1
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Zhou Y, Shen W, Gao Y, Peng J, Li Q, Wei X, Liu S, Lam FS, Mayol-Llinàs J, Zhao G, Li G, Li Y, Sun H, Cao Y, Li X. Protein-templated ligand discovery via the selection of DNA-encoded dynamic libraries. Nat Chem 2024; 16:543-555. [PMID: 38326646 DOI: 10.1038/s41557-024-01442-y] [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: 02/13/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
DNA-encoded chemical libraries (DELs) have become a powerful technology platform in drug discovery. Dual-pharmacophore DELs display two sets of small molecules at the termini of DNA duplexes, thereby enabling the identification of synergistic binders against biological targets, and have been successfully applied in fragment-based ligand discovery and affinity maturation of known ligands. However, dual-pharmacophore DELs identify separate binders that require subsequent linking to obtain the full ligands, which is often challenging. Here we report a protein-templated DEL selection approach that can identify full ligand/inhibitor structures from DNA-encoded dynamic libraries (DEDLs) without the need for subsequent fragment linking. Our approach is based on dynamic DNA hybridization and target-templated in situ ligand synthesis, and it incorporates and encodes the linker structures in the library, along with the building blocks, to be sampled by the target protein. To demonstrate the performance of this method, 4.35-million- and 3.00-million-member DEDLs with different library architectures were prepared, and hit selection was achieved against four therapeutically relevant target proteins.
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Grants
- AoE/P-705/16, 17301118, 17111319, 17303220, 17300321, 17318322, C7005-20G, C7016-22G, and 2122-7S04 Research Grants Council, University Grants Committee (RGC, UGC)
- 21877093, 22222702, and 91953119 National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)
- Health@InnoHK Innovation and Technology Commission (ITF)
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Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Gao
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qingrong Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xueying Wei
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shihao Liu
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Joan Mayol-Llinàs
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Hongzhe Sun
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
| | - Yan Cao
- School of Pharmacy, Naval Medical University, Shanghai, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
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2
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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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3
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Kupihár Z, Ferenc G, Petrovicz VL, Fáy VR, Kovács L, Martinek TA, Hegedüs Z. Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates. Pharmaceutics 2023; 15:pharmaceutics15010248. [PMID: 36678876 PMCID: PMC9865093 DOI: 10.3390/pharmaceutics15010248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which are often carried out on the 5' or 3' end. Modifying oligonucleotides in the middle of the sequence opens the possibility to ligate the conjugates and create DNA strands bearing multiple different ligands. Our goal was to establish a complete workflow that can be applied for such purposes from monomer synthesis to templated ligation. To achieve this, a monomer is required with an orthogonal functional group that can be incorporated internally into the oligonucleotide sequence. This is followed by conjugation with different molecules and ligation with the help of a complementary template. Here, we show the synthesis and the application of a thiol-modified thymidine nucleoside phosphoramidite to prepare ligatable oligonucleotide conjugates. The conjugations were performed both in solution and on solid phase, resulting in conjugates that can be assembled into multivalent oligonucleotides decorated with tissue-targeting peptides using templated ligation.
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Affiliation(s)
- Zoltán Kupihár
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre, Eötvös Lóránd Research Network, H-6726 Szeged, Hungary
| | - Vencel L. Petrovicz
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Viktória R. Fáy
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Lajos Kovács
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Tamás A. Martinek
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network, H-6720 Szeged, Hungary
- Correspondence: (T.A.M.); (Z.H.)
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
- Correspondence: (T.A.M.); (Z.H.)
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4
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Shi B, Zhou Y, Li X. Recent advances in DNA-encoded dynamic libraries. RSC Chem Biol 2022; 3:407-419. [PMID: 35441147 PMCID: PMC8985084 DOI: 10.1039/d2cb00007e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.
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Affiliation(s)
- Bingbing Shi
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Jining Medical University Jining Shandong 272067 P. R. China
| | - Yu Zhou
- 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
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission Units 1503-1511 15/F. Building 17W Hong Kong SAR China
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5
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Masaki Y, Maruyama A, Yoshida K, Tomori T, Kishimura T, Seio K. Oligodeoxynucleotides Modified with 2'- O-(Cysteinylaminobutyl)carbamoylethylribothymidine Residues for Native Chemical Ligation with Peptide at Internal Positions. Bioconjug Chem 2022; 33:272-278. [PMID: 35129971 DOI: 10.1021/acs.bioconjchem.1c00575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We used native chemical ligation (NCL) to synthesize a 2'-O-{N-[N-(S-tert-butylthiocysteinyl)aminobutyl]carbamoylethyl} (CysBCE) ribothymidine-derived oligonucleotide to expand the variety of peptide conjugation sites, allowing the incorporation of peptides at the 2'-hydroxy group when the oligonucleotide forms a duplex with the complementary strand. The NCL reaction with a peptide thioester and the modified oligonucleotide proceeded smoothly even when the CysBCE modification was in the middle of the oligonucleotide sequence. In addition, we incorporated two CysBCEs into an oligonucleotide to conjugate two peptides to one oligonucleotide. The results indicated that the tandem NCL reactions proceeded efficiently when the oligonucleotide hybridized to the complementary strand to avoid intramolecular disulfide formation between the two CysBCE groups. This method could be useful for peptide conjugation on the 2'-position.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Keita Yoshida
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Takahito Tomori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Tomohiro Kishimura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
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6
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Pimentel EB, Peters-Clarke TM, Coon JJ, Martell JD. DNA-Scaffolded Synergistic Catalysis. J Am Chem Soc 2021; 143:21402-21409. [PMID: 34898209 PMCID: PMC9101022 DOI: 10.1021/jacs.1c10757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report DNA-scaffolded synergistic catalysis, a concept that combines the diverse reaction scope of synergistic catalysis with the ability of DNA to precisely preorganize abiotic groups and undergo stimuli-triggered conformational changes. As an initial demonstration of this concept, we focus on Cu-TEMPO-catalyzed aerobic alcohol oxidation, using DNA as a scaffold to hold a copper cocatalyst and an organic radical cocatalyst (TEMPO) in proximity. The DNA-scaffolded catalyst maintained a high turnover number upon dilution and exhibited 190-fold improvement in catalyst turnover number relative to the unscaffolded cocatalysts. By incorporating the cocatalysts into a DNA hairpin-containing scaffold, we demonstrate that the rate of the synergistic catalytic reaction can be controlled through a reversible DNA conformational change that alters the distance between the cocatalysts. This work demonstrates the compatibility of synergistic catalytic reactions with DNA scaffolding, opening future avenues in reaction discovery, sensing, responsive materials, and chemical biology.
