized, replicated,
and evolved providing access to a rich sequence, structure, and phenotypic
space. “Synthetic genetics”, that is, the exploration
of these spaces, will illuminate the chemical parameter range for
en- and decoding information, 3D folding, and catalysis and yield
novel ligands, catalysts, and nanostructures and devices for applications
in biotechnology and medicine.
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Affiliation(s)
- Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
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22
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Xiao L, Xiang Y. Quantification of total phosphorothioate in bacterial DNA by a bromoimane-based fluorescent method. Biotechnol J 2016; 11:824-30. [PMID: 27168171 DOI: 10.1002/biot.201500432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 03/16/2016] [Accepted: 05/09/2016] [Indexed: 01/09/2023]
Abstract
The discovery of phosphorothioate (PT) modifications in bacterial DNA has challenged our understanding of conserved phosphodiester backbone structure of cellular DNA. This exclusive DNA modification in bacteria is not found in animal cells yet, and its biological function in bacteria is still poorly understood. Quantitative information about the bacterial PT modifications is thus important for the investigation of their possible biological functions. In this study, we have developed a simple fluorescence method for selective quantification of total PTs in bacterial DNA, based on fluorescent labeling of PTs and subsequent release of the labeled fluorophores for absolute quantification. The method was highly selective to PTs and not interfered by the presence of reactive small molecules or proteins. The quantification of PTs in an E. coli DNA sample was successfully achieved using our method and gave a result of about 455 PTs per million DNA nucleotides, while almost no detectable PTs were found in a mammalian calf thymus DNA. With this new method, the content of phosphorothioate in bacterial DNA could be successfully quantified, serving as a simple method suitable for routine use in biological phosphorothioate related studies.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China.
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23
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Prakash TP, Kinberger GA, Murray HM, Chappell A, Riney S, Graham MJ, Lima WF, Swayze EE, Seth PP. Synergistic effect of phosphorothioate, 5'-vinylphosphonate and GalNAc modifications for enhancing activity of synthetic siRNA. Bioorg Med Chem Lett 2016; 26:2817-2820. [PMID: 27161280 DOI: 10.1016/j.bmcl.2016.04.063] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 12/30/2022]
Abstract
Chemical modifications are essential to improve metabolic stability and pharmacokinetic properties of siRNA to enable their systemic delivery. We investigated the effect of combing the phosphorothioate (PS) modification with metabolically stable phosphate analog (E)-5'-vinylphosphonate and GalNAc cluster conjugation on the activity of fully 2'-modified siRNA in cell culture and mice. Our data suggest that integrating multiple chemical approaches in one siRNA molecule improved potency 5-10 fold and provide a roadmap for developing more efficient siRNA drugs.
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Affiliation(s)
- Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States.
| | - Garth A Kinberger
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Heather M Murray
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Alfred Chappell
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Stan Riney
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Mark J Graham
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Walt F Lima
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
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24
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Application of locked nucleic acid-based probes in fluorescence in situ hybridization. Appl Microbiol Biotechnol 2016; 100:5897-906. [PMID: 26969040 DOI: 10.1007/s00253-016-7429-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/19/2016] [Accepted: 02/24/2016] [Indexed: 02/07/2023]
Abstract
Fluorescence in situ hybridization (FISH) employing nucleic acid mimics as probes is becoming an emerging molecular tool in the microbiology area for the detection and visualization of microorganisms. However, the impact that locked nucleic acid (LNA) and 2'-O-methyl (2'-OMe) RNA modifications have on the probe that is targeting microorganisms is unknown. In this study, the melting and hybridization efficiency properties of 18 different probes in regards to their use in FISH for the detection of the 16S rRNA of Helicobacter pylori were compared. For the same sequence and target, probe length and the type of nucleic acid mimics used as mixmers in LNA-based probes strongly influence the efficiency of detection. LNA probes with 10 to 15 mers showed the highest efficiency. Additionally, the combination of 2'-OMe RNA with LNA allowed an increase on the fluorescence intensities of the probes. Overall, these results have significant implications for the design and applications of LNA probes for the detection of microorganisms.
