1
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Chen K, Mao M, Huo L, Wang G, Pu Z, Zhang Y. Flexible DNA Nanoclaws Offer Multivalent and Powerful Spatial Pattern-Recognition for Tumor Cells. ACS APPLIED MATERIALS & INTERFACES 2024; 16:29760-29769. [PMID: 38813974 DOI: 10.1021/acsami.4c03382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Multivalent receptor-ligand interactions (RLIs) exhibit excellent affinity for binding when targeting cell membrane receptors with low expression. However, existing strategies only allow for limited control of the valency and spacing of ligands for a certain receptor, lacking recognition patterns for multiple interested receptors with complex spatial distributions. Here, we developed flexible DNA nanoclaws with multivalent aptamers to achieve powerful cell recognition by controlling the spacing of aptamers to match the spatial patterns of receptors. The DNA nanoclaw with spacing-controllable binding sites was constructed via hybrid chain reaction (HCR), enabling dual targeting of HER2 and EpCAM molecules. The results demonstrate that the binding affinity of multivalent DNA nanoclaws to tumor cells is enhanced. We speculate that the flexible structure may conform better to irregularly shaped membrane surfaces, increasing the probability of intermolecular contact. The capture efficiency of circulating tumor cells successfully verified the high affinity and selectivity of this spatial pattern. This strategy will further promote the potential application of DNA frameworks in future disease diagnosis and treatment.
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Affiliation(s)
- Kang Chen
- Department of Laboratory Medicine, Zhongshan City People's Hospital, 528403 Zhongshan, Guangdong, China
| | - Miao Mao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
| | - Lian Huo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
| | - Guanzhao Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
| | - Zhe Pu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
| | - Yuanqing Zhang
- Department of Laboratory Medicine, Zhongshan City People's Hospital, 528403 Zhongshan, Guangdong, China
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
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2
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Ye T, Xu Y, Chen H, Yuan M, Cao H, Hao L, Wu X, Yin F, Xu F. A trivalent aptasensor by using DNA tetrahedron as scaffold for label-free determination of antibiotics. Biosens Bioelectron 2024; 251:116127. [PMID: 38382272 DOI: 10.1016/j.bios.2024.116127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/23/2024]
Abstract
Owing to advantage in high sensitivity and fast response, aptamer based electrochemical biosensors have attracted much more attention. However, inappropriate interfacial engineering strategy leads to poor recognition performance, which ascribe to the following factors of immobilized oligonucleotide strand including steric hindrance, interchain entanglement, and unfavorable conformation. In this work, we proposed a DNA tetrahedron based diblock aptamer immobilized strategy for the construction of label-free electrochemical biosensor. The diblock aptamer sequence is composite of T-rich anchor domain and recognition domain, where T-rich domain enabling anchored on the edge of DNA tetrahedron via Hoogsteen hydrogen bond at neutral condition. The DNA tetrahedron scaffold offers an appropriate lateral space for target recognition of diblock aptamer. More importantly, this trivalent aptamer recognition interface can be regenerated by simply adjusting the pH environment to alkaline, resulting in the dissociation of diblock aptamer. Under the optimum condition, proposed electrochemical aptasensor manifested a satisfied sensitivity for aminoglycosides antibiotic, kanamycin with a limit of detection of 0.69 nM, which is 45-fold lower than traditional Au-S immobilization strategy. Moreover, the proposed aptasensor had also successfully been extended to ampicillin detection by changing the sequence of recognition domain in diblock aptamer. This work paves a new way for the rational design of aptamer-based electrochemical sensor.
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Affiliation(s)
- Tai Ye
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yimin Xu
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Haohao Chen
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Min Yuan
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hui Cao
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Liling Hao
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xiuxiu Wu
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Fengqin Yin
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Fei Xu
- Shanghai Engineering Research Center of Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
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3
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Basaran R, Ning X, Budhadev D, Hondow N, Guo Y, Zhou D. Probing the pH-dependency of DC-SIGN/R multivalent lectin-glycan interactions using polyvalent glycan-gold nanoparticles. NANOSCALE ADVANCES 2024; 6:2198-2208. [PMID: 38633047 PMCID: PMC11019501 DOI: 10.1039/d3na01013a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
The dendritic cell tetrameric lectin, DC-SIGN, and its closely related endothelial cell lectin, DC-SIGNR (collectively abbreviated as DC-SIGN/R) play a key role in the binding and transmission of deadly viruses, including Ebola, HIV, HCV, and SARS-CoV-2. Their virus binding/release processes involve a gradually acidifying environment following the natural intracellular trafficking pathways. Therefore, understanding DC-SIGN/R's pH-dependent binding properties with glycan ligands is of great importance. We have recently developed densely glycosylated gold nanoparticles (glycan-GNPs) as a powerful new tool for probing DC-SIGN/R multivalent lectin-glycan interaction (MLGI) mechanisms. They can provide not only quantitative MLGI affinities but also important structural information, such as binding site orientation and binding modes. Herein, we further employ the glycan-GNP probes to investigate the pH dependency of DC-SIGN/R MLGI properties. We find that DC-SIGN/R MLGIs exhibit distinct pH dependence over the normal physiological (7.4) to lysosomal (∼4.6) pH range. DC-SIGN binds glycan-GNPs strongly and stably from pH 7.4 to ∼5.8, but the binding is weakened significantly as pH decreases to ≤5.4 and may be fully dissociated at pH 4.6. This behaviour is fully consistent with DC-SIGN's role as an endocytic recycling receptor. In contrast, DC-SIGNR's affinity with glycan-GNPs is enhanced with the decreasing pH from 7.4 to 5.4, peaking at pH 5.4, and then reduced as pH is further lowered. Interestingly, both DC-SIGN/R binding with glycan-GNPs are found to be partially reversible in a pH-dependent manner.
