1
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Choi JH, Kim S, Kang OY, Choi SY, Hyun JY, Lee HS, Shin I. Selective fluorescent labeling of cellular proteins and its biological applications. Chem Soc Rev 2024; 53:9446-9489. [PMID: 39109465 DOI: 10.1039/d4cs00094c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Proteins, which are ubiquitous in cells and critical to almost all cellular functions, are indispensable for life. Fluorescence imaging of proteins is key to understanding their functions within their native milieu, as it provides insights into protein localization, dynamics, and trafficking in living systems. Consequently, the selective labeling of target proteins with fluorophores has emerged as a highly active research area, encompassing bioorganic chemistry, chemical biology, and cell biology. Various methods for selectively labeling proteins with fluorophores in cells and tissues have been established and are continually being developed to visualize and characterize proteins. This review highlights research findings reported since 2018, with a focus on the selective labeling of cellular proteins with small organic fluorophores and their biological applications in studying protein-associated biological events. We also discuss the strengths and weaknesses of each labeling approach for their utility in living systems.
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Affiliation(s)
- Joo Hee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Sooin Kim
- Department of Chemistry, Sogang University, 04107 Seoul, Republic of Korea.
| | - On-Yu Kang
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Seong Yun Choi
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
- Pharmaceutical Chemistry, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
- Pharmaceutical Chemistry, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 04107 Seoul, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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2
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Xiang Z, Lu J, Ming Y, Guo W, Chen X, Sun W. Engineering of a DNA/γPNA Hybrid Nanoreporter for ctDNA Mutation Detection via γPNA Urinalysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310225. [PMID: 38958527 PMCID: PMC11434236 DOI: 10.1002/advs.202310225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Detection of circulating tumor DNA (ctDNA) mutations, which are molecular biomarkers present in bodily fluids of cancer patients, can be applied for tumor diagnosis and prognosis monitoring. However, current profiling of ctDNA mutations relies primarily on polymerase chain reaction (PCR) and DNA sequencing and these techniques require preanalytical processing of blood samples, which are time-consuming, expensive, and tedious procedures that increase the risk of sample contamination. To overcome these limitations, here the engineering of a DNA/γPNA (gamma peptide nucleic acid) hybrid nanoreporter is disclosed for ctDNA biosensing via in situ profiling and recording of tumor-specific DNA mutations. The low tolerance of γPNA to single mismatch in base pairing with DNA allows highly selective recognition and recording of ctDNA mutations in peripheral blood. Owing to their remarkable biostability, the detached γPNA strands triggered by mutant ctDNA will be enriched in kidneys and cleared into urine for urinalysis. It is demonstrated that the nanoreporter has high specificity for ctDNA mutation in peripheral blood, and urinalysis of cleared γPNA can provide valuable information for tumor progression and prognosis evaluation. This work demonstrates the potential of the nanoreporter for urinary monitoring of tumor and patient prognosis through in situ biosensing of ctDNA mutations.
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Affiliation(s)
- Zhichu Xiang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
| | - Jianhua Lu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yang Ming
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
| | - Weisheng Guo
- Department of Minimally Invasive Interventional Radiology, The State Key Laboratory of Respiratory Disease, School of Biomedical Engineering & The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Theranostics Center of Excellence (TCE), Yong Loo Lin School of Medicine, National University of Singapore, 11 Biopolis Way, Helios, Singapore, 138667, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Weijian Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
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3
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Xiong T, Chen Y, Peng Q, Li M, Lu S, Chen X, Fan J, Wang L, Peng X. Pyrazolone-Protein Interaction Enables Long-Term Retention Staining and Facile Artificial Biorecognition on Cell Membranes. J Am Chem Soc 2024; 146:24158-24166. [PMID: 39138141 DOI: 10.1021/jacs.4c08987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Cell membrane genetic engineering has been utilized to confer cell membranes with functionalities for diagnostic and therapeutic purposes but concerns over cost and variable modification results. Although nongenetic chemical modification and phospholipid insertion strategies are more convenient, they still face bottlenecks in either biosafety or stability of the modifications. Herein, we show that pyrazolone-bearing molecules can bind to proteins with high stability, which is mainly contributed to by the multiple interactions between pyrazolone and basic amino acids. This new binding model offers a simple and versatile noncovalent approach for cell membrane functionalization. By binding to cell membrane proteins, pyrazolone-bearing dyes enabled precise cell tracking in vitro (>96 h) and in vivo (>21 days) without interfering with the protein function or causing cell death. Furthermore, the convenient anchor of pyrazolone-bearing biotin on cell membranes rendered the biorecognition to avidin, showing the potential for artificially creating cell targetability.
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Affiliation(s)
- Tao Xiong
- State Key Laboratory of Fine Chemicals, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518071, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yingchao Chen
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, China
| | - Qiang Peng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, China
| | - Mingle Li
- State Key Laboratory of Fine Chemicals, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518071, China
| | - Sheng Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xiaoqiang Chen
- State Key Laboratory of Fine Chemicals, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518071, China
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, China
| | - Lei Wang
- State Key Laboratory of Fine Chemicals, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518071, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518071, China
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, China
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4
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Ai H, Pan M, Liu L. Chemical Synthesis of Human Proteoforms and Application in Biomedicine. ACS CENTRAL SCIENCE 2024; 10:1442-1459. [PMID: 39220697 PMCID: PMC11363345 DOI: 10.1021/acscentsci.4c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Limited understanding of human proteoforms with complex posttranslational modifications and the underlying mechanisms poses a major obstacle to research on human health and disease. This Outlook discusses opportunities and challenges of de novo chemical protein synthesis in human proteoform studies. Our analysis suggests that to develop a comprehensive, robust, and cost-effective methodology for chemical synthesis of various human proteoforms, new chemistries of the following types need to be developed: (1) easy-to-use peptide ligation chemistries allowing more efficient de novo synthesis of protein structural domains, (2) robust temporary structural support strategies for ligation and folding of challenging targets, and (3) efficient transpeptidative protein domain-domain ligation methods for multidomain proteins. Our analysis also indicates that accurate chemical synthesis of human proteoforms can be applied to the following aspects of biomedical research: (1) dissection and reconstitution of the proteoform interaction networks, (2) structural mechanism elucidation and functional analysis of human proteoform complexes, and (3) development and evaluation of drugs targeting human proteoforms. Overall, we suggest that through integrating chemical protein synthesis with in vivo functional analysis, mechanistic biochemistry, and drug development, synthetic chemistry would play a pivotal role in human proteoform research and facilitate the development of precision diagnostics and therapeutics.
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Affiliation(s)
- Huasong Ai
- New
Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life
Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and
Chemical Biology, Center for Synthetic and Systems Biology, Department
of Chemistry, Tsinghua University, Beijing 100084, China
- Institute
of Translational Medicine, School of Pharmacy, School of Chemistry
and Chemical Engineering, National Center for Translational Medicine
(Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Man Pan
- Institute
of Translational Medicine, School of Pharmacy, School of Chemistry
and Chemical Engineering, National Center for Translational Medicine
(Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- New
Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life
Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and
Chemical Biology, Center for Synthetic and Systems Biology, Department
of Chemistry, Tsinghua University, Beijing 100084, China
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5
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Bian T, Pei Y, Gao S, Zhou S, Sun X, Dong M, Song J. Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application. Adv Healthc Mater 2024:e2401207. [PMID: 39036821 DOI: 10.1002/adhm.202401207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 07/23/2024]
Abstract
Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.