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25
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Chumakov AM, Yuhina ES, Frolova EI, Kravchenko JE, Chumakov SP. Expanding the application potential of DNA aptamers by their functionalization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Xiong W, Zhao G, Yu H, He X. Interactions of Dnd proteins involved in bacterial DNA phosphorothioate modification. Front Microbiol 2015; 6:1139. [PMID: 26539172 PMCID: PMC4611135 DOI: 10.3389/fmicb.2015.01139] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
DNA phosphorothioation (PT) is the first discovered physiological DNA backbone modification, in which a non-bridging oxygen atom of the phosphodiester bond is replaced with a sulfur atom in Rp (rectus for plane) configuration. PT modification is governed by a highly conserved gene cluster dndA/iscS-dndBCDE that is widespread across bacterial and archaeal species. However, little is known about how these proteins coordinately react with each other to perform oxygen–sulfur swap. We here demonstrated that IscS, DndC, DndD and DndE form a protein complex of which the molecular ratio for four proteins in the complex is approximate 1:1:1:1. DndB here displayed little or weak affinity to the complex and the constructs harboring dndACDE can confer the host in vivo PT modification. Using co-purification and pull down strategy, we demonstrated that the four proteins assemble into a pipeline in collinear to its gene organization, namely, IscS binding to DndC, DndC binding to DndD, and DndD binding to DndE. Moreover, weak interactions between DndE and IscS, DndE and DndC were also identified.
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Affiliation(s)
- Wei Xiong
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University Shanghai, China
| | - Gong Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University Shanghai, China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University Shanghai, China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University Shanghai, China
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27
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Urmann K, Tenenbaum E, Walter JG, Segal E. Porous Silicon Biosensors Employing Emerging Capture Probes. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-20346-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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28
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Abstract
Multi-site-saturation mutagenesis allows altering of "localizable" properties such as activity and selectivity and enables the discovery of cooperative amino acid substitutions which are unlikely to be discovered by saturating single codons individually or iteratively. The herein presented method "OmniChange" does not require any DNA modifying enzyme (e.g., endonucleases or ligases), and diverse mutant libraries with up to five simultaneously saturated positions are generated in a robust and technically simple manner in four steps. The key feature of the OmniChange method is a highly efficient chemical cleavage of phosphorothiolated nucleotides by ethanol-iodine to generate 12-nucleotide-long 5' overhangs in double-stranded DNA. The generated vector and inserts can be hybridized in a one-pot assembly leading to fully functional mutagenic plasmids, and the employed E. coli host can easily ligate up to 10 DNA nicks without any further enzymatic treatment. OmniChange is furthermore a reliable and general tool for multi-DNA fragment assembly which is DNA sequence independent.
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29
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DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks. Sci Rep 2014; 4:6642. [PMID: 25319634 PMCID: PMC4198939 DOI: 10.1038/srep06642] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/29/2014] [Indexed: 01/13/2023] Open
Abstract
The modification of DNA by phosphorothioate (PT) occurs when the non-bridging oxygen in the sugar-phosphate backbone of DNA is replaced with sulfur. This DNA backbone modification was recently discovered and is governed by the dndABCDE genes in a diverse group of bacteria and archaea. However, the biological function of DNA PT modifications is poorly understood. In this study, we employed the RNA-seq analysis to characterize the global transcriptional changes in response to PT modifications. Our results show that DNA without PT protection is susceptible to DNA damage caused by the dndFGHI gene products. The DNA double-stranded breaks then trigger the SOS response, cell filamentation and prophage induction. Heterologous expression of dndBCDE conferring DNA PT modifications at GPSA and GPST prevented the damage in Salmonella enterica. Our data provide insights into the physiological role of the DNA PT system.