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Affiliation(s)
- Rahman Basaran
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
| | - Xinyu Ning
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
| | - Darshita Budhadev
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
| | - Nicole Hondow
- School of Chemical and Process Engineering, University of Leeds Leeds LS2 9JT UK
| | - Yuan Guo
- School of Food Science and Nutrition, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
| | - Dejian Zhou
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
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4
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Liang Y, Schettini R, Kern N, Manciocchi L, Izzo I, Spichty M, Bodlenner A, Compain P. Deconstructing Best-in-Class Neoglycoclusters as a Tool for Dissecting Key Multivalent Processes in Glycosidase Inhibition. Chemistry 2024; 30:e202304126. [PMID: 38221894 DOI: 10.1002/chem.202304126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/16/2024]
Abstract
Multivalency represents an appealing option to modulate selectivity in enzyme inhibition and transform moderate glycosidase inhibitors into highly potent ones. The rational design of multivalent inhibitors is however challenging because global affinity enhancement relies on several interconnected local mechanistic events, whose relative impact is unknown. So far, the largest multivalent effects ever reported for a non-polymeric glycosidase inhibitor have been obtained with cyclopeptoid-based inhibitors of Jack bean α-mannosidase (JBα-man). Here, we report a structure-activity relationship (SAR) study based on the top-down deconstruction of best-in-class multivalent inhibitors. This approach provides a valuable tool to understand the complex interdependent mechanisms underpinning the inhibitory multivalent effect. Combining SAR experiments, binding stoichiometry assessments, thermodynamic modelling and atomistic simulations allowed us to establish the significant contribution of statistical rebinding mechanisms and the importance of several key parameters, including inhitope accessibility, topological restrictions, and electrostatic interactions. Our findings indicate that strong chelate-binding, resulting from the formation of a cross-linked complex between a multivalent inhibitor and two dimeric JBα-man molecules, is not a sufficient condition to reach high levels of affinity enhancements. The deconstruction approach thus offers unique opportunities to better understand multivalent binding and provides important guidelines for the design of potent and selective multiheaded inhibitors.
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Affiliation(s)
- Yan Liang
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67087, Strasbourg, France)
| | - Rosaria Schettini
- Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di, Salerno, 84084, Fisciano (Salerno), Italy
| | - Nicolas Kern
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67087, Strasbourg, France)
| | - Luca Manciocchi
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042)-IRJBD, 3 bis rue Alfred Werner, 68057, Mulhouse Cedex, France
| | - Irene Izzo
- Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di, Salerno, 84084, Fisciano (Salerno), Italy
| | - Martin Spichty
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042)-IRJBD, 3 bis rue Alfred Werner, 68057, Mulhouse Cedex, France
| | - Anne Bodlenner
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67087, Strasbourg, France)
| | - Philippe Compain
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67087, Strasbourg, France)
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5
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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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6
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Alešković M, Šekutor M. Overcoming barriers with non-covalent interactions: supramolecular recognition of adamantyl cucurbit[ n]uril assemblies for medical applications. RSC Med Chem 2024; 15:433-471. [PMID: 38389878 PMCID: PMC10880950 DOI: 10.1039/d3md00596h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 02/24/2024] Open
Abstract
Adamantane, a staple in medicinal chemistry, recently became a cornerstone of a supramolecular host-guest drug delivery system, ADA/CB[n]. Owing to a good fit between the adamantane cage and the host cavity of the cucurbit[n]uril macrocycle, formed strong inclusion complexes find applications in drug delivery and controlled drug release. Note that the cucurbit[n]uril host is not solely a delivery vehicle of the ADA/CB[n] system but rather influences the bioactivity and bioavailability of drug molecules and can tune drug properties. Namely, as host-guest interactions are capable of changing the intrinsic properties of the guest molecule, inclusion complexes can become more soluble, bioavailable and more resistant to metabolic conditions compared to individual non-complexed molecules. Such synergistic effects have implications for practical bioapplicability of this complex system and provide a new viewpoint to therapy, beyond the traditional single drug molecule approach. By achieving a balance between guest encapsulation and release, the ADA/CB[n] system has also found use beyond just drug delivery, in fields like bioanalytics, sensing assays, bioimaging, etc. Thus, chemosensing in physiological conditions, indicator displacement assays, in vivo diagnostics and hybrid nanostructures are just some recent examples of the ADA/CB[n] applicability, be it for displacements purposes or as cargo vehicles.