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Affiliation(s)
- Edward B. Pimentel
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA, Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA, National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA, Morgridge Institute for Research, Madison, WI, 53515, USA
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA,
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7
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Guo H, Wang L, Deng Y, Ye J. Novel perspectives of environmental proteomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147588. [PMID: 34023612 DOI: 10.1016/j.scitotenv.2021.147588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/08/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
The connection among genome expression, proteome alteration, metabolism regulation and phenotype change under environmental stresses is very vague. It is a tough task for the traditional research approaches to reveal the related scientific mechanisms of the above connection at molecular and systematic levels. Proteomics approach is an insightful tool for revealing the biological functions, metabolic networks and functional protein interaction networks of cells and organisms under stresses at the systematic level. The purpose of this review is to provide an insightful guideline on how to set up a proteomic investigation for revealing biomolecule mechanisms, protein biomarkers and metabolism networks related to stress response, pollutant recognition, transport and biodegradation, and providing an insightful high-throughput approach for screening functional enzymes and effective microbes based on bioinformatics and functional verification method. Furthermore, the toxicity evaluation of pollutants and byproducts by proteomics approaches provides a scientific insight for early diagnosis of ecological risk and determination of the effectiveness of pollutant treatment techniques.
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Affiliation(s)
- Huiying Guo
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Institute of Orthopedic Diseases, Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Lili Wang
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ying Deng
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
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8
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Kong G, Xiong M, Liu L, Hu L, Meng HM, Ke G, Zhang XB, Tan W. DNA origami-based protein networks: from basic construction to emerging applications. Chem Soc Rev 2021; 50:1846-1873. [PMID: 33306073 DOI: 10.1039/d0cs00255k] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
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Affiliation(s)
- Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Ling Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Hong-Min Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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9
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He L, Mu J, Gang O, Chen X. Rationally Programming Nanomaterials with DNA for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003775. [PMID: 33898180 PMCID: PMC8061415 DOI: 10.1002/advs.202003775] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/23/2020] [Indexed: 05/05/2023]
Abstract
DNA is not only a carrier of genetic information, but also a versatile structural tool for the engineering and self-assembling of nanostructures. In this regard, the DNA template has dramatically enhanced the scalability, programmability, and functionality of the self-assembled DNA nanostructures. These capabilities provide opportunities for a wide range of biomedical applications in biosensing, bioimaging, drug delivery, and disease therapy. In this review, the importance and advantages of DNA for programming and fabricating of DNA nanostructures are first highlighted. The recent progress in design and construction of DNA nanostructures are then summarized, including DNA conjugated nanoparticle systems, DNA-based clusters and extended organizations, and DNA origami-templated assemblies. An overview on biomedical applications of the self-assembled DNA nanostructures is provided. Finally, the conclusion and perspectives on the self-assembled DNA nanostructures are presented.
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Affiliation(s)
- Liangcan He
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
| | - Jing Mu
- Institute of Precision MedicinePeking University Shenzhen HospitalShenzhen518036China
| | - Oleg Gang
- Department of Chemical Engineering and Department of Applied Physics and Applied MathematicsColumbia UniversityNew YorkNY10027USA
- Center for Functional NanomaterialsBrookhaven National LaboratoryUptonNY11973USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
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10
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Weinhold E, Chakraborty B. DNA modification and visualization on an origami-based enzyme nano-factory. NANOSCALE 2021; 13:2465-2471. [PMID: 33471009 DOI: 10.1039/d0nr07618j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The past decade has seen enormous progress in DNA nanotechnology through the advent of DNA origami. Functionalizing the DNA origami for multiple applications is the recent focus of this field. Here we have constructed a novel DNA enzyme nano-factory, which modifies target DNA embedded on a DNA origami platform. The enzyme is programmed to reside in close proximity to the target DNA which enhances significantly the local concentration compared to solution-based DNA modification. To demonstrate this we have immobilized DNA methyltransferase M·TaqI next to the target DNA on the DNA origami and used this enzyme to sequence-specifically modify the target DNA with biotin using a cofactor analogue. Streptavidin binding to biotin is applied as a topographic marker to follow the machine cycle of this enzyme nano-factory using atomic force microscopy imaging. The nano-factory is demonstrated to be recyclable and holds the potential to be expanded to a multi-enzyme, multi-substrate operating system controlled by simple to complex molecules made of DNA, RNA or proteins.
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Affiliation(s)
- Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India.
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11
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Dems D, Freeman R, Riker KD, Coradin T, Stupp SI, Aimé C. Multivalent Clustering of Adhesion Ligands in Nanofiber-Nanoparticle Composites. Acta Biomater 2021; 119:303-311. [PMID: 33171314 DOI: 10.1016/j.actbio.2020.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/17/2020] [Accepted: 11/04/2020] [Indexed: 02/07/2023]
Abstract
Because the positioning and clustering of biomolecules within the extracellular matrix dictates cell behaviors, the engineering of biomaterials incorporating bioactive epitopes with spatial organization tunable at the nanoscale is of primary importance. Here we used a highly modular composite approach combining peptide amphiphile (PA) nanofibers and silica nanoparticles, which are both easily functionalized with one or several bioactive signals. We show that the surface of silica nanoparticles allows the clustering of RGDS bioactive signals leading to improved adhesion and spreading of fibroblast cells on composite hydrogels at an epitope concentration much lower than in PA-only based matrices. Most importantly, by combining the two integrin-binding sequences RGDS and PHSRN on nanoparticle surfaces, we improved cell adhesion on the PA nanofiber/particle composite hydrogels, which is attributed to synergistic interactions known to be effective only for peptide intermolecular distance of ca. 5 nm. Such composites with soft and hard nanostructures offer a strategy for the design of advanced scaffolds to display multiple signals and control cell behavior.