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30
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Lai C, Wu X, Chen C, Huang T, Xiong X, Wu S, Gu M, Deng Z, Chen X, Chen S, Wang L. In vivo mutational characterization of DndE involved in DNA phosphorothioate modification. PLoS One 2014; 9:e107981. [PMID: 25269084 PMCID: PMC4182426 DOI: 10.1371/journal.pone.0107981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/22/2014] [Indexed: 12/05/2022] Open
Abstract
DNA phosphorothioate (PT) modification is a recently identified epigenetic modification that occurs in the sugar-phosphate backbone of prokaryotic DNA. Previous studies have demonstrated that DNA PT modification is governed by the five DndABCDE proteins in a sequence-selective and RP stereo-specific manner. Bacteria may have acquired this physiological modification along with dndFGH as a restriction-modification system. However, little is known about the biological function of Dnd proteins, especially the smallest protein, DndE, in the PT modification pathway. DndE was reported to be a DNA-binding protein with a preference for nicked dsDNA in vitro; the binding of DndE to DNA occurs via six positively charged lysine residues on its surface. The substitution of these key lysine residues significantly decreased the DNA binding affinities of DndE proteins to undetectable levels. In this study, we conducted site-directed mutagenesis of dndE on a plasmid and measured DNA PT modifications under physiological conditions by mass spectrometry. We observed distinctive differences from the in vitro binding assays. Several mutants with lysine residues mutated to alanine decreased the total frequency of PT modifications, but none of the mutants completely eliminated PT modification. Our results suggest that the nicked dsDNA-binding capacity of DndE may not be crucial for PT modification and/or that DndE may have other biological functions in addition to binding to dsDNA.
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Affiliation(s)
- Chongde Lai
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaolin Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Chao Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Teng Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xiaolin Xiong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Shuangju Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Meijia Gu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- * E-mail: (SC); (LW)
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- * E-mail: (SC); (LW)
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31
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Wang LX, Su L, Li JH, Li NB, Peng ZH, Li YY, Xu XH. Simple and Convenient Method for the Synthesis of Aryltellurophosphates Catalyzed by Cesium Hydroxide. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.879897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ling Xiao Wang
- a College of Chemistry and Chemical Engineering , Hunan University , Changsha , China
| | - Liu Su
- a College of Chemistry and Chemical Engineering , Hunan University , Changsha , China
| | - Jian Hua Li
- a College of Chemistry and Chemical Engineering , Hunan University , Changsha , China
| | - Ning Bo Li
- a College of Chemistry and Chemical Engineering , Hunan University , Changsha , China
| | - Zhi Hong Peng
- a College of Chemistry and Chemical Engineering , Hunan University , Changsha , China
| | - Yuan Yuan Li
- a College of Chemistry and Chemical Engineering , Hunan University , Changsha , China
| | - Xin Hua Xu
- a College of Chemistry and Chemical Engineering , Hunan University , Changsha , China
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Cao B, Chen C, DeMott MS, Cheng Q, Clark TA, Xiong X, Zheng X, Butty V, Levine SS, Yuan G, Boitano M, Luong K, Song Y, Zhou X, Deng Z, Turner SW, Korlach J, You D, Wang L, Chen S, Dedon PC. Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences. Nat Commun 2014; 5:3951. [PMID: 24899568 DOI: 10.1038/ncomms4951] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 04/25/2014] [Indexed: 01/29/2023] Open
Abstract
Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. Here we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: single molecule, real-time sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of GpsAAC/GpsTTC motifs, but with only 12% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at CpsCA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT-modification proteins and rule out known R-M mechanisms.