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Affiliation(s)
- Marija Alešković
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute Bijenička 54 10 000 Zagreb Croatia
| | - Marina Šekutor
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute Bijenička 54 10 000 Zagreb Croatia
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7
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Gräwe A, Spruit CM, de Vries RP, Merkx M. Bioluminescent detection of viral surface proteins using branched multivalent protein switches. RSC Chem Biol 2024; 5:148-157. [PMID: 38333197 PMCID: PMC10849123 DOI: 10.1039/d3cb00164d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/22/2023] [Indexed: 02/10/2024] Open
Abstract
Fast and reliable virus diagnostics is key to prevent the spread of viruses in populations. A hallmark of viruses is the presence of multivalent surface proteins, a property that can be harnessed to control conformational switching in sensor proteins. Here, we introduce a new sensor platform (dark-LUX) for the detection of viral surface proteins consisting of a general bioluminescent framework that can be post-translationally functionalized with separately expressed binding domains. The platform relies on (1) plug-and-play bioconjugation of different binding proteins via SpyTag/SpyCatcher technology to create branched protein structures, (2) an optimized turn-on bioluminescent switch based on complementation of the split-luciferase NanoBiT upon target binding and (3) straightforward exploration of the protein linker space. The influenza A virus (IAV) surface proteins hemagglutinin (HA) and neuraminidase (NA) were used as relevant multivalent targets to establish proof of principle and optimize relevant parameters such as linker properties, choice of target binding domains and the optimal combination of the competing NanoBiT components SmBiT and DarkBiT. The sensor framework allows rapid conjugation and exchange of various binding domains including scFvs, nanobodies and de novo designed binders for a variety of targets, including the construction of a heterobivalent switch that targets the head and stem region of hemagglutinin. The modularity of the platform thus allows straightforward optimization of binding domains and scaffold properties for existing viral targets, and is well suited to quickly adapt bioluminescent sensor proteins to effectively detect newly evolving viral epitopes.
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Affiliation(s)
- Alexander Gräwe
- Laboratory of Protein Engineering, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Cindy M Spruit
- Utrecht Institute for Pharmaceutical Sciences, Department of Chemical Biology and Drug Discovery Utrecht The Netherlands
| | - Robert P de Vries
- Utrecht Institute for Pharmaceutical Sciences, Department of Chemical Biology and Drug Discovery Utrecht The Netherlands
| | - Maarten Merkx
- Laboratory of Protein Engineering, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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8
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Mayer I, Karimian T, Gordiyenko K, Angelin A, Kumar R, Hirtz M, Mikut R, Reischl M, Stegmaier J, Zhou L, Ma R, Nienhaus GU, Rabe KS, Lanzerstorfer P, Domínguez CM, Niemeyer CM. Surface-Patterned DNA Origami Rulers Reveal Nanoscale Distance Dependency of the Epidermal Growth Factor Receptor Activation. NANO LETTERS 2024; 24:1611-1619. [PMID: 38267020 PMCID: PMC10853960 DOI: 10.1021/acs.nanolett.3c04272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The nanoscale arrangement of ligands can have a major effect on the activation of membrane receptor proteins and thus cellular communication mechanisms. Here we report on the technological development and use of tailored DNA origami-based molecular rulers to fabricate "Multiscale Origami Structures As Interface for Cells" (MOSAIC), to enable the systematic investigation of the effect of the nanoscale spacing of epidermal growth factor (EGF) ligands on the activation of the EGF receptor (EGFR). MOSAIC-based analyses revealed that EGF distances of about 30-40 nm led to the highest response in EGFR activation of adherent MCF7 and Hela cells. Our study emphasizes the significance of DNA-based platforms for the detailed investigation of the molecular mechanisms of cellular signaling cascades.