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Affiliation(s)
- Dounia Dems
- Sorbonne Université, CNRS, Collège de France, Laboratoire de Chimie de la Matière Condensée de Paris, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Ronit Freeman
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA.; Department of Applied Physical Sciences, University of North Carolina, 121 South Rd, Chapel Hill, North Carolina, 27514, United States
| | - Kyle D Riker
- Department of Applied Physical Sciences, University of North Carolina, 121 South Rd, Chapel Hill, North Carolina, 27514, United States
| | - Thibaud Coradin
- Sorbonne Université, CNRS, Collège de France, Laboratoire de Chimie de la Matière Condensée de Paris, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Samuel I Stupp
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA.; Department of Materials and Science & Engineering; Department of Chemistry; Department of Biomedical Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States; Department of Medicine, Northwestern University, 676 North St. Clair Street, Chicago, Illinois 60611, United States
| | - Carole Aimé
- Sorbonne Université, CNRS, Collège de France, Laboratoire de Chimie de la Matière Condensée de Paris, 4 place Jussieu, 75252 Paris cedex 05, France.
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12
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Live cell PNA labelling enables erasable fluorescence imaging of membrane proteins. Nat Chem 2020; 13:15-23. [PMID: 33288896 DOI: 10.1038/s41557-020-00584-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/02/2020] [Indexed: 12/18/2022]
Abstract
DNA nanotechnology is an emerging field that promises fascinating opportunities for the manipulation and imaging of proteins on a cell surface. The key to progress is the ability to create a nucleic acid-protein junction in the context of living cells. Here we report a covalent labelling reaction that installs a biostable peptide nucleic acid (PNA) tag. The reaction proceeds within minutes and is specific for proteins carrying a 2 kDa coiled-coil peptide tag. Once installed, the PNA label serves as a generic landing platform that enables the recruitment of fluorescent dyes via nucleic acid hybridization. We demonstrate the versatility of this approach by recruiting different fluorophores, assembling multiple fluorophores for increased brightness and achieving reversible labelling by way of toehold-mediated strand displacement. Additionally, we show that labelling can be carried out using two different coiled-coil systems, with epidermal growth factor receptor and endothelin receptor type B, on both HEK293 and CHO cells. Finally, we apply the method to monitor internalization of epidermal growth factor receptor on CHO cells.
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13
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Bachem G, Wamhoff E, Silberreis K, Kim D, Baukmann H, Fuchsberger F, Dernedde J, Rademacher C, Seitz O. Rational Design of a DNA‐Scaffolded High‐Affinity Binder for Langerin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Gunnar Bachem
- Department of Chemistry Humboldt-Universität zu Berlin 12489 Berlin Germany
| | - Eike‐Christian Wamhoff
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces 14424 Potsdam Germany
| | - Kim Silberreis
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry Charité-Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health 13353 Berlin Germany
| | - Dongyoon Kim
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces 14424 Potsdam Germany
| | - Hannes Baukmann
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces 14424 Potsdam Germany
| | - Felix Fuchsberger
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces 14424 Potsdam Germany
| | - Jens Dernedde
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry Charité-Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health 13353 Berlin Germany
| | - Christoph Rademacher
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces 14424 Potsdam Germany
| | - Oliver Seitz
- Department of Chemistry Humboldt-Universität zu Berlin 12489 Berlin Germany
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14
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Bachem G, Wamhoff E, Silberreis K, Kim D, Baukmann H, Fuchsberger F, Dernedde J, Rademacher C, Seitz O. Rational Design of a DNA-Scaffolded High-Affinity Binder for Langerin. Angew Chem Int Ed Engl 2020; 59:21016-21022. [PMID: 32749019 PMCID: PMC7693190 DOI: 10.1002/anie.202006880] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/24/2020] [Indexed: 11/17/2022]
Abstract
Binders of langerin could target vaccines to Langerhans cells for improved therapeutic effect. Since langerin has low affinity for monovalent glycan ligands, highly multivalent presentation has previously been key for targeting. Aiming to reduce the amount of ligand required, we rationally designed molecularly defined high-affinity binders based on the precise display of glycomimetic ligands (Glc2NTs) on DNA-PNA scaffolds. Rather than mimicking langerin's homotrimeric structure with a C3-symmetric scaffold, we developed readily accessible, easy-to-design bivalent binders. The method considers the requirements for bridging sugar binding sites and statistical rebinding as a means to both strengthen the interactions at single binding sites and amplify the avidity enhancement provided by chelation. This gave a 1150-fold net improvement over the affinity of the free ligand and provided a nanomolar binder (IC50 =300 nM) for specific internalization by langerin-expressing cells.
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Affiliation(s)
- Gunnar Bachem
- Department of ChemistryHumboldt-Universität zu Berlin12489BerlinGermany
| | - Eike‐Christian Wamhoff
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces14424PotsdamGermany
| | - Kim Silberreis
- Institute of Laboratory Medicine, Clinical Chemistry and PathobiochemistryCharité-Universitätsmedizin Berlincorporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health13353BerlinGermany
| | - Dongyoon Kim
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces14424PotsdamGermany
| | - Hannes Baukmann
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces14424PotsdamGermany
| | - Felix Fuchsberger
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces14424PotsdamGermany
| | - Jens Dernedde
- Institute of Laboratory Medicine, Clinical Chemistry and PathobiochemistryCharité-Universitätsmedizin Berlincorporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health13353BerlinGermany
| | - Christoph Rademacher
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces14424PotsdamGermany
| | - Oliver Seitz
- Department of ChemistryHumboldt-Universität zu Berlin12489BerlinGermany
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15
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Yeldell SB, Seitz O. Nucleic acid constructs for the interrogation of multivalent protein interactions. Chem Soc Rev 2020; 49:6848-6865. [DOI: 10.1039/d0cs00518e] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequence-programmed self-assembly provides multivalent nucleic acid–ligand constructs used as tailor-made probes for unravelling and exploiting the mechanisms of multivalency-enhanced interactions on protein receptors.