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Affiliation(s)
- Tianyuan Bian
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, 300072, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yufeng Pei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Shitao Gao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- College of Materials Science and Engineering, Zhejiang University of Technology, ChaoWang Road 18, HangZhou, 310014, China
| | - Songtao Zhou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinyu Sun
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Aarhus, DK-8000, Denmark
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
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6
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López-Tena M, Winssinger N. Impact of charges on the hybridization kinetics and thermal stability of PNA duplexes. Org Biomol Chem 2024; 22:5759-5767. [PMID: 38920402 PMCID: PMC11253249 DOI: 10.1039/d4ob00887a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Peptide nucleic acid (PNA) is a prominent artificial nucleic acid mimetic and modifications at the γ-position of the peptidic backbone are known to further enhance the desirable properties of PNA in terms of duplex stability. Here, we leveraged a propargyl ether modification at this position for late stage functionalization of PNA to obtain positively charged (cationic amino and guanidinium groups), negatively charged (anionic carboxylate and alkyl phosphonate groups) and neutral (PEG) PNAs to assess the impact of these charges on DNA : PNA and PNA : PNA duplex formation. Thermal stability analysis findings concurred with prior studies showing PNA : DNA duplexes are moderately more stable with cationic PNAs than anionic PNAs at physiological salt concentrations. We show that this effect is derived predominantly from differences in the association kinetics. For PNA : PNA duplexes, anionic PNAs were found to form the most stable duplexes, more stable than neutral PNA : PNA duplexes.
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Affiliation(s)
- Miguel López-Tena
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
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7
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Carson LM, Watson EE. Peptide Nucleic Acids: From Origami to Editing. Chempluschem 2024:e202400305. [PMID: 38972843 DOI: 10.1002/cplu.202400305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/09/2024]
Abstract
Peptide nucleic acids (PNAs) combine the programmability of native nucleic acids with the robustness and ease of synthesis of a peptide backbone. These designer biomolecules have demonstrated tremendous utility across a broad range of applications, from the formation of bespoke biosupramolecular architectures to biosensing and gene regulation. Herein, we explore some of the key developments in the application of PNA in chemical biology and biotechnology in the last 5 years and present anticipated key areas of future development.
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Affiliation(s)
- Liam M Carson
- Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Emma E Watson
- Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
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8
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Reiber T, Dose C, Yushchenko DA. A novel dual-release scaffold for fluorescent labels improves cyclic immunofluorescence. RSC Chem Biol 2024; 5:684-690. [PMID: 38966675 PMCID: PMC11221530 DOI: 10.1039/d4cb00007b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/22/2024] [Indexed: 07/06/2024] Open
Abstract
Cyclic immunofluorescence is a powerful method to generate high-content imaging datasets for investigating cell biology and developing therapies. This method relies on fluorescent labels that determine the quality of immunofluorescence and the maximum number of staining cycles that can be performed. Here we present a novel fluorescent labelling strategy, based on antibodies conjugated to a scaffold containing two distinct sites for enzymatic cleavage of fluorophores. The scaffold is composed of a dextran decorated with short ssDNA that upon hybridization with complementary dye-modified oligos result in fluorescent molecules. The developed fluorescent labels exhibit specific staining and remarkable brightness in flow cytometry and fluorescence microscopy. We showed that the combination of DNase-mediated degradation of DNA and dextranse-mediated degradation of the dextran as two complementary enzymatic release mechanisms in one molecule, improves signal erasure from labelled epitopes. We envision that such dual-release labels with high brightness and efficient and specific erasure will advance multiplexed cyclic immunofluorescence approaches and thereby will contribute to gaining new insights in cell biology.
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Affiliation(s)
- Thorge Reiber
- Department of Chemical Biology, Miltenyi Biotec GmbH Friedrich-Ebert Straße 68 Bergisch Gladbach 51429 Germany
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Str. 2 Berlin 12489 Germany
| | - Christian Dose
- Department of Chemical Biology, Miltenyi Biotec GmbH Friedrich-Ebert Straße 68 Bergisch Gladbach 51429 Germany
| | - Dmytro A Yushchenko
- Department of Chemical Biology, Miltenyi Biotec GmbH Friedrich-Ebert Straße 68 Bergisch Gladbach 51429 Germany
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9
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Pichon M, Hollenstein M. Controlled enzymatic synthesis of oligonucleotides. Commun Chem 2024; 7:138. [PMID: 38890393 PMCID: PMC11189433 DOI: 10.1038/s42004-024-01216-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage of information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not as efficient as that to read (i.e., sequencing) DNA/RNA. Alternative, biocatalytic methods for the de novo synthesis of natural or modified oligonucleotides are in dire need to circumvent the limitations of traditional synthetic approaches. This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into immobilized primers by polymerases. While robust protocols have been established for DNA, RNA or XNA synthesis is more challenging. Nevertheless, using a suitable combination of protected nucleotides and polymerase has shown promises to produce RNA oligonucleotides even though the production of long DNA/RNA/XNA sequences (>1000 nt) remains challenging. We surmise that merging ligase- and polymerase-based synthesis would help to circumvent the current shortcomings of controlled enzymatic synthesis.
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Affiliation(s)
- Maëva Pichon
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, Rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, Rue du Docteur Roux, 75724, Paris Cedex 15, France.
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10
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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11
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Mir MH, Parmar S, Singh C, Kalia D. Location-agnostic site-specific protein bioconjugation via Baylis Hillman adducts. Nat Commun 2024; 15:859. [PMID: 38286847 PMCID: PMC10825175 DOI: 10.1038/s41467-024-45124-2] [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: 07/14/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Proteins labelled site-specifically with small molecules are valuable assets for chemical biology and drug development. The unique reactivity profile of the 1,2-aminothiol moiety of N-terminal cysteines (N-Cys) of proteins renders it highly attractive for regioselective protein labelling. Herein, we report an ultrafast Z-selective reaction between isatin-derived Baylis Hillman adducts and 1,2-aminothiols to form a bis-heterocyclic scaffold, and employ it for stable protein bioconjugation under both in vitro and live-cell conditions. We refer to our protein bioconjugation technology as Baylis Hillman orchestrated protein aminothiol labelling (BHoPAL). Furthermore, we report a lipoic acid ligase-based technology for introducing the 1,2-aminothiol moiety at any desired site within proteins, rendering BHoPAL location-agnostic (not limited to N-Cys). By using this approach in tandem with BHoPAL, we generate dually labelled protein bioconjugates appended with different labels at two distinct specific sites on a single protein molecule. Taken together, the protein bioconjugation toolkit that we disclose herein will contribute towards the generation of both mono and multi-labelled protein-small molecule bioconjugates for applications as diverse as biophysical assays, cellular imaging, and the production of therapeutic protein-drug conjugates. In addition to protein bioconjugation, the bis-heterocyclic scaffold we report herein will find applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Mudassir H Mir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Sangeeta Parmar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Chhaya Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Dimpy Kalia
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India.
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12
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Yang Y, Jiang Q, Zhang F. Nanocrystals for Deep-Tissue In Vivo Luminescence Imaging in the Near-Infrared Region. Chem Rev 2024; 124:554-628. [PMID: 37991799 DOI: 10.1021/acs.chemrev.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
In vivo imaging technologies have emerged as a powerful tool for both fundamental research and clinical practice. In particular, luminescence imaging in the tissue-transparent near-infrared (NIR, 700-1700 nm) region offers tremendous potential for visualizing biological architectures and pathophysiological events in living subjects with deep tissue penetration and high imaging contrast owing to the reduced light-tissue interactions of absorption, scattering, and autofluorescence. The distinctive quantum effects of nanocrystals have been harnessed to achieve exceptional photophysical properties, establishing them as a promising category of luminescent probes. In this comprehensive review, the interactions between light and biological tissues, as well as the advantages of NIR light for in vivo luminescence imaging, are initially elaborated. Subsequently, we focus on achieving deep tissue penetration and improved imaging contrast by optimizing the performance of nanocrystal fluorophores. The ingenious design strategies of NIR nanocrystal probes are discussed, along with their respective biomedical applications in versatile in vivo luminescence imaging modalities. Finally, thought-provoking reflections on the challenges and prospects for future clinical translation of nanocrystal-based in vivo luminescence imaging in the NIR region are wisely provided.