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Affiliation(s)
- Ivy Mayer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Tina Karimian
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Klavdiya Gordiyenko
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Alessandro Angelin
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ravi Kumar
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Michael Hirtz
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ralf Mikut
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Markus Reischl
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Johannes Stegmaier
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute
of Imaging and Computer Vision, RWTH Aachen
University, 52074 Aachen, Germany
| | - Lu Zhou
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Rui Ma
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
- Institute
of Biological and Chemical Systems (IBCS) and Institute of Nanotechnology
(INT), Karlsruhe Institute of Technology
(KIT), 76021 Karlsruhe, Germany
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kersten S. Rabe
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Peter Lanzerstorfer
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Carmen M. Domínguez
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
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9
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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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10
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Guo AD, Yan KN, Hu H, Zhai L, Hu TF, Su H, Chi Y, Zha J, Xu Y, Zhao D, Lu X, Xu YJ, Zhang J, Tan M, Chen XH. Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors. Nat Chem 2023:10.1038/s41557-023-01196-z. [PMID: 37106095 DOI: 10.1038/s41557-023-01196-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Precise dissection of DNA-protein interactions is essential for elucidating the recognition basis, dynamics and gene regulation mechanism. However, global profiling of weak and dynamic DNA-protein interactions remains a long-standing challenge. Here, we establish the light-induced lysine (K) enabled crosslinking (LIKE-XL) strategy for spatiotemporal and global profiling of DNA-protein interactions. Harnessing unique abilities to capture weak and transient DNA-protein interactions, we demonstrate that LIKE-XL enables the discovery of low-affinity transcription-factor/DNA interactions via sequence-specific DNA baits, determining the binding sites for transcription factors that have been previously unknown. More importantly, we successfully decipher the dynamics of the transcription factor subproteome in response to drug treatment in a time-resolved manner, and find downstream target transcription factors from drug perturbations, providing insight into their dynamic transcriptional networks. The LIKE-XL strategy offers a complementary method to expand the DNA-protein profiling toolbox and map accurate DNA-protein interactomes that were previously inaccessible via non-covalent strategies, for better understanding of protein function in health and disease.
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Affiliation(s)
- An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke-Nian Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Teng-Fei Hu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yijia Chi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyin Zha
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dongxin Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Jiang Xu
- School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Jian Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China.
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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11
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Vu TQ, Sant'Anna LE, Kamat NP. Tuning Targeted Liposome Avidity to Cells via Lipid Phase Separation. Biomacromolecules 2023; 24:1574-1584. [PMID: 36943688 PMCID: PMC10874583 DOI: 10.1021/acs.biomac.2c01338] [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] [Indexed: 03/23/2023]
Abstract
The addition of both cell-targeting moieties and polyethylene glycol (PEG) to nanoparticle (NP) drug delivery systems is a standard approach to improve the biodistribution, specificity, and uptake of therapeutic cargo. The spatial presentation of these molecules affects avidity of the NP to target cells in part through an interplay between the local ligand concentration and the steric hindrance imposed by PEG molecules. Here, we show that lipid phase separation in nanoparticles can modulate liposome avidity by changing the proximity of PEG and targeting protein molecules on a nanoparticle surface. Using lipid-anchored nickel-nitrilotriacetic acid (Ni-NTA) as a model ligand, we demonstrate that the attachment of lipid anchored Ni-NTA and PEG molecules to distinct lipid domains in nanoparticles can enhance liposome binding to cancer cells by increasing ligand clustering and reducing steric hindrance. We then use this technique to enhance the binding of RGD-modified liposomes, which can bind to integrins overexpressed on many cancer cells. These results demonstrate the potential of lipid phase separation to modulate the spatial presentation of targeting and shielding molecules on lipid nanocarriers, offering a powerful tool to enhance the efficacy of NP drug delivery systems.
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Affiliation(s)
- Timothy Q Vu
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Lucas E Sant'Anna
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Neha P Kamat
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
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12
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Berehova N, Buckle T, van Meerbeek MP, Bunschoten A, Velders AH, van Leeuwen FWB. Nerve Targeting via Myelin Protein Zero and the Impact of Dimerization on Binding Affinity. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27249015. [PMID: 36558148 PMCID: PMC9786614 DOI: 10.3390/molecules27249015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Surgically induced nerve damage is a common but debilitating side effect. By developing tracers that specifically target the most abundant protein in peripheral myelin, namely myelin protein zero (P0), we intend to support fluorescence-guided nerve-sparing surgery. To that end, we aimed to develop a dimeric tracer that shows a superior affinity for P0. METHODS Following truncation of homotypic P0 protein-based peptide sequences and fluorescence labeling, the lead compound Cy5-P0101-125 was selected. Using a bifunctional fluorescent dye, the dimeric Cy5-(P0101-125)2 was created. Assessment of the performance of the mono- and bi-labeled compounds was based on (photo)physical evaluation. This was followed by in vitro assessment in P0 expressing Schwannoma cell cultures by means of fluorescence confocal imaging (specificity, location of binding) and flow cytometry (binding affinity; KD). RESULTS Dimerization resulted in a 1.5-fold increase in affinity compared to the mono-labeled counterpart (70.3 +/- 10.0 nM vs. 104.9 +/- 16.7 nM; p = 0.003) which resulted in a 4-fold increase in staining efficiency in P0 expressing Schwannoma cells. Presence of two targeting vectors also improves a pharmacokinetics of labeled compounds by lowering serum binding and optical stability by preventing dye stacking. CONCLUSIONS Dimerization of the nerve-targeting peptide P0101-125 proves a valid strategy to improve P0 targeting.