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Affiliation(s)
- Sean B. Yeldell
- Department of Chemistry
- Humboldt-Universität zu Berlin
- Brook-Taylor-Str. 2
- 12489 Berlin
- Germany
| | - Oliver Seitz
- Department of Chemistry
- Humboldt-Universität zu Berlin
- Brook-Taylor-Str. 2
- 12489 Berlin
- Germany
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16
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Seitz O. Templated chemistry for bioorganic synthesis and chemical biology. J Pept Sci 2019; 25:e3198. [PMID: 31309674 PMCID: PMC6771651 DOI: 10.1002/psc.3198] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/24/2022]
Abstract
In light of the 2018 Max Bergmann Medal, this review discusses advancements on chemical biology-driven templated chemistry developed in the author's laboratories. The focused review introduces the template categories applied to orient functional units such as functional groups, chromophores, biomolecules, or ligands in space. Unimolecular templates applied in protein synthesis facilitate fragment coupling of unprotected peptides. Templating via bimolecular assemblies provides control over proximity relationships between functional units of two molecules. As an instructive example, the coiled coil peptide-templated labelling of receptor proteins on live cells will be shown. Termolecular assemblies provide the opportunity to put the proximity of functional units on two (bio)molecules under the control of a third party molecule. This allows the design of conditional bimolecular reactions. A notable example is DNA/RNA-triggered peptide synthesis. The last section shows how termolecular and multimolecular assemblies can be used to better characterize and understand multivalent protein-ligand interactions.
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Affiliation(s)
- Oliver Seitz
- Department of ChemistryHumboldt University BerlinBerlinGermany
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17
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Dubel N, Liese S, Scherz F, Seitz O. Untersuchungen zu Grenzen der Bivalenz mit DNA-basierter räumlicher Rasterung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Natali Dubel
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Susanne Liese
- Institut für Theoretische Physik; Freie Universität Berlin; Arnimallee 14 14195 Berlin Deutschland
| | - Franziska Scherz
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Oliver Seitz
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
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18
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Dubel N, Liese S, Scherz F, Seitz O. Exploring the Limits of Bivalency by DNA-Based Spatial Screening. Angew Chem Int Ed Engl 2018; 58:907-911. [DOI: 10.1002/anie.201810996] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/19/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Natali Dubel
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Susanne Liese
- Institute for Theoretical Physics; Free University Berlin; Arnimallee 14 14195 Berlin Germany
| | - Franziska Scherz
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Oliver Seitz
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
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19
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Zhou Y, Li C, Peng J, Xie L, Meng L, Li Q, Zhang J, Li XD, Li X, Huang X, Li X. DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery. J Am Chem Soc 2018; 140:15859-15867. [DOI: 10.1021/jacs.8b09277] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yu Zhou
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Chen Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
| | - Jianzhao Peng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Liangxu Xie
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water
Bay, Kowloon, Hong Kong, Hong Kong
| | - Ling Meng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Qingrong Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Jianfu Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water
Bay, Kowloon, Hong Kong, Hong Kong
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
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20
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Freeman R, Stephanopoulos N, Álvarez Z, Lewis JA, Sur S, Serrano CM, Boekhoven J, Lee SS, Stupp SI. Instructing cells with programmable peptide DNA hybrids. Nat Commun 2017; 8:15982. [PMID: 28691701 PMCID: PMC5508132 DOI: 10.1038/ncomms15982] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/19/2017] [Indexed: 12/12/2022] Open
Abstract
The native extracellular matrix is a space in which signals can be displayed dynamically and reversibly, positioned with nanoscale precision, and combined synergistically to control cell function. Here we describe a molecular system that can be programmed to control these three characteristics. In this approach we immobilize peptide-DNA (P-DNA) molecules on a surface through complementary DNA tethers directing cells to adhere and spread reversibly over multiple cycles. The DNA can also serve as a molecular ruler to control the distance-dependent synergy between two peptides. Finally, we use two orthogonal DNA handles to regulate two different bioactive signals, with the ability to independently up- or downregulate each over time. This enabled us to discover that neural stem cells, derived from the murine spinal cord and organized as neurospheres, can be triggered to migrate out in response to an exogenous signal but then regroup into a neurosphere as the signal is removed.
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Affiliation(s)
- Ronit Freeman
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
| | - Nicholas Stephanopoulos
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
| | - Zaida Álvarez
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
| | - Jacob A Lewis
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Shantanu Sur
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
| | - Chris M Serrano
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, USA
| | - Job Boekhoven
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
| | - Sungsoo S. Lee
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
| | - Samuel I. Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, USA
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
- Department of Medicine, Northwestern University, 251 East Huron Street, Chicago, Illinois 60611, USA
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21
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Abstract
Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging.
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Affiliation(s)
- Margherita Di Pisa
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
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22
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Machida T, Novoa A, Gillon É, Zheng S, Claudinon J, Eierhoff T, Imberty A, Römer W, Winssinger N. Dynamic Cooperative Glycan Assembly Blocks the Binding of Bacterial Lectins to Epithelial Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700813] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Takuya Machida
- Department of Organic Chemistry; NCCR Chemical Biology; Faculty of Science; University of Geneva; Quai Ernest Ansermet 30 1211 Geneva Switzerland
| | - Alexandre Novoa
- Department of Organic Chemistry; NCCR Chemical Biology; Faculty of Science; University of Geneva; Quai Ernest Ansermet 30 1211 Geneva Switzerland
| | - Émilie Gillon
- CERMAV UPR5301, CNRS; Université Grenoble Alpes, BP 53; 38041 Grenoble cedex 9 France
| | - Shuangshuang Zheng
- Faculty of Biology; Centre for Biological Signalling Studies (BIOSS); Albert-Ludwigs-University Freiburg; Schänzlestraße 18 79104 Freiburg Germany
| | - Julie Claudinon
- Faculty of Biology; Centre for Biological Signalling Studies (BIOSS); Albert-Ludwigs-University Freiburg; Schänzlestraße 18 79104 Freiburg Germany
| | - Thorsten Eierhoff
- Faculty of Biology; Centre for Biological Signalling Studies (BIOSS); Albert-Ludwigs-University Freiburg; Schänzlestraße 18 79104 Freiburg Germany
- Present address: Institute of Biochemistry; Heinrich-Heine-University Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
| | - Anne Imberty
- CERMAV UPR5301, CNRS; Université Grenoble Alpes, BP 53; 38041 Grenoble cedex 9 France
| | - Winfried Römer
- Faculty of Biology; Centre for Biological Signalling Studies (BIOSS); Albert-Ludwigs-University Freiburg; Schänzlestraße 18 79104 Freiburg Germany
| | - Nicolas Winssinger
- Department of Organic Chemistry; NCCR Chemical Biology; Faculty of Science; University of Geneva; Quai Ernest Ansermet 30 1211 Geneva Switzerland
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23
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Machida T, Novoa A, Gillon É, Zheng S, Claudinon J, Eierhoff T, Imberty A, Römer W, Winssinger N. Dynamic Cooperative Glycan Assembly Blocks the Binding of Bacterial Lectins to Epithelial Cells. Angew Chem Int Ed Engl 2017; 56:6762-6766. [PMID: 28504473 DOI: 10.1002/anie.201700813] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/20/2017] [Indexed: 11/06/2022]
Abstract
Pathogens frequently rely on lectins for adhesion and cellular entry into the host. Since these interactions typically result from multimeric binding of lectins to cell-surface glycans, novel therapeutic strategies are being developed with the use of glycomimetics as competitors of such interactions. Herein we study the benefit of nucleic acid based oligomeric assemblies with PNA-fucose conjugates. We demonstrate that the interactions of a lectin with epithelial cells can be inhibited with conjugates that do not form stable assemblies in solution but benefit from cooperativity between ligand-protein interactions and PNA hybridization to achieve high affinity. A dynamic dimeric assembly fully blocked the binding of the fucose-binding lectin BambL of Burkholderia ambifaria, a pathogenic bacterium, to epithelial cells with an efficiency of more than 700-fold compared to l-fucose.