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Affiliation(s)
- Yang Yang
- College of Energy Materials and Chemistry, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Qunying Jiang
- College of Energy Materials and Chemistry, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Fan Zhang
- College of Energy Materials and Chemistry, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200433, China
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13
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Krishnaiah P, Atchudan R, Perumal S, Gangadaran P, Manoj D, Ahn BC, Kumar RS, Almansour AI, Lee YR, Jeon BH. Multifunctional carbon dots originated from waste garlic peel for rapid sensing of heavy metals and fluorescent imaging of 2D and 3D spheroids cultured fibroblast cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123422. [PMID: 37734247 DOI: 10.1016/j.saa.2023.123422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023]
Abstract
Here, we prepared sulfur and nitrogen self-doped carbon dots derived from garlic peel extract (GPSNCDs) using a hydrothermal method. The as-synthesized GPSNCDs were confirmed using Fourier-transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy. The analytical techniques indicate that the resulting GPSNCDs exhibit distinct emissive carbon-core with functionalities (owing to various ligands in the GPSNCDs). These functionalities are responsible for excellent hydrophilic and optical properties, including excitation-dependent emission and anti-photobleaching. Fluorescence intensities of GPSNCDs were quenched in the existence of Mn2+ and Fe3+ ions. This indicates that the GPSNCDs were sensitive to Fe3+ and Mn2+ ions with a limited range from 5 to 50 µM and showed lower recognition at ∼0.75 and 0.95 µM, respectively. In addition, the sensing results were generated in a short time (20 s). The cytotoxicity of GPSNCDs was tested to demonstrate that they are sufficiently safe to use for cellular imaging. The novel fluorescent GPSNCDs-based sensor can be used as a high-performance sensor for environmental monitoring. Further, GPSNCDs showed greater biocompatibility with normal fibroblast cells, and In Vitro fluorescent imaging of GPSNCDs revealed strong fluorescence signals in the two-dimensional (2D) and three-dimensional (3D) spheroids cultured fibroblast cells. The properties mentioned above demonstrate that the GPSNCDs can be applied to imaging normal cells without further modifications.
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Affiliation(s)
- Prakash Krishnaiah
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, South Korea
| | - Raji Atchudan
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea; Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India.
| | - Suguna Perumal
- Department of Chemistry, Sejong University, Seoul 143‑747, Republic of Korea
| | - Prakash Gangadaran
- BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, Republic of Korea
| | - Devaraj Manoj
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India; Centre for Material Chemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
| | - Byeong-Cheol Ahn
- BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, Republic of Korea
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yong Rok Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea.
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, South Korea.
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14
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Nithun RV, Yao YM, Lin X, Habiballah S, Afek A, Jbara M. Deciphering the Role of the Ser-Phosphorylation Pattern on the DNA-Binding Activity of Max Transcription Factor Using Chemical Protein Synthesis. Angew Chem Int Ed Engl 2023; 62:e202310913. [PMID: 37642402 DOI: 10.1002/anie.202310913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 08/31/2023]
Abstract
The chemical synthesis of site-specifically modified transcription factors (TFs) is a powerful method to investigate how post-translational modifications (PTMs) influence TF-DNA interactions and impact gene expression. Among these TFs, Max plays a pivotal role in controlling the expression of 15 % of the genome. The activity of Max is regulated by PTMs; Ser-phosphorylation at the N-terminus is considered one of the key regulatory mechanisms. In this study, we developed a practical synthetic strategy to prepare homogeneous full-length Max for the first time, to explore the impact of Max phosphorylation. We prepared a focused library of eight Max variants, with distinct modification patterns, including mono-phosphorylated, and doubly phosphorylated analogues at Ser2/Ser11 as well as fluorescently labeled variants through native chemical ligation. Through comprehensive DNA binding analyses, we discovered that the phosphorylation position plays a crucial role in the DNA-binding activity of Max. Furthermore, in vitro high-throughput analysis using DNA microarrays revealed that the N-terminus phosphorylation pattern does not interfere with the DNA sequence specificity of Max. Our work provides insights into the regulatory role of Max's phosphorylation on the DNA interactions and sequence specificity, shedding light on how PTMs influence TF function.
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Affiliation(s)
- Raj V Nithun
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Yumi Minyi Yao
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Xiaoxi Lin
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shaimaa Habiballah
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ariel Afek
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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15
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Beutel J, Tannig P, Di Vincenzo R, Schumacher T, Überla K, Eichler J. Bind&Bite: covalently stabilized heterodimeric coiled-coil peptides for the site-selective, cysteine-free chemical modification of proteins. RSC Chem Biol 2023; 4:794-803. [PMID: 37799587 PMCID: PMC10549240 DOI: 10.1039/d3cb00122a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023] Open
Abstract
Ensuring site-selectivity in covalent chemical modification of proteins is one of the major challenges in chemical biology and related biomedical disciplines. Most current strategies either utilize the selectivity of proteases, or are based on reactions involving the thiol groups of cysteine residues. We have modified a pair of heterodimeric coiled-coil peptides to enable the selective covalent stabilization of the dimer without using enzymes or cysteine moieties. Fusion of one peptide to the protein of interest, in combination with linking the desired chemical modification to the complementary peptide, facilitates stable, regio-selective attachment of the chemical moiety to the protein, through the formation of the covalently stabilized coiled-coil. This ligation method, which is based on the formation of isoeptide and squaramide bonds, respectively, between the coiled-coil peptides, was successfully used to selectively modify the HIV-1 envelope glycoprotein. Covalent stabilization of the coiled-coil also facilitated truncation of the peptides by one heptad sequence. Furthermore, selective addressing of individual positions of the peptides enabled the generation of mutually selective coiled-coils. The established method, termed Bind&Bite, can be expected to be beneficial for a range of biotechnological and biomedical applications, in which chemical moieties need to be stably attached to proteins in a site-selective fashion.
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Affiliation(s)
- Jannis Beutel
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg (FAU) Erlangen Germany
- Institut Virion-Serion GmbH Würzburg Germany
| | - Pierre Tannig
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | - Riccardo Di Vincenzo
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | | | - Klaus Überla
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg (FAU) Erlangen Germany
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16
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Winer L, Motiei L, Margulies D. Fluorescent Investigation of Proteins Using DNA-Synthetic Ligand Conjugates. Bioconjug Chem 2023; 34:1509-1522. [PMID: 37556353 PMCID: PMC10515487 DOI: 10.1021/acs.bioconjchem.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/27/2023] [Indexed: 08/11/2023]
Abstract
The unfathomable role that fluorescence detection plays in the life sciences has prompted the development of countless fluorescent labels, sensors, and analytical techniques that can be used to detect and image proteins or investigate their properties. Motivated by the demand for simple-to-produce, modular, and versatile fluorescent tools to study proteins, many research groups have harnessed the advantages of oligodeoxynucleotides (ODNs) for scaffolding such probes. Tight control over the valency and position of protein binders and fluorescent dyes decorating the polynucleotide chain and the ability to predict molecular architectures through self-assembly, inherent solubility, and stability are, in a nutshell, the important properties of DNA probes. This paper reviews the progress in developing DNA-based, fluorescent sensors or labels that navigate toward their protein targets through small-molecule (SM) or peptide ligands. By describing the design, operating principles, and applications of such systems, we aim to highlight the versatility and modularity of this approach and the ability to use ODN-SM or ODN-peptide conjugates for various applications such as protein modification, labeling, and imaging, as well as for biomarker detection, protein surface characterization, and the investigation of multivalency.
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Affiliation(s)
- Lulu Winer
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
| | - Leila Motiei
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
| | - David Margulies
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
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17
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Gasse C, Srivastava P, Schepers G, Jose J, Hollenstein M, Marlière P, Herdewijn P. Controlled E. coli Aggregation Mediated by DNA and XNA Hybridization. Chembiochem 2023; 24:e202300191. [PMID: 37119472 DOI: 10.1002/cbic.202300191] [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: 03/10/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/01/2023]
Abstract
Chemical cell surface modification is a fast-growing field of research, due to its enormous potential in tissue engineering, cell-based immunotherapy, and regenerative medicine. However, engineering of bacterial tissues by chemical cell surface modification has been vastly underexplored and the identification of suitable molecular handles is in dire need. We present here, an orthogonal nucleic acid-protein conjugation strategy to promote artificial bacterial aggregation. This system gathers the high selectivity and stability of linkage to a protein Tag expressed at the cell surface and the modularity and reversibility of aggregation due to oligonucleotide hybridization. For the first time, XNA (xeno nucleic acids in the form of 1,5-anhydrohexitol nucleic acids) were immobilized via covalent, SNAP-tag-mediated interactions on cell surfaces to induce bacterial aggregation.