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Affiliation(s)
- Nataliia Berehova
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC Leiden, The Netherlands
| | - Tessa Buckle
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC Leiden, The Netherlands
| | - Maarten P. van Meerbeek
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC Leiden, The Netherlands
| | - Anton Bunschoten
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Aldrik H. Velders
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Fijs W. B. van Leeuwen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC Leiden, The Netherlands
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
- Correspondence:
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13
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Wang M, Yang D, Lu Q, Liu L, Cai Z, Wang Y, Wang HH, Wang P, Nie Z. Spatially Reprogramed Receptor Organization to Switch Cell Behavior Using a DNA Origami-Templated Aptamer Nanoarray. NANO LETTERS 2022; 22:8445-8454. [PMID: 36255126 DOI: 10.1021/acs.nanolett.2c02489] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Receptor oligomerization is a highly complex molecular process that modulates divergent cell signaling. However, there is a lack of molecular tools for systematically interrogating how receptor oligomerization governs the signaling response. Here, we developed a DNA origami-templated aptamer nanoarray (DOTA) that enables precise programming of the oligomerization of receptor tyrosine kinases (RTK) with defined valency, distribution, and stoichiometry at the ligand-receptor interface. The DOTA allows for advanced receptor manipulations by arraying either monomeric aptamer ligands (mALs) that oligamerize receptor monomers to elicit artificial signaling or dimeric aptamer ligands (dALs) that preorganize the receptor dimer to recapitulate natural activation. We demonstrated that the multivalency and nanoscale spacing of receptor oligomerization coordinately influence the activation level of receptor tyrosine kinase signaling. Furthermore, we illustrated that DOTA-modulated receptor oligomerization could function as a signaling switch to promote the transition from epithelia to mesenchymal-like cells, demonstrating robust control over cellular behaviors. Together, we present a versatile all-in-one DNA nanoplatform for the systematical investigation and regulation of receptor-mediated cellular response.
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Affiliation(s)
- Miao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qin Lu
- GeneMind Biosciences Company Limited, Shenzhen, Guangdong 518000, China
| | - Lin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Zixin Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Yirong Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
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14
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Watson EE, Winssinger N. Synthesis of Protein-Oligonucleotide Conjugates. Biomolecules 2022; 12:biom12101523. [PMID: 36291732 PMCID: PMC9599799 DOI: 10.3390/biom12101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids and proteins form two of the key classes of functional biomolecules. Through the ability to access specific protein-oligonucleotide conjugates, a broader range of functional molecules becomes accessible which leverages both the programmability and recognition potential of nucleic acids and the structural, chemical and functional diversity of proteins. Herein, we summarize the available conjugation strategies to access such chimeric molecules and highlight some key case study examples within the field to showcase the power and utility of such technology.
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Affiliation(s)
- Emma E. Watson
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (E.E.W.); (N.W.)
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, CH-1205 Geneva, Switzerland
- Correspondence: (E.E.W.); (N.W.)
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15
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Sheng L, Jin Y, Hou H, Huang Y, Zhao R. Hydrazone bond-oriented molecularly imprinted nanocomposites for the selective separation of protein via the well-defined recognition sites. Mikrochim Acta 2022; 189:246. [PMID: 35674804 DOI: 10.1007/s00604-022-05308-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/15/2022] [Indexed: 11/27/2022]
Abstract
The development of hydrazone bond-oriented epitope imprinting strategy is reported to synthesize the polymeric binders for the selective recognition of a protein-β2-microglobulin through either its N- or C-terminal epitope. The dynamic reversibility of hydrazone bond facilitated not only the oriented assembly of the template peptide hydrazides onto the substrate but also the efficient removal of them from the imprinted cavities. The well-defined surface imprinted layer was successfully constructed through the precise control over the polymerization of silicate esters. Binding performance of the C-terminal peptide imprinted nanocomposite was significantly improved after tuning the non-covalent interactions using the sequence-matching aromatic co-monomers. The dissociation constant (Kd) between the optimized nanocomposite and epitope peptide was 0.5 µmol L-1. The nanomaterial was utilized for the selective extraction and determination of β2-microglobulin from human urine by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and HPLC-UV with satisfied recoveries of 93.1-112.3% in a concentration range 1.0-50.0 μg⋅mL-1.