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Affiliation(s)
- Bo Cao
- 1] State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200233, China [2] Department of Biological Engineering, Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3]
| | - Chao Chen
- 1] Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China [2]
| | - Michael S DeMott
- 1] Department of Biological Engineering, Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2]
| | - Qiuxiang Cheng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Tyson A Clark
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Xiaolin Xiong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiaoqing Zheng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Vincent Butty
- Department of Biological Engineering, Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Stuart S Levine
- Department of Biological Engineering, Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - George Yuan
- Pacific Biosciences, Menlo Park, California 94025, USA
| | | | - Khai Luong
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Yi Song
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Xiufen Zhou
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200233, China
| | | | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Delin You
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Peter C Dedon
- Department of Biological Engineering, Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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33
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Kaur M, Rob A, Caton-Williams J, Huang Z. Biochemistry of Nucleic Acids Functionalized with Sulfur, Selenium, and Tellurium: Roles of the Single-Atom Substitution. ACTA ACUST UNITED AC 2013. [DOI: 10.1021/bk-2013-1152.ch005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Manindar Kaur
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Abdur Rob
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | | | - Zhen Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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34
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Ruff AJ, Dennig A, Schwaneberg U. To get what we aim for - progress in diversity generation methods. FEBS J 2013; 280:2961-78. [DOI: 10.1111/febs.12325] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Anna J. Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Germany
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35
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Jeong J, Cho N, Jung D, Bang D. Genome-scale genetic engineering in Escherichia coli. Biotechnol Adv 2013; 31:804-10. [PMID: 23624241 DOI: 10.1016/j.biotechadv.2013.04.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 04/13/2013] [Accepted: 04/15/2013] [Indexed: 12/23/2022]
Abstract
Genome engineering has been developed to create useful strains for biological studies and industrial uses. However, a continuous challenge remained in the field: technical limitations in high-throughput screening and precise manipulation of strains. Today, technical improvements have made genome engineering more rapid and efficient. This review introduces recent advances in genome engineering technologies applied to Escherichia coli as well as multiplex automated genome engineering (MAGE), a recent technique proposed as a powerful toolkit due to its straightforward process, rapid experimental procedures, and highly efficient properties.
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Affiliation(s)
- Jaehwan Jeong
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
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Zhang YC, Liang J, Lian P, Han Y, Chen Y, Bai L, Wang Z, Liang J, Deng Z, Zhao YL. Theoretical study on steric effects of DNA phosphorothioation: B-helical destabilization in Rp-phosphorothioated DNA. J Phys Chem B 2012; 116:10639-48. [PMID: 22857608 DOI: 10.1021/jp302494b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Phosphorothioation, with sulfur replacing a nonbridging oxygen of phosphate, has surfaced in bacterial DNA electrophoresis. To understand structural characteristics of the thio-substituted DNA, we have investigated the correlation between the relative energy of phosphate/phosphorothioate linkage and the backbone torsions. The relative energies (R.E.) computed by the quantum mechanical method, the PBE1PBE(CPCM, solvent=water)//PBE1PBE/6-31+G(2df) level of theory, were used to construct energy-scoring functions against backbone torsion variables, resulting in the squared correlation coefficients r(2) of 0.90-0.95. Then, the DNA energy alteration by phosphorothioation is estimated with the relative energy difference (ΔR.E.) between phosphate and phosphorothioate of the phosphate linkages in the DNA crystallographic database (NDB). As a result, Rp-phosphorothioation shifts the relative energy of B-helical structures by 2.7 ± 3.4 kcal/mol, destabilizing about 95% linkages, while Sp-phosphorothioation by -1.4 ± 2.4 kcal/mol, stabilizing over 84% linkages in the data sets. The B-helical destabilization is likely caused by the steric effect between the sulfur atom of Rp-phosphorothioate and the neighboring C-H groups of deoxyribose on the groove wall in B-helix. The unfavorable interaction may be magnified by the increasing rigidness of P-O-involving backbone torsions α and ζ upon the nonbridging phosphorothioations. Since B-helix is the most prevalent DNA double-helical structure and Rp-phosphorothioation is the exclusive configuration in bacteria thio-DNA found to date, the observed stereospecificity-destabilization correlation may reflect a structure-function relationship of biological DNA-phosphorothiation.
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Affiliation(s)
- Yi-Chao Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
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37
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Govan JM, Uprety R, Hemphill J, Lively MO, Deiters A. Regulation of transcription through light-activation and light-deactivation of triplex-forming oligonucleotides in mammalian cells. ACS Chem Biol 2012; 7:1247-56. [PMID: 22540192 DOI: 10.1021/cb300161r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Triplex-forming oligonucleotides (TFOs) are efficient tools to regulate gene expression through the inhibition of transcription. Here, nucleobase-caging technology was applied to the temporal regulation of transcription through light-activated TFOs. Through site-specific incorporation of caged thymidine nucleotides, the TFO:DNA triplex formation is blocked, rendering the TFO inactive. However, after a brief UV irradiation, the caging groups are removed, activating the TFO and leading to the inhibition of transcription. Furthermore, the synthesis and site-specific incorporation of caged deoxycytidine nucleotides within TFO inhibitor sequences was developed, allowing for the light-deactivation of TFO function and thus photochemical activation of gene expression. After UV-induced removal of the caging groups, the TFO forms a DNA dumbbell structure, rendering it inactive, releasing it from the DNA, and activating transcription. These are the first examples of light-regulated TFOs and their application in the photochemical activation and deactivation of gene expression. In addition, hairpin loop structures were found to significantly increase the efficacy of phosphodiester DNA-based TFOs in tissue culture.