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Affiliation(s)
- Cécile Gasse
- Génomique Métabolique, Genoscope Institut François Jacob, CEA, CNRS Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Puneet Srivastava
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstr. 48, D-48149, Münster, Germany
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Philippe Marlière
- The European Syndicate of Synthetic Scientists and Industrialists (TESSSI), 81 rue Réaumur, 75002, Paris, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
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18
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Xi X, Wu Z, Zhang X, Li Y, Zhao Y, Wen W, Wang S. Endogenous Protease-Activatable Nanosensor Based on PNA-Peptide-DNA Engineering for AND-Gated and Dual-Model Detection of MicroRNA in Single Living Tumor Cells. ACS APPLIED MATERIALS & INTERFACES 2023; 15:21917-21928. [PMID: 37105764 DOI: 10.1021/acsami.3c02012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The in situ detection of low-content cancer biomarkers by an endogenous activator instead of an exogenous initiator in vitro remains a great challenge, leaving a gap in the development of a tumor-specific nanosensor with an endogenous protease-activatable manner. Herein, we proposed an endogenous protease-activatable nanosensor (PA-NS) guided by peptide nucleic acid-peptide-DNA copolymers to realize AND-gated and dual-model sensing of miRNA-21 (miR-21) by combining electrochemical detection with optical imaging in living tumor cells, without an additional introduction of an exogenous activator or nanomaterials. Moreover, the PA-NS can only be activated by "dual keys" (overexpressed miR-21 and cathepsin B protease in tumor cells) simultaneously, which enables effective improvement of the tumor-to-healthy cells ratio. The fluorescence intensity measured in single tumor cells was ∼3.5-fold higher than that in single healthy cells, and the electrochemical response decreased ∼30% in the presence of target miRNA. Furthermore, studies on regulation of the protease activity and miR-21 fluctuation under external stimulation have contributed to our understanding of the biological processes and drug screenings underlying disease development. This specific endogenous protease-mediated manner for dual-model detection of miRNA guarantees excellent tumor-selective capability, which offers new opportunities to study cell heterogeneity and provides more reliable fundamentals for the diagnosis and treatment of cancer down to the single-cell level.
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Affiliation(s)
- Xiaoxue Xi
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Zhen Wu
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Xiuhua Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Yuebin Li
- Faculty of Physics and Electronic Sciences, Wuhan 430062, Hubei, P. R. China
| | - Yuandi Zhao
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioformatics and Molecular Imaging Key Laboratory, Department of Biomedicine Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Wei Wen
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Shengfu Wang
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
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19
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Guo AD, Yan KN, Hu H, Zhai L, Hu TF, Su H, Chi Y, Zha J, Xu Y, Zhao D, Lu X, Xu YJ, Zhang J, Tan M, Chen XH. Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors. Nat Chem 2023:10.1038/s41557-023-01196-z. [PMID: 37106095 DOI: 10.1038/s41557-023-01196-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Precise dissection of DNA-protein interactions is essential for elucidating the recognition basis, dynamics and gene regulation mechanism. However, global profiling of weak and dynamic DNA-protein interactions remains a long-standing challenge. Here, we establish the light-induced lysine (K) enabled crosslinking (LIKE-XL) strategy for spatiotemporal and global profiling of DNA-protein interactions. Harnessing unique abilities to capture weak and transient DNA-protein interactions, we demonstrate that LIKE-XL enables the discovery of low-affinity transcription-factor/DNA interactions via sequence-specific DNA baits, determining the binding sites for transcription factors that have been previously unknown. More importantly, we successfully decipher the dynamics of the transcription factor subproteome in response to drug treatment in a time-resolved manner, and find downstream target transcription factors from drug perturbations, providing insight into their dynamic transcriptional networks. The LIKE-XL strategy offers a complementary method to expand the DNA-protein profiling toolbox and map accurate DNA-protein interactomes that were previously inaccessible via non-covalent strategies, for better understanding of protein function in health and disease.
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Affiliation(s)
- An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke-Nian Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Teng-Fei Hu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yijia Chi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyin Zha
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dongxin Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Jiang Xu
- School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Jian Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China.
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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20
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Harel O, Jbara M. Chemical Synthesis of Bioactive Proteins. Angew Chem Int Ed Engl 2023; 62:e202217716. [PMID: 36661212 DOI: 10.1002/anie.202217716] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/21/2023]
Abstract
Nature has developed a plethora of protein machinery to operate and maintain nearly every task of cellular life. These processes are tightly regulated via post-expression modifications-transformations that modulate intracellular protein synthesis, folding, and activation. Methods to prepare homogeneously and precisely modified proteins are essential to probe their function and design new bioactive modalities. Synthetic chemistry has contributed remarkably to protein science by allowing the preparation of novel biomacromolecules that are often challenging or impractical to prepare via common biological means. The ability to chemically build and precisely modify proteins has enabled the production of new molecules with novel physicochemical properties and programmed activity for biomedical research, diagnostic, and therapeutic applications. This minireview summarizes recent developments in chemical protein synthesis to produce bioactive proteins, with emphasis on novel analogs with promising in vitro and in vivo activity.
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Affiliation(s)
- Omer Harel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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21
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Smiley AT, Tompkins KJ, Pawlak MR, Krueger AJ, Evans RL, Shi K, Aihara H, Gordon WR. Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases. mBio 2023; 14:e0258722. [PMID: 36541758 PMCID: PMC9973303 DOI: 10.1128/mbio.02587-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair's identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps. IMPORTANCE Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses are a ubiquitous group of viruses that infect organisms across all domains of life. These viruses negatively impact both agriculture and human health. All members of this viral family employ a multifunctional nuclease (Rep) to initiate replication. Reps are structurally similar throughout this family, making them targets of interest for viral inhibition strategies. Here, we investigate the functional dependencies of the Rep protein from Muscovy duck circovirus for ssDNA interaction. We demonstrate that this Rep requires an intramolecular Watson-Crick base pairing for origin of replication (Ori) recognition and interaction. We show that noncognate base pair swaps are well tolerated, highlighting a local structural specificity over sequence specificity. Bioinformatic analysis found that the vast majority of CRESS-DNA Oris form base pairs in conserved positions, suggesting this pairing is a universal requirement for replication initiation in the CRESS-DNA virus family.
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Affiliation(s)
- Adam T. Smiley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kassidy J. Tompkins
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matthew R. Pawlak
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - August J. Krueger
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Robert L. Evans
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wendy R. Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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22
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Wang Y, Yan T, Mei K, Rao D, Wu W, Chen Y, Peng Y, Wang J, Wu S, Zhang Q. Nanomechanical assay for ultrasensitive and rapid detection of SARS-CoV-2 based on peptide nucleic acid. NANO RESEARCH 2023; 16:1183-1195. [PMID: 35610981 PMCID: PMC9118818 DOI: 10.1007/s12274-022-4333-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 05/14/2023]
Abstract
UNLABELLED The massive global spread of the COVID-19 pandemic makes the development of more effective and easily popularized assays critical. Here, we developed an ultrasensitive nanomechanical method based on microcantilever array and peptide nucleic acid (PNA) for the detection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) RNA. The method has an extremely low detection limit of 0.1 fM (105 copies/mL) for N-gene specific sequence (20 bp). Interestingly, it was further found that the detection limit of N gene (pharyngeal swab sample) was even lower, reaching 50 copies/mL. The large size of the N gene dramatically enhances the sensitivity of the nanomechanical sensor by up to three orders of magnitude. The detection limit of this amplification-free assay method is an order of magnitude lower than RT-PCR (500 copies/mL) that requires amplification. The non-specific signal in the assay is eliminated by the in-situ comparison of the array, reducing the false-positive misdiagnosis rate. The method is amplification-free and label-free, allowing for accurate diagnosis within 1 h. The strong specificity and ultra-sensitivity allow single base mutations in viruses to be distinguished even at very low concentrations. Also, the method remains sensitive to fM magnitude lung cancer marker (miRNA-155). Therefore, this ultrasensitive, amplification-free and inexpensive assay is expected to be used for the early diagnosis of COVID-19 patients and to be extended as a broad detection tool. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (experimental section, N gene sequences and all nucleic acid sequences used in the study, Figs. S1-S6, and Tables S1-S3) is available in the online version of this article at 10.1007/s12274-022-4333-3.