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Affiliation(s)
- Le Sheng
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, People's Republic of China.,School of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yulong Jin
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, People's Republic of China. .,School of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huiqing Hou
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, People's Republic of China.,School of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyan Huang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, People's Republic of China.,School of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, People's Republic of China. .,School of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Chen S, Zhang L, Yuan Q, Tan J. Current Advances in Aptamer-based Biomolecular Recognition and Biological Process Regulation. Chem Res Chin Univ 2022; 38:847-855. [PMID: 35573821 PMCID: PMC9077342 DOI: 10.1007/s40242-022-2087-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 12/01/2022]
Abstract
The interaction between biomolecules with their target ligands plays a great role in regulating biological functions. Aptamers are short oligonucleotide sequences that can specifically recognize target biomolecules via structural complementarity and thus regulate related biological functions. In the past ten years, aptamers have made great progress in target biomolecule recognition, becoming a powerful tool to regulate biological functions. At present, there are many reviews on aptamers applied in biomolecular recognition, but few reviews pay attention to aptamer-based regulation of biological functions. Here, we summarize the approaches to enhancing aptamer affinity and the advancements of aptamers in regulating enzymatic activity, cellular immunity and cellular behaviors. Furthermore, this review discusses the challenges and future perspectives of aptamers in target recognition and biological functions regulation, aiming to provide some promising ideas for future regulation of biomolecular functions in a complex biological environment.
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Affiliation(s)
- Sisi Chen
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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17
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Xu J, Xiang J, Chen J, Wan T, Deng H, Li D. High sensitivity detection of tumor cells in biological samples using a multivalent aptamer strand displacement strategy. Analyst 2022; 147:634-644. [PMID: 35040831 DOI: 10.1039/d1an01949j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Monitoring the cell surface-expressed nucleolin facilitates early cancer diagnosis. Herein, we developed a multivalent aptamer displacement strand duplex strategy on cell membranes using a multi-receptor co-recognition design for improving the sensitivity and specificity of cancer cell recognition with an ultra-low background. The AS1411 aptamer labeled with the FAM fluorophore can be quenched using a partial complementary sequence modified with a BHQ1 tag which is partially hybridized with the AS1411 aptamer to create a receptor-activating aptamer. The multi-AS1411 activable probe based on the strand displacement strategy was constructed using multiple copies of the structure-switching AS1411 aptamer (bearing a short poly-A tail) linked together using the poly-T long chain (as a scaffold) which was synthesized by Terminal Deoxynucleotidyl Transferase (TDT)-mediated extension. We demonstrated the promising efficacy and sensitivity of our method in recognizing tumor cells in both cell mixtures and clinical cytology specimens. Due to its simple and fast operation with excellent cell recognition sensitivity and accuracy, it is expected to achieve the detection of low abundance target cells. Our approach will have broad application in clinical rapid detection and personalized medicine.
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Affiliation(s)
- Jieru Xu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jiahui Xiang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jialing Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Tao Wan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Hongli Deng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Dairong Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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18
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Huang Y, Li Y, Li X. Strategies for developing DNA-encoded libraries beyond binding assays. Nat Chem 2022; 14:129-140. [PMID: 35121833 DOI: 10.1038/s41557-021-00877-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
DNA-encoded chemical libraries (DELs) have emerged as a powerful technology in drug discovery. The wide adoption of DELs in the pharmaceutical industry and the rapid advancements of DEL-compatible chemistry have further fuelled its development and applications. In general, a DEL has been considered as a massive binding assay to identify physical binders for individual protein targets. However, recent innovations demonstrate the capability of DELs to operate in the complex milieu of biological systems. In this Perspective, we discuss the recent progress in using DNA-encoded chemical libraries to interrogate complex biological targets and their potential to identify structures that elicit function or possess other useful properties. Future breakthroughs in these aspects are expected to catapult DEL to become a momentous technology platform not only for drug discovery but also to explore fundamental biology.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 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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19
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Liu Q, Tian J, Liu J, Zhu M, Gao Z, Hu X, Midgley AC, Wu J, Wang X, Kong D, Zhuang J, Liu J, Yan X, Huang X. Modular Assembly of Tumor-Penetrating and Oligomeric Nanozyme Based on Intrinsically Self-Assembling Protein Nanocages. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2103128. [PMID: 34350648 DOI: 10.1002/adma.202103128] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/26/2021] [Indexed: 06/13/2023]
Abstract
Biomimetic design of nanomaterials with enzyme-like characteristics has emerged as a promising method for the generation of novel therapeutics. However, synthesis of nanomaterials while maintaining a high degree of control over both geometry and valency poses a prominent challenge. Herein, the authors introduce a nanomaterial-based synthetic biology strategy for accurate and quantitative tailoring of high-ordered nanostructures that uses a "bottom-up" hierarchical incorporation of protein building blocks. The assembled nano-oligomers possessed tunable protein motifs and multivalent binding domains, which facilitated prolonged blood circulation time, accumulation within tumor cells through direct targeting of cell receptors, and deep tumor tissue penetration via a transcytosis mechanism. Using these protein/protein nano-oligomers as scaffolds, the authors created a new series of artificial nano-scaled metalloenzymes (nanozymes) by the in situ incorporation of metal nanoclusters within the cavity of the protein nanocages. Nanozymes were capable of mimicking peroxidase-like activity and generated cytotoxic free radicals. Compared to nanozyme alone, the systemic delivery of oligomeric nanozymes demonstrated significantly enhanced therapeutic and anti-tumor benefits. This study shows a new insight into nanotechnology by taking advantage of synthetic biotechnology.