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Affiliation(s)
- Jeane M. Govan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - Rajendra Uprety
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - James Hemphill
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - Mark O. Lively
- Center
for Structural Biology, Wake Forest University School of Medicine, Winston-Salem,
North Carolina 27157, United States
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
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38
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Marienhagen J, Dennig A, Schwaneberg U. Phosphorothioate-based DNA recombination: an enzyme-free method for the combinatorial assembly of multiple DNA fragments. Biotechniques 2012; 52:000113865. [DOI: 10.2144/000113865] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/09/2012] [Indexed: 11/23/2022] Open
Abstract
Rational guided generation of protein chimeras has developed into an attractive approach in protein engineering for tailoring catalytic and biophysical properties of enzymes. Combinatorial recombination of structural elements or whole protein domains is still technically challenging due to sequence dependent biases diminishing the overall quality of resulting chimeric libraries. Since methods for generating such libraries are often limited by a low frequency of crossover points and suffer from challenges in handling, we developed the phosphorothioate-based DNA recombination method (PTRec). PTRec is an enzyme-free method and only requires a short stretch of four amino acids that is identical among the proteins to be recombined in order to define a single crossover point. In a PTRec-generated chimeric library that shuffled five domains of phytase using genes from three different species, 88% of 42 randomly picked and sequenced genes were efficiently recombined. Furthermore, PTRec is a technically simple, fast, and reliable method that can be used for domain-and exon-shuffling or recombination of DNA fragments in general.
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Affiliation(s)
- Jan Marienhagen
- Department of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Alexander Dennig
- Department of Biotechnology, RWTH Aachen University, Aachen, Germany
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Hu W, Wang C, Liang J, Zhang T, Hu Z, Wang Z, Lan W, Li F, Wu H, Ding J, Wu G, Deng Z, Cao C. Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification. Cell Res 2012; 22:1203-6. [PMID: 22525332 DOI: 10.1038/cr.2012.66] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Ponomarov O, Laws AP, Hanusek J. 1,2,4-Dithiazole-5-ones and 5-thiones as efficient sulfurizing agents of phosphorus(iii) compounds – a kinetic comparative study. Org Biomol Chem 2012; 10:8868-76. [DOI: 10.1039/c2ob26460a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Maxwell CI, Liu CT, Neverov AA, Mosey NJ, Brown RS. Transition from concerted to stepwise processes as a function of leaving group ability: density functional theory and experimental study of lyoxide-promoted cleavages of phosphorothioate and phosphate triesters in water and methanol. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - C. Tony Liu
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Nicholas J. Mosey
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Robert Stan Brown
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
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Dennig A, Shivange AV, Marienhagen J, Schwaneberg U. OmniChange: the sequence independent method for simultaneous site-saturation of five codons. PLoS One 2011; 6:e26222. [PMID: 22039444 PMCID: PMC3198389 DOI: 10.1371/journal.pone.0026222] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/22/2011] [Indexed: 12/20/2022] Open
Abstract
Focused mutant library generation methods have been developed to improve mainly "localizable" enzyme properties such as activity and selectivity. Current multi-site saturation methods are restricted by the gene sequence, require subsequent PCR steps and/or additional enzymatic modifications. Here we report, a multiple site saturation mutagenesis method, OmniChange, which simultaneously and efficiently saturates five independent codons. As proof of principle, five chemically cleaved DNA fragments, each carrying one NNK-degenerated codon, were generated and assembled to full gene length in a one-pot-reaction without additional PCR-amplification or use of restriction enzymes or ligases. Sequencing revealed the presence of up to 27 different codons at individual positions, corresponding to 84.4% of the theoretical diversity offered by NNK-degeneration. OmniChange is absolutely sequence independent, does not require a minimal distance between mutated codons and can be accomplished within a day.