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Affiliation(s)
- Yu Wang
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Tianhao Yan
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Kainan Mei
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Depeng Rao
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Wenjie Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Ye Chen
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Yongpei Peng
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Jianye Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, 230022 China
| | - Shangquan Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Qingchuan Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
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23
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Liu H, Chen Y, Ju H. Functional DNA structures for cytosensing. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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24
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Watson EE, Winssinger N. Synthesis of Protein-Oligonucleotide Conjugates. Biomolecules 2022; 12:biom12101523. [PMID: 36291732 PMCID: PMC9599799 DOI: 10.3390/biom12101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids and proteins form two of the key classes of functional biomolecules. Through the ability to access specific protein-oligonucleotide conjugates, a broader range of functional molecules becomes accessible which leverages both the programmability and recognition potential of nucleic acids and the structural, chemical and functional diversity of proteins. Herein, we summarize the available conjugation strategies to access such chimeric molecules and highlight some key case study examples within the field to showcase the power and utility of such technology.
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Affiliation(s)
- Emma E. Watson
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (E.E.W.); (N.W.)
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, CH-1205 Geneva, Switzerland
- Correspondence: (E.E.W.); (N.W.)
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25
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Yin D, Yao C, Chen Y, He Z, Yu P, Sun X, Wang S, Zhang F. HClO-Activated Near-Infrared Fluorogenic Aza-BODIPY-Bisferrocene Triad with High Turn-on Ratio for In Vivo Biosensing. Adv Healthc Mater 2022; 11:e2201139. [PMID: 35815541 DOI: 10.1002/adhm.202201139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 01/27/2023]
Abstract
Optically monitoring hypochlorous acid (HClO) in living body favors diagnosis and study of inflammatory diseases. However, this has been hampered by limited strategies to develop highly fluorogenic tools in the deep-penetration near-infrared spectrum. Herein, a near-infrared aza-BODIPY-bisferrocene triad Fc2 -CBDP that unexpectedly achieves an exceptionally sensitive and selective fluorescence turn-on (>220-fold) response toward HClO through single-ferrocene oxidation and boron-alkynyl hydrolysis cascade is reported. Mechanism insight shows that Fc2 -CBDP features "enhanced charge transfer"-caused quenching due to intramolecular bisferrocene electronic coupling, which is decoupled in the reaction with HClO. The utility of Fc2 -CBDP for intracellular HClO imaging is evaluated and, more importantly, in vivo high-contrast deep-tissue imaging of lymphatic inflammation and colitis is realized. This work provides new insights into both HClO and ferrocene chemistry, and extends the reach of fluorogenic strategies in the near-infrared biosensing.
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Affiliation(s)
- Dongrui Yin
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials and iChem, Fudan University, Shanghai, 200433, China
| | - Chenzhi Yao
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials and iChem, Fudan University, Shanghai, 200433, China
| | - Ying Chen
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials and iChem, Fudan University, Shanghai, 200433, China
| | - Zuyang He
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials and iChem, Fudan University, Shanghai, 200433, China
| | - Peng Yu
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials and iChem, Fudan University, Shanghai, 200433, China
| | - Xingwen Sun
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials and iChem, Fudan University, Shanghai, 200433, China
| | - Shangfeng Wang
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials and iChem, Fudan University, Shanghai, 200433, China
| | - Fan Zhang
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials and iChem, Fudan University, Shanghai, 200433, China
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26
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Efficient DNA fluorescence labeling via base excision trapping. Nat Commun 2022; 13:5043. [PMID: 36028479 PMCID: PMC9418136 DOI: 10.1038/s41467-022-32494-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/03/2022] [Indexed: 01/19/2023] Open
Abstract
Fluorescence labeling of DNAs is broadly useful, but methods for labeling are expensive and labor-intensive. Here we describe a general method for fluorescence labeling of oligonucleotides readily and cost-efficiently via base excision trapping (BETr), employing deaminated DNA bases to mark label positions, which are excised by base excision repair enzymes generating AP sites. Specially designed aminooxy-substituted rotor dyes trap the AP sites, yielding high emission intensities. BETr is orthogonal to DNA synthesis by polymerases, enabling multi-uracil incorporation into an amplicon and in situ BETr labeling without washing. BETr also enables labeling of dsDNA such as genomic DNA at a high labeling density in a single tube by use of nick translation. Use of two different deaminated bases facilitates two-color site-specific labeling. Use of a multi-labeled DNA construct as a bright fluorescence tag is demonstrated through the conjugation to an antibody for imaging proteins. Finally, double-strand selectivity of a repair enzyme is harnessed in sensitive reporting on the presence of a target DNA or RNA in a mixture with isothermal turnover and single nucleotide specificity. Overall, the results document a convenient and versatile method for general fluorescence labeling of DNAs.
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27
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Di Z, Lu X, Zhao J, Jaklenec A, Zhao Y, Langer R, Li L. Mild Acidosis-Directed Signal Amplification in Tumor Microenvironment via Spatioselective Recruitment of DNA Amplifiers. Angew Chem Int Ed Engl 2022; 61:e202205436. [PMID: 35652128 DOI: 10.1002/anie.202205436] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 12/29/2022]
Abstract
DNA biotechnology offers intriguing opportunities for amplification-based sensitive detection. However, spatiotemporally-controlled manipulation of signal amplification for in situ imaging of the tumor microenvironment remains an outstanding challenge. Here, we demonstrate a DNA-based strategy that can spatial-selectively amplify the acidic signal in the extracellular milieu of the tumor to achieve specific imaging with improved sensitivity. The strategy, termed mild acidosis-targeted amplification (MAT-amp), leverages the specific acidic microenvironment to engineer tumor cells with artificial DNA receptors through a pH (low) insertion peptide, which permits controlled recruitment of fluorescent amplifiers via a hybridization chain reaction. The acidosis-responsive amplification cascade enables significant fluorescence enhancement in tumors with a reduced background signal in normal tissues, leading to improved signal-to-background ratio. These results highlight the utility of MAT-amp for in situ imaging of the microenvironment characterized by pH disequilibrium.
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Affiliation(s)
- Zhenghan Di
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueguang Lu
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ana Jaklenec
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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28
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Lu Z, Liu Y, Deng Y, Jia B, Ding X, Zheng P, Li Z. OaAEP1-mediated PNA-protein conjugation enables erasable imaging of membrane proteins. Chem Commun (Camb) 2022; 58:8448-8451. [PMID: 35797663 DOI: 10.1039/d2cc02153f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the use of a protein ligase to covalently ligate a protein to a peptide nucleic acid (PNA). The rapid ligation demands only an N-terminal GL dipeptide in the target protein and a C-terminal NGL tripeptide in the PNA. We demonstrate the versatility of this approach by attaching a PNA strand to three different proteins. Lastly, we show that erasable imaging of EGFR on HEK293 cell membranes is achieved with DNA origami nanostructures and toehold-mediated strand displacement.
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Affiliation(s)
- Zhangwei Lu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Yutong Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Bin Jia
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Xuan Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
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29
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Di Z, Lu X, Zhao J, Jaklenec A, Zhao Y, Langer R, Li L. Mild Acidosis‐Directed Signal Amplification in Tumor Microenvironment via Spatioselective Recruitment of DNA Amplifiers. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Zhenghan Di
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
| | - Xueguang Lu
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- David H. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
| | - Ana Jaklenec
- David H. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
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30
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Vermeer B, Schmid S. Can DyeCycling break the photobleaching limit in single-molecule FRET? NANO RESEARCH 2022; 15:9818-9830. [PMID: 35582137 PMCID: PMC9101981 DOI: 10.1007/s12274-022-4420-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 05/03/2023]
Abstract
Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce "DyeCycling", a measurement scheme with which we aim to break the photobleaching limit in smFRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide > 100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range. Electronic Supplementary Material Supplementary material is available for this article at 10.1007/s12274-022-4420-5 and is accessible for authorized users.