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Affiliation(s)
- Takuya Machida
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
| | - Alexandre Novoa
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
| | - Émilie Gillon
- CERMAV UPR5301, CNRS, Université Grenoble Alpes, BP 53, 38041, Grenoble cedex 9, France
| | - Shuangshuang Zheng
- Faculty of Biology, Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Julie Claudinon
- Faculty of Biology, Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Thorsten Eierhoff
- Faculty of Biology, Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany.,Present address: Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Anne Imberty
- CERMAV UPR5301, CNRS, Université Grenoble Alpes, BP 53, 38041, Grenoble cedex 9, France
| | - Winfried Römer
- Faculty of Biology, Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
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24
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Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
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25
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Peri-Naor R, Motiei L, Margulies D. Mimicking the Function of Signaling Proteins: Toward Artificial Signal Transduction Therapy. J Vis Exp 2016. [PMID: 27768030 DOI: 10.3791/54396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Signal transduction pathways, which control the response of cells to various environmental signals, are mediated by the function of signaling proteins that interact with each other and activate one other with high specificity. Synthetic agents that mimic the function of these proteins might therefore be used to generate unnatural signal transduction steps and consequently, alter the cell's function. We present guidelines for designing 'chemical transducers' that can induce artificial communication between native proteins. In addition, we present detailed protocols for synthesizing and testing a specific 'transducer', which can induce communication between two unrelated proteins: platelet-derived growth-factor (PDGF) and glutathione-S-transferase (GST). The way by which this unnatural PDGF-GST communication could be used to control the cleavage of an anticancer prodrug is also presented, indicating the potential for using such systems in 'artificial signal transduction therapy'. This work is intended to facilitate developing additional 'transducers' of this class, which may be used to mediate intracellular protein-protein communication and consequently, to induce artificial cell signaling pathways.
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Affiliation(s)
- Ronny Peri-Naor
- Department of Organic Chemistry, Weizmann Institute of Science
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science;
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26
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Su X, Zhou X, Zhang N, Zhu M, Zhang H, Jayawickramarajah J. A stable bidentate protein binder achieved via DNA self-assembly driven ligand migration. Chem Commun (Camb) 2016. [PMID: 26225890 DOI: 10.1039/c5cc03213j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herein we disclose the development of two complementary single stranded DNA-small molecule chimeras (DCs) that by themselves only bind weakly to a protein target (human serum albumin; HSA). However, upon self-assembly, the DC duplex facilitates a ligand migration reaction leading to a covalently fastened high-affinity, bidentate, protein-binder that resides at the terminus of only one of the DC strands. Due to this specific localization, the bidentate projection remains intact—and thus the system continues to strongly bind HSA—even under conditions that denature and degrade the DNA scaffolds.
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Affiliation(s)
- Xiaoye Su
- Department of Chemistry, Tulane University, Louisiana 70118, USA.
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27
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Orbach R, Willner B, Willner I. Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: from basic principles to practical applications. Chem Commun (Camb) 2015; 51:4144-60. [PMID: 25612298 DOI: 10.1039/c4cc09874a] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This feature article addresses the implementation of catalytic nucleic acids as functional units for the construction of logic gates and computing circuits, and discusses the future applications of these systems. The assembly of computational modules composed of DNAzymes has led to the operation of a universal set of logic gates, to field programmable logic gates and computing circuits, to the development of multiplexers/demultiplexers, and to full-adder systems. Also, DNAzyme cascades operating as logic gates and computing circuits were demonstrated. DNAzyme logic systems find important practical applications. These include the use of DNAzyme-based systems for sensing and multiplexed analyses, for the development of controlled release and drug delivery systems, for regulating intracellular biosynthetic pathways, and for the programmed synthesis and operation of cascades.
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Affiliation(s)
- Ron Orbach
- Institute of Chemistry and the Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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28
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Gupta P, Rastede EE, Appella DH. Multivalent LKγ-PNA oligomers bind to a human telomere DNA G-rich sequence to form quadruplexes. Bioorg Med Chem Lett 2015; 25:4757-4760. [PMID: 26259805 PMCID: PMC5603266 DOI: 10.1016/j.bmcl.2015.07.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 12/15/2022]
Abstract
We report G-quadruplex formation between peptide nucleic acids (PNAs) composed of (L)Kγ-PNA-G monomers and a known portion of human telomeric DNA that adopts three G3 tracts via intramolecular hydrogen bonding. The resulting complex is a bimolecular PNA-DNA heteroquadruplex. In this Letter, we show that introduction of a γ-modification and addition of a peptide ligand does not disrupt the heteroquadruplex. Although the unmodified PNA1 forms a quadruplex with itself, the γ-substituted PNAs (PNA2-PNA6) do not form G-quadruplexes on their own, at even high concentrations. The selectivity of these PNAs could influence the design of new quadruplex-targeting molecules or allow the quadruplex structure to be used as a scaffold for multivalent display of protein binding ligands.
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Affiliation(s)
- Pankaj Gupta
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD 20892, USA
| | | | - Daniel H Appella
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD 20892, USA.