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Affiliation(s)
- Alexander Dennig
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Amol V. Shivange
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Jan Marienhagen
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- * E-mail:
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43
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Lassila JK, Zalatan JG, Herschlag D. Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annu Rev Biochem 2011; 80:669-702. [PMID: 21513457 DOI: 10.1146/annurev-biochem-060409-092741] [Citation(s) in RCA: 295] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phosphoryl-transfer reactions are central to biology. These reactions also have some of the slowest nonenzymatic rates and thus require enormous rate accelerations from biological catalysts. Despite the central importance of phosphoryl transfer and the fascinating catalytic challenges it presents, substantial confusion persists about the properties of these reactions. This confusion exists despite decades of research on the chemical mechanisms underlying these reactions. Here we review phosphoryl-transfer reactions with the goal of providing the reader with the conceptual and experimental background to understand this body of work, to evaluate new results and proposals, and to apply this understanding to enzymes. We describe likely resolutions to some controversies, while emphasizing the limits of our current approaches and understanding. We apply this understanding to enzyme-catalyzed phosphoryl transfer and provide illustrative examples of how this mechanistic background can guide and deepen our understanding of enzymes and their mechanisms of action. Finally, we present important future challenges for this field.
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Affiliation(s)
- Jonathan K Lassila
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
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44
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Abstract
Aptamers are single-stranded structured oligonucleotides (DNA or RNA) that can bind to a wide range of targets ("apatopes") with high affinity and specificity. These nucleic acid ligands, generated from pools of random-sequence by an in vitro selection process referred to as systematic evolution of ligands by exponential enrichment (SELEX), have now been identified as excellent tools for chemical biology, therapeutic delivery, diagnosis, research, and monitoring therapy in real-time imaging. Today, aptamers represent an interesting class of modern Pharmaceuticals which with their low immunogenic potential mimic extend many of the properties of monoclonal antibodies in diagnostics, research, and therapeutics. More recently, chimeric aptamer approach employing many different possible types of chimerization strategies has generated more stable and efficient chimeric aptamers with aptamer-aptamer, aptamer-nonaptamer biomacromolecules (siRNAs, proteins) and aptamer-nanoparticle chimeras. These chimeric aptamers when conjugated with various biomacromolecules like locked nucleic acid (LNA) to potentiate their stability, biodistribution, and targeting efficiency, have facilitated the accurate targeting in preclinical trials. We developed LNA-aptamer (anti-nucleolin and EpCAM) complexes which were loaded in iron-saturated bovine lactofeerin (Fe-blf)-coated dopamine modified surface of superparamagnetic iron oxide (Fe3O4) nanoparticles (SPIONs). This complex was used to deliver the specific aptamers in tumor cells in a co-culture model of normal and cancer cells. This review focuses on the chimeric aptamers, currently in development that are likely to find future practical applications in concert with other therapeutic molecules and modalities.
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Affiliation(s)
- Jagat R Kanwar
- Nanomedicine Laboratory of Immunology and Molecular Biomedical Research (LIMBR), Centre for Biotechnology and Interdisciplinary Biosciences (BioDeakin), Institute for Technology and Research Innovation (ITRI), Geelong Technology Precinct (GTP), Deakin University, Victoria, Australia.
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Wang L, Chen S, Vergin KL, Giovannoni SJ, Chan SW, DeMott MS, Taghizadeh K, Cordero OX, Cutler M, Timberlake S, Alm EJ, Polz MF, Pinhassi J, Deng Z, Dedon PC. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci U S A 2011; 108:2963-8. [PMID: 21285367 PMCID: PMC3041111 DOI: 10.1073/pnas.1017261108] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.