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Affiliation(s)
- Benjamin Vermeer
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
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31
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Ranallo S, Sorrentino D, Delibato E, Ercolani G, Plaxco KW, Ricci F. Protein–Protein Communication Mediated by an Antibody‐Responsive DNA Nanodevice**. Angew Chem Int Ed Engl 2022; 61:e202115680. [DOI: 10.1002/anie.202115680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Simona Ranallo
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
- Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara CA 93106 USA
| | - Daniela Sorrentino
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health Istituto Superiore di Sanità Viale Regina Elena 299 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara CA 93106 USA
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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32
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Yang S, Zhao G, Gao Y, Sun Y, Zhang G, Fan X, Li Y, Li Y. In-solution direct oxidative coupling for the integration of sulfur/selenium into DNA-encoded chemical libraries. Chem Sci 2022; 13:2604-2613. [PMID: 35340849 PMCID: PMC8890091 DOI: 10.1039/d1sc06268a] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/29/2022] [Indexed: 12/27/2022] Open
Abstract
Sulfur/selenium-containing electron-rich arenes (ERAs) exist in a wide range of both approved and investigational drugs with diverse pharmacological activities. These unique chemical structures and bioactive properties, if combined with the emerging DNA-encoded chemical library (DEL) technique, would facilitate drug and chemical probe discovery. However, it remains challenging, as there is no general DNA-compatible synthetic methodology available for the formation of C-S and C-Se bonds in aqueous solution. Herein, an in-solution direct oxidative coupling procedure that could efficiently integrate sulfur/selenium into the ERA under mild conditions is presented. This method features simple DNA-conjugated electron-rich arenes with a broad substrate scope and a transition-metal free process. Furthermore, this synthetic methodology, examined by a scale-up reaction test and late-stage precise modification in a mock peptide-like DEL synthesis, will enable its utility for the synthesis of sulfur/selenium-containing DNA-encoded libraries and the discovery of bioactive agents.
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Affiliation(s)
- Shilian Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Yang Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Xiaohong Fan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
- Pharmaceutical Department of Chongqing Three Gorges Central Hospital, Chongqing University Chongqing 404100 P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University Chongqing 400044 P. R. China
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33
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Ranallo S, Sorrentino D, Delibato E, Ercolani G, Plaxco KW, Ricci F. Protein–Protein Communication Mediated by an Antibody‐Responsive DNA Nanodevice**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Simona Ranallo
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
- Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara CA 93106 USA
| | - Daniela Sorrentino
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health Istituto Superiore di Sanità Viale Regina Elena 299 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara CA 93106 USA
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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34
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Wang X, Wen C, Davis B, Shi P, Abune L, Lee K, Dong C, Wang Y. Synthetic DNA for Cell Surface Engineering: Experimental Comparison between Click Conjugation and Lipid Insertion in Terms of Cell Viability, Engineering Efficiency, and Displaying Stability. ACS APPLIED MATERIALS & INTERFACES 2022; 14:3900-3909. [PMID: 35020367 DOI: 10.1021/acsami.1c22774] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The cell surface can be engineered with synthetic DNA for various applications ranging from cancer immunotherapy to tissue engineering. However, while elegant methods such as click conjugation and lipid insertion have been developed to engineer the cell surface with DNA, little effort has been made to systematically evaluate and compare these methods. Resultantly, it is often challenging to choose a right method for a certain application or to interpret data from different studies. In this study, we systematically evaluated click conjugation and lipid insertion in terms of cell viability, engineering efficiency, and displaying stability. Cells engineered with both methods can maintain high viability when the concentration of modified DNA is less than 25-50 μM. However, lipid insertion is faster and more efficient in displaying DNA on the cell surface than click conjugation. The efficiency of displaying DNA with lipid insertion is 10-40 times higher than that with click conjugation for a large range of DNA concentration. However, the half-life of physically inserted DNA on the cell surface is 3-4 times lower than that of covalently conjugated DNA, which depends on the working temperature. While the half-life of physically inserted DNA molecules on the cell surface is shorter than that of DNA molecules clicked onto the cell surface, lipid insertion is more effective than click conjugation in the promotion of cell-cell interactions under the two different experimental settings. The data acquired in this work are expected to act as a guideline for choosing an approximate method for engineering the cell surface with synthetic DNA or even other biomolecules.
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Affiliation(s)
- Xuelin Wang
- Department of Biomedical Engineering, The Pennsylvania State University University Park, State College, Pennsylvania 16802, United States
| | - Connie Wen
- Department of Biomedical Engineering, The Pennsylvania State University University Park, State College, Pennsylvania 16802, United States
| | - Brandon Davis
- Department of Biomedical Engineering, The Pennsylvania State University University Park, State College, Pennsylvania 16802, United States
| | - Peng Shi
- Department of Biomedical Engineering, The Pennsylvania State University University Park, State College, Pennsylvania 16802, United States
| | - Lidya Abune
- Department of Biomedical Engineering, The Pennsylvania State University University Park, State College, Pennsylvania 16802, United States
| | - Kyungsene Lee
- Department of Biomedical Engineering, The Pennsylvania State University University Park, State College, Pennsylvania 16802, United States
| | - Cheng Dong
- Department of Biomedical Engineering, The Pennsylvania State University University Park, State College, Pennsylvania 16802, United States
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University University Park, State College, Pennsylvania 16802, United States
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35
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Chen Y, Gong X, Gao Y, Shang Y, Shang J, Yu S, Li R, He S, Liu X, Wang F. Bioorthogonal regulation of DNA circuits for smart intracellular microRNA imaging. Chem Sci 2021; 12:15710-15718. [PMID: 35003602 PMCID: PMC8654030 DOI: 10.1039/d1sc05214d] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Catalytic DNA circuits represent a versatile toolbox for tracking intracellular biomarkers yet are constrained with low anti-interference capacity originating from their severe off-site activation. Herein, by introducing an unprecedented endogenous DNA repairing enzyme-powered pre-selection strategy, we develop a sequential and specific on-site activated catalytic DNA circuit for achieving the cancer cell-selective imaging of microRNA with high anti-interference capacity. Initially, the circuitry reactant is firmly caged by an elongated stabilizing duplex segment with a recognition/cleavage site of a cell-specific DNA repairing enzyme, which can prevent undesired signal leakage prior to its exposure to target cells. Then, the intrinsic DNA repairing enzyme of target cells can liberate the DNA probe for efficient intracellular microRNA imaging via the multiply guaranteed molecular recognition/activation procedures. This bioorthogonal regulated DNA circuit presents a modular and programmable amplification strategy for highly reliable assays of intracellular biomarkers, and provides a pivotal molecular toolbox for living systems. An on-site bioorthogonal regulated DNA circuit was developed by introducing an endogenous DNA repairing enzyme-mediated sequential activation strategy to achieve cancer cell-selective microRNA imaging with high anti-interference ability.![]()
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Affiliation(s)
- Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Xue Gong
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Yuhui Gao
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Yu Shang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China.,Research Institute of Shenzhen, Wuhan University Shenzhen 518057 P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China.,Research Institute of Shenzhen, Wuhan University Shenzhen 518057 P. R. China
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36
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Wolf P, Mohr A, Gavins G, Behr V, Mörl K, Seitz O, Beck-Sickinger AG. Orthogonal Peptide-Templated Labeling Elucidates Lateral ET A R/ET B R Proximity and Reveals Altered Downstream Signaling. Chembiochem 2021; 23:e202100340. [PMID: 34699123 PMCID: PMC9298254 DOI: 10.1002/cbic.202100340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/03/2021] [Indexed: 12/21/2022]
Abstract
Fine‐tuning of G protein‐coupled receptor (GPCR) signaling is important to maintain cellular homeostasis. Recent studies demonstrated that lateral GPCR interactions in the cell membrane can impact signaling profiles. Here, we report on a one‐step labeling method of multiple membrane‐embedded GPCRs. Based on short peptide tags, complementary probes transfer the cargo (e. g. a fluorescent dye) by an acyl transfer reaction with high spatial and temporal resolution within 5 min. We applied this approach to four receptors of the cardiovascular system: the endothelin receptor A and B (ETAR and ETBR), angiotensin II receptor type 1, and apelin. Wild type‐like G protein activation after N‐terminal modification was demonstrated for all receptor species. Using FRET‐competent dyes, a constitutive proximity between hetero‐receptors was limited to ETAR/ETBR. Further, we demonstrate, that ETAR expression regulates the signaling of co‐expressed ETBR. Our orthogonal peptide‐templated labeling of different GPCRs provides novel insight into the regulation of GPCR signaling.