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29
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Flory JD, Johnson T, Simmons CR, Lin S, Ghirlanda G, Fromme P. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage. ARTIFICIAL DNA, PNA & XNA 2015; 5:1-8. [PMID: 25760314 DOI: 10.4161/1949095x.2014.992181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PNA is hybrid molecule ideally suited for bridging the functional landscape of polypeptides with the structural diversity that can be engineered with DNA nanostructures. However, PNA can be more challenging to work with in aqueous solvents due to its hydrophobic nature. A solution phase method using strain promoted, copper free click chemistry was developed to conjugate the fluorescent dye Cy5 to 2 bifunctional PNA strands as a first step toward building cyclic PNA-polypeptides that can be arranged within 3D DNA nanoscaffolds. A 3D DNA nanocage was designed with binding sites for the 2 fluorescently labeled PNA strands in close proximity to mimic protein active sites. Denaturing polyacrylamide gel electrophoresis (PAGE) is introduced as an efficient method for purifying charged, dye-labeled PNA conjugates from large excesses of unreacted dye and unreacted, neutral PNA. Elution from the gel in water was monitored by fluorescence and found to be more efficient for the more soluble PNA strand. Native PAGE shows that both PNA strands hybridize to their intended binding sites within the DNA nanocage. Förster resonance energy transfer (FRET) with a Cy3 labeled DNA nanocage was used to determine the dissociation temperature of one PNA-Cy5 conjugate to be near 50°C. Steady-state and time resolved fluorescence was used to investigate the dye orientation and interactions within the various complexes. Bifunctional, thermostable PNA molecules are intriguing candidates for controlling the assembly and orientation of peptides within small DNA nanocages for mimicking protein catalytic sites.
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Key Words
- DBCO, dibenzocyclooctyl
- DNA nanotechnology
- DTNB, 5, 5′-dithiobis-(2-nitrobenzoic acid)
- EtBr, ethidium bromide
- IEX-FPLC, ion-exchange fast protein liquid chromatography
- MALDI-MS, matrix assisted laser desorption ionization mass spectrometry
- PAGE, polyacrylamide gel electrophoresis
- PNA, peptide nucleic acid
- RP-HPLC, reverse-phase high pressure liquid chromatography
- TCEP, tris(2-carboxyethyl)phosphine
- biomimicry
- copper-free click chemistry
- fluorescence
- self-assembly
- γ-PNA
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Affiliation(s)
- Justin D Flory
- a Department of Chemistry and Biochemistry; Arizona State University ; Tempe , Arizona USA
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30
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Guo C, Watkins CP, Hili R. Sequence-Defined Scaffolding of Peptides on Nucleic Acid Polymers. J Am Chem Soc 2015; 137:11191-6. [DOI: 10.1021/jacs.5b07675] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Chun Guo
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602-2556, United States
| | - Christopher P. Watkins
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602-2556, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602-2556, United States
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31
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Chu X, Battle CH, Zhang N, Aryal GH, Mottamal M, Jayawickramarajah J. Bile Acid Conjugated DNA Chimera that Conditionally Inhibits Carbonic Anhydrase-II in the Presence of MicroRNA-21. Bioconjug Chem 2015; 26:1606-12. [PMID: 26191606 DOI: 10.1021/acs.bioconjchem.5b00231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In order to tackle the issue of systemic toxicity in chemotherapy, there is a need to develop novel mechanisms for the activation of protein inhibitors using biomarkers overexpressed in cancer cells. Many current strategies focus on using cancer associated enzymes as a triggering agent for prodrugs. Herein, we detail an alternative approach that harnesses a microRNA (miR-21) that is overexpressed in cancers as the trigger that activates an inhibitor of human carbonic anhydrase-II (hCA-II). Specifically, we have developed a DNA-small molecule chimera (DC) composed of an hCA-II binding lithocholic acid amide (LAA) headgroup that can transition from a rigid duplex state (that does not bind appreciably to hCA) to a single-stranded conformation via a miR-21 trigger. The activated single-stranded DC can project the LAA headgroup into the hCA-II active site and is a robust hCA-II inhibitor (K(i) of 3.12 μM). This work may spur research into developing new classes of cancer selective protein inhibitors.
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Affiliation(s)
- Xiaozhu Chu
- †Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Cooper H Battle
- †Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Nan Zhang
- †Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Gyan H Aryal
- †Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Madhusoodanan Mottamal
- ‡RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
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32
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Peri-Naor R, Ilani T, Motiei L, Margulies D. Protein-Protein Communication and Enzyme Activation Mediated by a Synthetic Chemical Transducer. J Am Chem Soc 2015; 137:9507-10. [PMID: 25955617 DOI: 10.1021/jacs.5b01123] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The design and function of a synthetic "chemical transducer" that can generate an unnatural communication channel between two proteins is described. Specifically, we show how this transducer enables platelet-derived growth factor to trigger (in vitro) the catalytic activity of glutathione-s-transferase (GST), which is not its natural enzyme partner. GST activity can be further controlled by adding specific oligonucleotides that switch the enzymatic reaction on and off. We also demonstrate that a molecular machine, which can regulate the function of an enzyme, could be used to change the way a prodrug is activated in a "programmable" manner.
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Affiliation(s)
- Ronny Peri-Naor
- †Departments of Organic Chemistry and ‡Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Ilani
- †Departments of Organic Chemistry and ‡Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Leila Motiei
- †Departments of Organic Chemistry and ‡Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Margulies
- †Departments of Organic Chemistry and ‡Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
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33
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Janssen BMG, Engelen W, Merkx M. DNA-directed control of enzyme-inhibitor complex formation: a modular approach to reversibly switch enzyme activity. ACS Synth Biol 2015; 4:547-53. [PMID: 25216042 DOI: 10.1021/sb500278z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA-templated reversible assembly of an enzyme-inhibitor complex is presented as a new and highly modular approach to control enzyme activity. TEM1-β-lactamase and its inhibitor protein BLIP were conjugated to different oligonucleotides, resulting in enzyme inhibition in the presence of template strand. Formation of a rigid dsDNA linker upon addition of a complementary target strand disrupts the enzyme-inhibitor complex and results in the restoration of enzyme activity, enabling detection of as little as 2 fmol DNA. The noncovalent assembly of the complex allows easy tuning of target and template strands without changing the oligonucleotide-functionalized enzyme and inhibitor domains. Using a panel of eight different template sequences, restoration of enzyme activity was only observed in the presence of the target viral DNA sequence. The use of stable, well-characterized protein domains and the intrinsic modularity of our system should allow easy integration with DNA/RNA-based logic circuits for applications in biomedicine and molecular diagnostics.