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Affiliation(s)
- Qiqi Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jingwei Tian
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jinjian Liu
- Key Laboratory of Radiopharmacokinetics for Innovative Drugs, Chinese Academy of Medical Sciences, and Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Mingsheng Zhu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Zhanxia Gao
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Xueyan Hu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Adam C Midgley
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jin Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xinyue Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Deling Kong
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Jie Zhuang
- School of Medicine, Nankai University, Tianjin, 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jianfeng Liu
- Key Laboratory of Radiopharmacokinetics for Innovative Drugs, Chinese Academy of Medical Sciences, and Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Xiyun Yan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin, 300071, China
- CAS Engineering Laboratory for Nanozymes, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinglu Huang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
- Joint Laboratory of Nanozymes, College of Life Sciences, Nankai University, Tianjin, 300071, China
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20
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Gavins GC, Gröger K, Reimann M, Bartoschek MD, Bultmann S, Seitz O. Orthogonal coiled coils enable rapid covalent labelling of two distinct membrane proteins with peptide nucleic acid barcodes. RSC Chem Biol 2021; 2:1291-1295. [PMID: 34458843 PMCID: PMC8341593 DOI: 10.1039/d1cb00126d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
Templated chemistry offers the prospect of addressing specificity challenges occurring in bioconjugation reactions. Here, we show two peptide-templated amide-bond forming reactions that enable the concurrent labelling of two different membrane proteins with two different peptide nucleic acid (PNA) barcodes. The reaction system is based on the mutually selective coiled coil interaction between two thioester-linked PNA–peptide conjugates and two cysteine peptides serving as genetically encoded peptide tags. Orthogonal coiled coil templated covalent labelling is highly specific, quantitative and proceeds within a minute. To demonstrate the usefulness, we evaluated receptor internalisation of two membranous receptors EGFR (epidermal growth factor) and ErbB2 (epidermal growth factor receptor 2) by first staining PNA-tagged proteins with fluorophore–DNA conjugates and then erasing signals from non-internalized receptors via toehold-mediated strand displacement. A pair of orthogonal coiled coils templates highly specific live cell bioconjugation of two different proteins. PNA tagging and hybridisation with fluorophore–DNA reporters enables rapid dual receptor internalisation analysis of EGFR and ErbB2.![]()
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Affiliation(s)
- Georgina C Gavins
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Katharina Gröger
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Marc Reimann
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Michael D Bartoschek
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstr. 1 Munich 81377 Germany
| | - Sebastian Bultmann
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstr. 1 Munich 81377 Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
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21
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Cremers GAO, Rosier BJHM, Meijs A, Tito NB, van Duijnhoven SMJ, van Eenennaam H, Albertazzi L, de Greef TFA. Determinants of Ligand-Functionalized DNA Nanostructure-Cell Interactions. J Am Chem Soc 2021; 143:10131-10142. [PMID: 34180666 PMCID: PMC8283757 DOI: 10.1021/jacs.1c02298] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Synthesis of ligand-functionalized
nanomaterials with control over
size, shape, and ligand orientation facilitates the design of targeted
nanomedicines for therapeutic purposes. DNA nanotechnology has emerged
as a powerful tool to rationally construct two- and three-dimensional
nanostructures, enabling site-specific incorporation of protein ligands
with control over stoichiometry and orientation. To efficiently target
cell surface receptors, exploration of the parameters that modulate
cellular accessibility of these nanostructures is essential. In this
study, we systematically investigate tunable design parameters of
antibody-functionalized DNA nanostructures binding to therapeutically
relevant receptors, including the programmed cell death protein 1,
the epidermal growth factor receptor, and the human epidermal growth
factor receptor 2. We show that, although the native affinity of antibody-functionalized
DNA nanostructures remains unaltered, the absolute number of bound
surface receptors is lower compared to soluble antibodies due to receptor
accessibility by the nanostructure. We explore structural determinants
of this phenomenon to improve efficiency, revealing that receptor
binding is mainly governed by nanostructure size and DNA handle location.
The obtained results provide key insights in the ability of ligand-functionalized
DNA nanostructures to bind surface receptors and yields design rules
for optimal cellular targeting.