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Affiliation(s)
- Lianrong Wang
- Department of Biological Engineering
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Shi Chen
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Kevin L. Vergin
- Department of Microbiology, Oregon State University, Corvallis, OR 97331; and
| | | | | | | | | | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael Cutler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Eric J. Alm
- Department of Biological Engineering
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jarone Pinhassi
- Marine Microbiology, School of Natural Sciences, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Zixin Deng
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Peter C. Dedon
- Department of Biological Engineering
- Center for Environmental Health Sciences, and
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Bobeck DR, Schinazi RF, Coats SJ. Advances in nucleoside monophosphate prodrugs as anti-HCV agents. Antivir Ther 2011; 15:935-50. [PMID: 21041908 DOI: 10.3851/imp1667] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleoside monophosphate prodrugs that are eventually bioconverted to the active nucleoside triphosphate (NTP) offer the potential to deliver increased intracellular NTP levels and/or organ-specific NTP enhancement. There are several classes of monophosphate prodrugs that have been applied to HCV drug discovery, and some of these approaches are currently being evaluated in humans. This review discusses recent advances in monophosphate prodrug approaches to improve oral absorption, stability and pharmacokinetic profile, including their advantages and potential pitfalls.
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Edwards DR, Neverov AA, Brown RS. Study on the Transesterification of Methyl Aryl Phosphorothioates in Methanol Promoted by Cd(II), Mn(II), and a Synthetic Pd(II) Complex. Inorg Chem 2011; 50:1786-97. [DOI: 10.1021/ic102220m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David R. Edwards
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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48
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Ozga M, Dolot R, Janicka M, Kaczmarek R, Krakowiak A. Histidine triad nucleotide-binding protein 1 (HINT-1) phosphoramidase transforms nucleoside 5'-O-phosphorothioates to nucleoside 5'-O-phosphates. J Biol Chem 2010; 285:40809-18. [PMID: 20940308 PMCID: PMC3003382 DOI: 10.1074/jbc.m110.162065] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/07/2010] [Indexed: 12/26/2022] Open
Abstract
Nucleoside 5'-O-phosphorothioates are formed in vivo as primary products of hydrolysis of oligo(nucleoside phosphorothioate)s (PS-oligos) that are applied as antisense therapeutic molecules. The biodistribution of PS-oligos and their pharmacokinetics have been widely reported, but little is known about their subsequent decay inside the organism. We suggest that the enzyme responsible for nucleoside 5'-O-monophosphorothioate ((d)NMPS) metabolism could be histidine triad nucleotide-binding protein 1 (Hint-1), a phosphoramidase belonging to the histidine triad (HIT) superfamily that is present in all forms of life. An additional, but usually ignored, activity of Hint-1 is its ability to catalyze the conversion of adenosine 5'-O-monophosphorothioate (AMPS) to 5'-O-monophosphate (AMP). By mutagenetic and biochemical studies, we defined the active site of Hint-1 and the kinetic parameters of the desulfuration reaction (P-S bond cleavage). Additionally, crystallographic analysis (resolution from 1.08 to 1.37 Å) of three engineered cysteine mutants showed the high similarity of their structures, which were not very different from the structure of WT Hint-1. Moreover, we found that not only AMPS but also other ribonucleoside and 2'-deoxyribonucleoside phosphorothioates are desulfurated by Hint-1 at the following relative rates: GMPS > AMPS > dGMPS ≥ CMPS > UMPS > dAMPS ≫ dCMPS > TMPS, and during the reaction, hydrogen sulfide, which is thought to be the third gaseous mediator, was released.
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Affiliation(s)
- Magdalena Ozga
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
| | - Rafal Dolot
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
| | - Magdalena Janicka
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
| | - Renata Kaczmarek
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
| | - Agnieszka Krakowiak
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
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49
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Ruman T, Długopolska K, Jurkiewicz A, Rut D, Frączyk T, Cieśla J, Leś A, Szewczuk Z, Rode W. Thiophosphorylation of free amino acids and enzyme protein by thiophosphoramidate ions. Bioorg Chem 2010; 38:74-80. [DOI: 10.1016/j.bioorg.2009.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 11/18/2009] [Accepted: 11/19/2009] [Indexed: 11/25/2022]
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50
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