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Affiliation(s)
- Brian M. G. Janssen
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
| | - Wouter Engelen
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
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34
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Dix A, Conroy JL, George Rosenker KM, Sibley DR, Appella DH. PNA-Based Multivalent Scaffolds Activate the Dopamine D2 Receptor. ACS Med Chem Lett 2015; 6:425-9. [PMID: 25893044 PMCID: PMC4394337 DOI: 10.1021/ml500478m] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/12/2015] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid scaffolds represent a promising tool to interrogate the multivalent effects of ligand binding to a membrane receptor. Dopamine D2 receptors (D2R) are a class of G-protein coupled receptors (GPCRs), and the formation of higher-ordered structures of these receptors has been associated with the progression of several neurological diseases. In this Letter, we describe the synthesis of a library of ligand-modified PNAs bearing a known D2R agonist, (±)-PPHT. The D2R activity for each construct was assessed, and the multivalent effects were evaluated.
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Affiliation(s)
- Andrew
V. Dix
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jennie L. Conroy
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kara M. George Rosenker
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David R. Sibley
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
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35
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Diezmann F, von Kleist L, Haucke V, Seitz O. Probing heterobivalent binding to the endocytic AP-2 adaptor complex by DNA-based spatial screening. Org Biomol Chem 2015; 13:8008-15. [DOI: 10.1039/c5ob00943j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The DNA-programmed peptide display in brain extract revealed a co-operation between the binding sites on the AP-2 alpha-appendage domain.
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Affiliation(s)
- F. Diezmann
- Humboldt-Universität zu Berlin
- Institut für Chemie
- D-12489 Berlin
- Germany
| | - L. von Kleist
- Freie Universität Berlin
- Department of Biology
- Chemistry and Pharmacy and Leibniz Institut für Molekulare Pharmakologie (FMP)
- D-13125 Berlin
- Germany
| | - V. Haucke
- Freie Universität Berlin
- Department of Biology
- Chemistry and Pharmacy and Leibniz Institut für Molekulare Pharmakologie (FMP)
- D-13125 Berlin
- Germany
| | - O. Seitz
- Humboldt-Universität zu Berlin
- Institut für Chemie
- D-12489 Berlin
- Germany
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36
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Flory JD, Simmons CR, Lin S, Johnson T, Andreoni A, Zook J, Ghirlanda G, Liu Y, Yan H, Fromme P. Low temperature assembly of functional 3D DNA-PNA-protein complexes. J Am Chem Soc 2014; 136:8283-95. [PMID: 24871902 DOI: 10.1021/ja501228c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteins have evolved to carry out nearly all the work required of living organisms within complex inter- and intracellular environments. However, systematically investigating the range of interactions experienced by a protein that influence its function remains challenging. DNA nanostructures are emerging as a convenient method to arrange a broad range of guest molecules. However, flexible methods are needed for arranging proteins in more biologically relevant 3D geometries under mild conditions that preserve protein function. Here we demonstrate how peptide nucleic acid (PNA) can be used to control the assembly of cytochrome c (12.5 kDa, pI 10.5) and azurin (13.9 kDa, pI 5.7) proteins into separate 3D DNA nanocages, in a process that maintains protein function. Toehold-mediated DNA strand displacement is introduced as a method to purify PNA-protein conjugates. The PNA-proteins were assembled within 2 min at room temperature and within 4 min at 11 °C, and hybridize with even greater efficiency than PNA conjugated to a short peptide. Gel electrophoresis and steady state and time-resolved fluorescence spectroscopy were used to investigate the effect of protein surface charge on its interaction with the negatively charged DNA nanocage. These data were used to generate a model of the DNA-PNA-protein complexes that show the negatively charged azurin protein repelled away from the DNA nanocage while the positively charged cytochrome c protein remains within and closely interacts with the DNA nanocage. When conjugated to PNA and incorporated into the DNA nanocage, the cytochrome c secondary structure and catalytic activity were maintained, and its redox potential was reduced modestly by 20 mV possibly due to neutralization of some positive surface charges. This work demonstrates a flexible new approach for using 3D nucleic acid (PNA-DNA) nanostructures to control the assembly of functional proteins, and facilitates further investigation of protein interactions as well as engineer more elaborate 3D protein complexes.
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Affiliation(s)
- Justin D Flory
- Department of Chemistry and Biochemistry, ‡Center for Bio-Inspired Solar Fuel Production, and §Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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37
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Motiei L, Pode Z, Koganitsky A, Margulies D. Targeted Protein Surface Sensors as a Tool for Analyzing Small Populations of Proteins in Biological Mixtures. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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38
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Motiei L, Pode Z, Koganitsky A, Margulies D. Targeted Protein Surface Sensors as a Tool for Analyzing Small Populations of Proteins in Biological Mixtures. Angew Chem Int Ed Engl 2014; 53:9289-93. [DOI: 10.1002/anie.201402501] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 01/11/2023]
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39
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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40
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Vázquez O, Seitz O. Cytotoxic peptide–PNA conjugates obtained by RNA-programmed peptidyl transfer with turnover. Chem Sci 2014. [DOI: 10.1039/c4sc00299g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A RNA triggered chemical peptidyl transfer reaction leads to a cytotoxic peptide conjugate that requires turnover in RNA for bioactivity.