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Affiliation(s)
- Glenn A O Cremers
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Bas J H M Rosier
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ab Meijs
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Nicholas B Tito
- Electric Ant Lab, Science Park 106, 1098 XG Amsterdam, The Netherlands
| | | | - Hans van Eenennaam
- Aduro Biotech Europe B.V., Kloosterstraat 9, 5349 AB Oss, The Netherlands
| | - Lorenzo Albertazzi
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Molecular Biosensing for Medical Diagnostics, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, 5600 MB Eindhoven, The Netherlands
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22
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Redman RL, Krauss IJ. Directed Evolution of 2'-Fluoro-Modified, RNA-Supported Carbohydrate Clusters That Bind Tightly to HIV Antibody 2G12. J Am Chem Soc 2021; 143:8565-8571. [PMID: 34096703 DOI: 10.1021/jacs.1c03194] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Carbohydrate binding proteins (CBPs) are attractive targets in medicine and biology. Multivalency, with several glycans binding to several binding pockets in the CBP, is important for high-affinity interactions. Herein, we describe a novel platform for design of multivalent carbohydrate cluster ligands by directed evolution, in which serum-stable 2'-fluoro modified RNA (F-RNA) backbones evolve to present the glycan in optimal clusters. We have validated this method by the selection of oligomannose (Man9) glycan clusters from a sequence pool of ∼1013 that bind to broadly neutralizing HIV antibody 2G12 with 13 to 36 nM affinities.
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Affiliation(s)
- Richard L Redman
- Department of Chemistry, Brandeis University, 415 South Street MS 015, Waltham, Massachusetts 02454, United States
| | - Isaac J Krauss
- Department of Chemistry, Brandeis University, 415 South Street MS 015, Waltham, Massachusetts 02454, United States
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23
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Li Z, Wang J, Shen R, Chen N, Qin X, Wang W, Yuan Q. Topological Radiated Dendrites Featuring Persistent Bactericidal Activity for Daily Personal Protection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100562. [PMID: 33969623 DOI: 10.1002/smll.202100562] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Many substances in nature show radiated topological structure and possess excellent bio-adhesion ability. Herein, regulating the topological structure of Zn2 GeO4 :Mn persistent phosphors is achieved with a molecular coordination method. The morphology of the Zn2 GeO4 :Mn phosphors is well-tuned from nanorods to radiated dendrites by changing the coordination capability of the surface ligand. Due to the structural matching and multivalent interactions, Zn2 GeO4 :Mn radiated dendrites show strong adhesion affinity toward organisms. Moreover, the porous radiated structure offers Zn2 GeO4 :Mn with a large surface area for photocatalysis. Efficient bacterial adhesion and good long persistent photocatalysis activity are observed in the Zn2 GeO4 :Mn radiated dendrites, which endows Zn2 GeO4 :Mn with persistent antibacterial activity even in the dark. Further, the Zn2 GeO4 :Mn spike flowers loaded fabrics exhibit potent persistent antibacterial properties. Mask and towel fabricated with the antibacterial fabrics can inhibit bacterial growth effectively and no bacteria are observed to pass through the antibacterial mask, suggesting that antibacterial mask can guarantee our health and can be utilized repeatedly. The developed Zn2 GeO4 :Mn dendrites possess ideal ability in long-term bacterial inhibition, making them valuable in the fields of medical protection and food packaging.
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Affiliation(s)
- Zhiheng Li
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan, 430072, China
| | - Jie Wang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan, 430072, China
| | - Ruichen Shen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Na Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan, 430072, China
| | - Xinyuan Qin
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan, 430072, China
| | - Wenjie Wang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Quan Yuan
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan, 430072, China
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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24
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Wang W, Arias DS, Deserno M, Ren X, Taylor RE. Emerging applications at the interface of DNA nanotechnology and cellular membranes: Perspectives from biology, engineering, and physics. APL Bioeng 2020; 4:041507. [PMID: 33344875 PMCID: PMC7725538 DOI: 10.1063/5.0027022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
DNA nanotechnology has proven exceptionally apt at probing and manipulating biological environments as it can create nanostructures of almost arbitrary shape that permit countless types of modifications, all while being inherently biocompatible. Emergent areas of particular interest are applications involving cellular membranes, but to fully explore the range of possibilities requires interdisciplinary knowledge of DNA nanotechnology, cell and membrane biology, and biophysics. In this review, we aim for a concise introduction to the intersection of these three fields. After briefly revisiting DNA nanotechnology, as well as the biological and mechanical properties of lipid bilayers and cellular membranes, we summarize strategies to mediate interactions between membranes and DNA nanostructures, with a focus on programmed delivery onto, into, and through lipid membranes. We also highlight emerging applications, including membrane sculpting, multicell self-assembly, spatial arrangement and organization of ligands and proteins, biomechanical sensing, synthetic DNA nanopores, biological imaging, and biomelecular sensing. Many critical but exciting challenges lie ahead, and we outline what strikes us as promising directions when translating DNA nanostructures for future in vitro and in vivo membrane applications.
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Affiliation(s)
- Weitao Wang
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - D. Sebastian Arias
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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