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Affiliation(s)
- Philipp Wolf
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Alexander Mohr
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Georgina Gavins
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Victoria Behr
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Karin Mörl
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Oliver Seitz
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Annette G Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
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37
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Manicardi A, Cadoni E, Madder A. Hydrolysis of 5-methylfuran-2-yl to 2,5-dioxopentanyl allows for stable bio-orthogonal proximity-induced ligation. Commun Chem 2021; 4:146. [PMID: 36697666 PMCID: PMC9814669 DOI: 10.1038/s42004-021-00584-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/14/2021] [Indexed: 01/28/2023] Open
Abstract
Ligation methodologies featuring bio-orthogonal units and leading to the formation of a stable adduct are the ideal candidates for being applied in a biological context. However, most of the available strategies rely on highly reactive species that require careful handling, or on the activation of pro-reactive functional groups. We here report on a proximity-induced ligation reaction that relies on a stable 2,5-dione, that can be conveniently generated under acidic conditions from a 2,5-dialkylfuran building block, and hydrazine nucleophiles. This bio-orthogonal ligation, which proceeds under physiological conditions, does not require any stimulus or trigger and leads to the formation of a pyridazinium adduct that demonstrates excellent stability under harsh conditions (24 h at 90 °C). The reaction was applied to the formation of PNA-PNA adducts, DNA- and RNA-templated ligations, and for the formation of peptide-peptide adducts in solution. This convenient methodology was further implemented on plastic and glass surfaces to realize self-addressable covalent constructs.
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Affiliation(s)
- Alex Manicardi
- grid.5342.00000 0001 2069 7798Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Enrico Cadoni
- grid.5342.00000 0001 2069 7798Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Annemieke Madder
- grid.5342.00000 0001 2069 7798Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
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38
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Wang W, Zhang Y, Zhao H, Zhuang X, Wang H, He K, Xu W, Kang Y, Chen S, Zeng S, Qian L. Real-time imaging of cell-surface proteins with antibody-based fluorogenic probes. Chem Sci 2021; 12:13477-13482. [PMID: 34777767 PMCID: PMC8528012 DOI: 10.1039/d1sc03065e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/08/2021] [Indexed: 12/29/2022] Open
Abstract
Cell-surface proteins, working as key agents in various diseases, are the targets for around 66% of approved human drugs. A general strategy to selectively detect these proteins in a real-time manner is expected to facilitate the development of new drugs and medical diagnoses. Although brilliant successes were attained using small-molecule probes, they could cover a narrow range of targets due to the lack of suitable ligands and some of them suffer from selectivity issues. We report herein an antibody-based fluorogenic probe prepared via a two-step chemical modification under physiological conditions, to fulfill the selective recognition and wash-free imaging of membrane proteins, establishing a modular strategy with broad implications for biochemical research and for therapeutics.
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Affiliation(s)
- Wenchao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
| | - Ying Zhang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
| | - Hong Zhao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
| | - Xinlei Zhuang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
| | - Haoting Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
| | - Kaifeng He
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
- Hangzhou Institute of Innovative Medicine, Zhejiang University Hangzhou 310018 China
| | - Wanting Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
- Hangzhou Institute of Innovative Medicine, Zhejiang University Hangzhou 310018 China
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University Hangzhou 310058 China
- Hangzhou Institute of Innovative Medicine, Zhejiang University Hangzhou 310018 China
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39
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Fuchs O, Trunschke S, Hanebrink H, Reimann M, Seitz O. Enabling Cysteine-Free Native Chemical Ligation at Challenging Junctions with a Ligation Auxiliary Capable of Base Catalysis. Angew Chem Int Ed Engl 2021; 60:19483-19490. [PMID: 34165893 PMCID: PMC8457107 DOI: 10.1002/anie.202107158] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 12/14/2022]
Abstract
Ligation auxiliaries are used in chemical protein synthesis to extend the scope of native chemical ligation (NCL) beyond cysteine. However, auxiliary-mediated ligations at sterically demanding junctions have been difficult. Often the thioester intermediate formed in the thiol exchange step of NCL accumulates because the subsequent S→N acyl transfer is extremely slow. Here we introduce the 2-mercapto-2-(pyridin-2-yl)ethyl (MPyE) group as the first auxiliary designed to aid the ligation reaction by catalysis. Notably, the MPyE auxiliary provides useful rates even for junctions containing proline or a β-branched amino acid. Quantum chemical calculations suggest that the pyridine nitrogen acts as an intramolecular base in a rate-determining proton transfer step. The auxiliary is prepared in two steps and conveniently introduced by reductive alkylation. Auxiliary cleavage is induced upon treatment with TCEP/morpholine in presence of a MnII complex as radical starter. The synthesis of a de novo designed 99mer peptide and an 80 aa long MUC1 peptide demonstrates the usefulness of the MPyE auxiliary.
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Affiliation(s)
- Olaf Fuchs
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Sebastian Trunschke
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Hendrik Hanebrink
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Marc Reimann
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
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40
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Ein zur Basenkatalyse befähigtes Ligationsauxiliar ermöglicht die cysteinfreie native chemische Ligation an anspruchsvollen Verknüpfungsstellen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Gavins GC, Gröger K, Reimann M, Bartoschek MD, Bultmann S, Seitz O. Orthogonal coiled coils enable rapid covalent labelling of two distinct membrane proteins with peptide nucleic acid barcodes. RSC Chem Biol 2021; 2:1291-1295. [PMID: 34458843 PMCID: PMC8341593 DOI: 10.1039/d1cb00126d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
Templated chemistry offers the prospect of addressing specificity challenges occurring in bioconjugation reactions. Here, we show two peptide-templated amide-bond forming reactions that enable the concurrent labelling of two different membrane proteins with two different peptide nucleic acid (PNA) barcodes. The reaction system is based on the mutually selective coiled coil interaction between two thioester-linked PNA–peptide conjugates and two cysteine peptides serving as genetically encoded peptide tags. Orthogonal coiled coil templated covalent labelling is highly specific, quantitative and proceeds within a minute. To demonstrate the usefulness, we evaluated receptor internalisation of two membranous receptors EGFR (epidermal growth factor) and ErbB2 (epidermal growth factor receptor 2) by first staining PNA-tagged proteins with fluorophore–DNA conjugates and then erasing signals from non-internalized receptors via toehold-mediated strand displacement. A pair of orthogonal coiled coils templates highly specific live cell bioconjugation of two different proteins. PNA tagging and hybridisation with fluorophore–DNA reporters enables rapid dual receptor internalisation analysis of EGFR and ErbB2.![]()
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Affiliation(s)
- Georgina C Gavins
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Katharina Gröger
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Marc Reimann
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Michael D Bartoschek
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstr. 1 Munich 81377 Germany
| | - Sebastian Bultmann
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstr. 1 Munich 81377 Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
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42
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Kabza AM, Kundu N, Zhong W, Sczepanski JT. Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1743. [PMID: 34328690 DOI: 10.1002/wnan.1743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/26/2021] [Accepted: 07/06/2021] [Indexed: 01/21/2023]
Abstract
Watson-Crick base pairing rules provide a powerful approach for engineering DNA-based nanodevices with programmable and predictable behaviors. In particular, DNA strand displacement reactions have enabled the development of an impressive repertoire of molecular devices with complex functionalities. By relying on DNA to function, dynamic strand displacement devices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation in living systems has been a slow process due to several persistent challenges, including nuclease degradation. To circumvent these issues, researchers are increasingly turning to chemically modified nucleotides as a means to increase device performance and reliability within harsh biological environments. In this review, we summarize recent progress toward the integration of chemically modified nucleotides with DNA strand displacement reactions, highlighting key successes in the development of robust systems and devices that operate in living cells and in vivo. We discuss the advantages and disadvantages of commonly employed modifications as they pertain to DNA strand displacement, as well as considerations that must be taken into account when applying modified oligonucleotide to living cells. Finally, we explore how chemically modified nucleotides fit into the broader goal of bringing dynamic DNA nanotechnology into the cell, and the challenges that remain. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing.