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Affiliation(s)
- O. Vázquez
- Institut für Chemie
- Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - O. Seitz
- Institut für Chemie
- Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
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41
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Li Y, Zhao P, Zhang M, Zhao X, Li X. Multistep DNA-Templated Synthesis Using a Universal Template. J Am Chem Soc 2013; 135:17727-30. [DOI: 10.1021/ja409936r] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yizhou Li
- Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of the Ministry of Education,
Beijing National Laboratory of Molecular Sciences (BNLMS), College
of Chemistry and Molecular Engineering, Peking University, 202
Chengfu Road, Beijing, China 100871
| | - Peng Zhao
- Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of the Ministry of Education,
Beijing National Laboratory of Molecular Sciences (BNLMS), College
of Chemistry and Molecular Engineering, Peking University, 202
Chengfu Road, Beijing, China 100871
| | - Mingda Zhang
- Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of the Ministry of Education,
Beijing National Laboratory of Molecular Sciences (BNLMS), College
of Chemistry and Molecular Engineering, Peking University, 202
Chengfu Road, Beijing, China 100871
| | - Xianyuan Zhao
- Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of the Ministry of Education,
Beijing National Laboratory of Molecular Sciences (BNLMS), College
of Chemistry and Molecular Engineering, Peking University, 202
Chengfu Road, Beijing, China 100871
| | - Xiaoyu Li
- Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of the Ministry of Education,
Beijing National Laboratory of Molecular Sciences (BNLMS), College
of Chemistry and Molecular Engineering, Peking University, 202
Chengfu Road, Beijing, China 100871
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42
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Xin L, Zhou C, Yang Z, Liu D. Regulation of an enzyme cascade reaction by a DNA machine. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3088-3091. [PMID: 23613449 DOI: 10.1002/smll.201300019] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 02/16/2013] [Indexed: 06/02/2023]
Abstract
A strategy for the regulation of enzyme cascade reaction efficiency by a DNA machine in vitro is presented. Two cascade enzymes (GOx and HRP) are attached to the DNA machine, and the enzyme cascade reaction shows much higher efficiency when the two enzymes are brought closer by the DNA machine than when they are distant.
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Affiliation(s)
- Ling Xin
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
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43
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Battle C, Chu X, Jayawickramarajah J. Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding. Supramol Chem 2013; 25. [PMID: 24187478 DOI: 10.1080/10610278.2013.810337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.
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Affiliation(s)
- Cooper Battle
- Department of Chemistry, Tulane University, New Orleans, LA, USA
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44
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Li G, Liu Y, Liu Y, Chen L, Wu S, Liu Y, Li X. Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry. Angew Chem Int Ed Engl 2013; 52:9544-9. [DOI: 10.1002/anie.201302161] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/14/2013] [Indexed: 01/07/2023]
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45
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Li G, Liu Y, Liu Y, Chen L, Wu S, Liu Y, Li X. Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302161] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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46
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Li S, Langenegger SM, Häner R. Control of aggregation-induced emission by DNA hybridization. Chem Commun (Camb) 2013; 49:5835-7. [PMID: 23702589 DOI: 10.1039/c3cc42706d] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Molecular aggregation and fluorescence of DATPEs are controlled by duplex formation.
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Affiliation(s)
- Shaoguang Li
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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47
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Li Y, Zhang M, Zhang C, Li X. Detection of bond formations by DNA-programmed chemical reactions and PCR amplification. Chem Commun (Camb) 2013; 48:9513-5. [PMID: 22899375 DOI: 10.1039/c2cc35230c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A system capable of performing both DNA-templated chemical reactions and detection of bond formations is reported. Photocleavable DNA templates direct reactions. Products from bond-forming events re-ligate original templates, amplifiable by PCR, therefore distinguishing bond formation from background. This system provides a novel approach for discovering potential new chemical reactions.
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Affiliation(s)
- Yizhou Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, 202 Chengfu Rd., Beijing, 100871, China
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48
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Scheibe C, Wedepohl S, Riese SB, Dernedde J, Seitz O. Carbohydrate-PNA and aptamer-PNA conjugates for the spatial screening of lectins and lectin assemblies. Chembiochem 2013; 14:236-50. [PMID: 23292704 DOI: 10.1002/cbic.201200618] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Indexed: 11/06/2022]
Abstract
Nucleic acid architectures offer intriguing opportunities for the interrogation of structural properties of protein receptors. In this study, we performed a DNA-programmed spatial screening to characterize two functionally distinct receptor systems: 1) structurally well-defined Ricinus communis agglutinin (RCA(120)), and 2) rather ill-defined assemblies of L-selectin on nanoparticles and leukocytes. A robust synthesis route that allowed the attachment both of carbohydrate ligands-such as N-acetyllactosamine (LacNAc), sialyl-Lewis-X (sLe(X)), and mannose-and of a DNA aptamer to PNAs was developed. A systematically assembled series of different PNA-DNA complexes served as multivalent scaffolds to control the spatial alignments of appended lectin ligands. The spatial screening of the binding sites of RCA(120) was in agreement with the crystal structure analysis. The study revealed that two appropriately presented LacNAc ligands suffice to provide unprecedented RCA(120) affinity (K(D) = 4 μM). In addition, a potential secondary binding site was identified. Less dramatic binding enhancements were obtained when the more flexible L-selectin assemblies were probed. This study involved the bivalent display both of the weak-affinity sLe(X) ligand and of a high-affinity DNA aptamer. Bivalent presentation led to rather modest (sixfold or less) enhancements of binding when the self-assemblies were targeted against L-selectin on gold nanoparticles. Spatial screening of L-selectin on the surfaces of leukocytes showed higher affinity enhancements (25-fold). This and the distance-activity relationships indicated that leukocytes permit dense clustering of L-selectin.
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Affiliation(s)
- Christian Scheibe
- Institut für Chemie, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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49
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Janssen BMG, Lempens EHM, Olijve LLC, Voets IK, van Dongen JLJ, de Greef TFA, Merkx M. Reversible blocking of antibodies using bivalent peptide–DNA conjugates allows protease-activatable targeting. Chem Sci 2013. [DOI: 10.1039/c3sc22033h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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50
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Schade M, Knoll A, Vogel A, Seitz O, Liebscher J, Huster D, Herrmann A, Arbuzova A. Remote control of lipophilic nucleic acids domain partitioning by DNA hybridization and enzymatic cleavage. J Am Chem Soc 2012; 134:20490-7. [PMID: 23163619 DOI: 10.1021/ja309256t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Lateral partitioning of lipid-modified molecules between liquid-disordered (ld) and liquid-ordered (lo) domains depends on the type of lipid modification, presence of a spacer, membrane composition, and temperature. Here, we show that the lo domain partitioning of the palmitoylated peptide nucleic acid (PNA) can be influenced by formation of a four-component complex with the ld domain partitioning tocopherol-modified DNA: the PNA-DNA complex partitioned into the ld domains. Enzymatic cleavage of the DNA linker led to the disruption of the complex and restored the initial distribution of the lipophilic nucleic acids into the respective domains. This modular system offers strategies for dynamic functionalization of biomimetic surfaces, for example, in nanostructuring and regulation of enzyme catalysis, and it provides a tool to study the molecular basis of controlled reorganization of lipid-modified proteins in membranes, for example, during signal transduction.
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Affiliation(s)
- Matthias Schade
- Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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