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Affiliation(s)
- Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Wenrui Zhong
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
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43
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Asiimwe N, Al Mazid MF, Murale DP, Kim YK, Lee J. Recent advances in protein modifications techniques for the targeting
N‐terminal
cysteine. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicholas Asiimwe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | | | | | - Yun Kyung Kim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | - Jun‐Seok Lee
- Department of Pharmacology Korea University College of Medicine Seoul Korea
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44
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Oehler S, Catalano M, Scapozza I, Bigatti M, Bassi G, Favalli N, Mortensen MR, Samain F, Scheuermann J, Neri D. Affinity Selections of DNA-Encoded Chemical Libraries on Carbonic Anhydrase IX-Expressing Tumor Cells Reveal a Dependence on Ligand Valence. Chemistry 2021; 27:8985-8993. [PMID: 33905156 DOI: 10.1002/chem.202100816] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 12/19/2022]
Abstract
DNA-encoded chemical libraries are typically screened against purified protein targets. Recently, cell-based selections with encoded chemical libraries have been described, commonly revealing suboptimal performance due to insufficient recovery of binding molecules. We used carbonic anhydrase IX (CAIX)-expressing tumor cells as a model system to optimize selection procedures with code-specific quantitative polymerase chain reaction (qPCR) as selection readout. Salt concentration and performing PCR on cell suspension had the biggest impact on selection performance, leading to 15-fold enrichment factors for high-affinity monovalent CAIX binders (acetazolamide; KD =8.7 nM). Surprisingly, the homobivalent display of acetazolamide at the extremities of both complementary DNA strands led to a substantial improvement of both ligand recovery and enrichment factors (above 100-fold). The optimized procedures were used for selections with a DNA-encoded chemical library comprising 1 million members against tumor cell lines expressing CAIX, leading to a preferential recovery of known and new ligands against this validated tumor-associated target. This work may facilitate future affinity selections on cells against target proteins which might be difficult to express otherwise.
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Affiliation(s)
- Sebastian Oehler
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Ilario Scapozza
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Martina Bigatti
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Michael R Mortensen
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Florent Samain
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Dario Neri
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
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45
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Wolf P, Gavins G, Beck‐Sickinger AG, Seitz O. Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags. Chembiochem 2021; 22:1717-1732. [PMID: 33428317 PMCID: PMC8248378 DOI: 10.1002/cbic.202000797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.
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Affiliation(s)
- Philipp Wolf
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Georgina Gavins
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| | - Annette G. Beck‐Sickinger
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Oliver Seitz
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
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46
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Riker KD, Daly ML, Papanikolas MJ, Jian T, Klawa SJ, Shin Sahin JYS, Liu D, Singh A, Miller AG, Freeman R. A Programmable Toolkit to Dynamically Signal Cells Using Peptide Strand Displacement. ACS APPLIED MATERIALS & INTERFACES 2021; 13:21018-21029. [PMID: 33938725 DOI: 10.1021/acsami.1c03370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The native extracellular matrix communicates and interacts with cells by dynamically displaying signals to control their behavior. Mimicking this dynamic environment in vitro is essential in order to unravel how cell-matrix interactions guide cell fate. Here, we present a synthetic platform for the temporal display of cell-adhesive signals using coiled-coil peptides. By designing an integrin-engaging coiled-coil pair to have a toehold (unpaired domain), we were able to use a peptide strand displacement reaction to remove the cell cue from the surface. This allowed us to test how the user-defined display of RGDS ligands at variable duration and periodicity of ligand exposure influence cell spreading degree and kinetics. Transient display of αVβ3-selective ligands instructed fibroblast cells to reversibly spread and contract in response to changes in ligand exposure over multiple cycles, exhibiting a universal kinetic response. Also, cells that were triggered to spread and contract repeatedly exhibited greater enrichment of integrins in focal adhesions versus cells cultured on persistent RGDS-displaying surfaces. This dynamic platform will allow us to uncover the molecular code by which cells sense and respond to changes in their environment and will provide insights into ways to program cellular behavior.
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Affiliation(s)
- Kyle D Riker
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Micah J Papanikolas
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Tengyue Jian
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline Yalin S Shin Sahin
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dingyuan Liu
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Anamika Singh
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - A Griffin Miller
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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47
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Jbara M, Rodriguez J, Dhanjee HH, Loas A, Buchwald SL, Pentelute BL. Oligonucleotide Bioconjugation with Bifunctional Palladium Reagents. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Muhammad Jbara
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Jacob Rodriguez
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Heemal H. Dhanjee
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Andrei Loas
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Stephen L. Buchwald
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
- The Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology 500 Main Street Cambridge MA 02142 USA
- Center for Environmental Health Sciences Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
- Broad Institute of MIT and Harvard 415 Main Street Cambridge MA 02142 USA
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48
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Jbara M, Rodriguez J, Dhanjee HH, Loas A, Buchwald SL, Pentelute BL. Oligonucleotide Bioconjugation with Bifunctional Palladium Reagents. Angew Chem Int Ed Engl 2021; 60:12109-12115. [PMID: 33730425 DOI: 10.1002/anie.202103180] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 01/01/2023]
Abstract
Organometallic reagents enable practical strategies for bioconjugation. Innovations in the design of water-soluble ligands and the enhancement of reaction rates have allowed for chemoselective cross-coupling reactions of peptides and proteins to be carried out in water. There are currently no organometallic-based methods for oligonucleotide bioconjugation to other biomolecules. Here we report bifunctional palladium(II)-oxidative addition complexes (OACs) as reagents for high-yielding oligonucleotide bioconjugation reactions. These bifunctional OACs react chemoselectively with amine-modified oligonucleotides to generate the first isolable, bench stable oligonucleotide-palladium(II) OACs. These complexes undergo site-selective C-S arylation with a broad range of native thiol-containing biomolecules at low micromolar concentrations in under one hour. This approach provided oligonucleotide-peptide, oligonucleotide-protein, oligonucleotide-small molecule, and oligonucleotide-oligonucleotide conjugates in >80 % yield and afforded conjugation of multiple copies of oligonucleotides onto a monoclonal antibody.
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Affiliation(s)
- Muhammad Jbara
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Jacob Rodriguez
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Heemal H Dhanjee
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA.,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02142, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
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Schoenit A, Cavalcanti-Adam EA, Göpfrich K. Functionalization of Cellular Membranes with DNA Nanotechnology. Trends Biotechnol 2021; 39:1208-1220. [PMID: 33722382 DOI: 10.1016/j.tibtech.2021.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
Due to its versatility and programmability, DNA nanotechnology has greatly expanded the experimental toolbox for biomedical research. Recent advances allow reliable and efficient functionalization of cellular plasma membranes with a variety of synthetic DNA constructs, ranging from single strands to complex 3D DNA origami. The scope for applications, which probe biophysical parameters or equip cells with novel functions, is rapidly increasing. These applications extend from programmed cellular connectivity and tissue engineering to molecular force measurements, controlled receptor-ligand interactions, membrane-anchored biosensors, and artificial transmembrane structures. Here, we give guidance on different strategies to functionalize cellular membranes with DNA nanotechnology and summarize current trends employing membrane-anchored DNA as a tool in biophysics, cell biology, and synthetic biology.
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Affiliation(s)
- Andreas Schoenit
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany; Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Elisabetta Ada Cavalcanti-Adam
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany.
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Huang Y, Deng Y, Zhang J, Meng L, Li X. Direct ligand screening against membrane proteins on live cells enabled by DNA-programmed affinity labelling. Chem Commun (Camb) 2021; 57:3769-3772. [DOI: 10.1039/d1cc00961c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA-programmed affinity labelling (DPAL) enables the screening of chemical compounds against membrane proteins directly on live cells.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Yuqing Deng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Jianfu Zhang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Ling Meng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
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