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Ma Y, Li X, Zhao R, Wu E, Du Q, Guo J, Wang L, Zhang F. Creating de novo peptide-based bioactivities: from assembly to origami. RSC Adv 2022; 12:25955-25961. [PMID: 36199601 PMCID: PMC9465703 DOI: 10.1039/d2ra03135c] [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: 05/18/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
DNA origami has created complex structures of various spatial dimensions. However, their versatility in terms of function is limited due to the lower number of the intrinsic building blocks, i.e. nucleotides, compared with the number of amino acids. Therefore, protein origami has been proposed and demonstrated to precisely fabricate artificial functional nanostructures. Despite their hierarchical folded structures, chain-like peptides and DNA share obvious similarities in both structures and properties, especially in terms of chain hybridization; therefore, replacing DNA with peptides to create bioactivities not only has high theoretical feasibility but also provides a new bottom-up synthetic strategy. However, designing functionalities with tens to hundreds of peptide chains using the similar principle of DNA origami has not been reported, although the origami strategy holds great potential to generate more complex bioactivities. In this perspective review, we have reviewed the recent progress in and highlighted the advantages of peptide assembly and origami on the orientation of artificially created bioactivities. With the great potential of peptide origami, we appeal to develop user-friendly softwares in combination with artificial intelligence.
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Affiliation(s)
- Yuxing Ma
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
- Inner Mongolia Key Laboratory of Tick-Borne Zoonotic Infectious Disease, Department of Medicine, Hetao College Bayannur 015000 China
| | - Xiaofang Li
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology Shanghai 200093 P. R. China
| | - Ruoyang Zhao
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
| | - Enqi Wu
- Inner Mongolia Key Laboratory of Tick-Borne Zoonotic Infectious Disease, Department of Medicine, Hetao College Bayannur 015000 China
| | - Qiqige Du
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
| | - Jun Guo
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology Shanghai 200093 P. R. China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Oral Disease, Stomatology Hospital, School of Biomedical Engineering, Guangzhou Medical University Guangzhou 511436 China
| | - Liping Wang
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
| | - Feng Zhang
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology Shanghai 200093 P. R. China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Oral Disease, Stomatology Hospital, School of Biomedical Engineering, Guangzhou Medical University Guangzhou 511436 China
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2
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Wang B, Fang H, Zhu W, Xu Y, Yang Y, Qian X. Dynamic Compartmentalization of Peptide-Oligonucleotide Conjugates with Reversible Nanovesicle-Microdroplet Phase Transition Behaviors. ACS APPLIED MATERIALS & INTERFACES 2022; 14:36998-37008. [PMID: 35925804 DOI: 10.1021/acsami.2c05268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Developing artificial microsystems based on liquid-liquid phase separation (LLPS) to mimic cellular dynamic compartmentalization has gained increasing attention. However, limitations including complicated components and laborious fabrication techniques have hindered their development. Herein, we describe a new single-component dynamic compartmentalization system using peptide-oligonucleotide conjugates (POCs) produced from short elastin-like polypeptides (sELPs) and oligonucleotides (ONs), which can perform thermoreversible phase transition between a nanovesicle and a microdroplet. The phase transition of sELP-ONs is thoroughly investigated, of which the transition temperature can be controlled by concentration, length of sELPs and ONs, base sequences, and salt. Moreover, the sELP-ON microcompartment can enrich a variety of functional molecules including small molecules, polysaccharides, proteins, and nucleic acids. Two sELP-ON compartments are used as nano- and microreactors for enzymatic reactions, separately, in which chemical activities are successfully regulated under different-scaled confinement effects, demonstrating their broad potential application in matter exchange and artificial cells.
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Affiliation(s)
- Bin Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Honglong Fang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weiping Zhu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yangyang Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor, East China University of Science and Technology, Shanghai 200237, China
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3
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Li ZY, Li DY, Huang L, Hu R, Yang T, Yang YH. An electrochemical aptasensor based on intelligent walking DNA nanomachine with cascade signal amplification powered by nuclease for Mucin 1 assay. Anal Chim Acta 2022; 1214:339964. [DOI: 10.1016/j.aca.2022.339964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/05/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023]
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4
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Heinritz C, Lamberger Z, Kocourková K, Minařík A, Humenik M. DNA Functionalized Spider Silk Nanohydrogels for Specific Cell Attachment and Patterning. ACS NANO 2022; 16:7626-7635. [PMID: 35521760 DOI: 10.1021/acsnano.1c11148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nucleated protein self-assembly of an azido modified spider silk protein was employed in the preparation of nanofibrillar networks with hydrogel-like properties immobilized on coatings of the same protein. Formation of the networks in a mild aqueous environment resulted in thicknesses between 2 and 60 nm, which were controlled only by the protein concentration. Incorporated azido groups in the protein were used to "click" short nucleic acid sequences onto the nanofibrils, which were accessible to specific hybridization-based modifications, as proved by fluorescently labeled DNA complements. A lipid modifier was used for efficient incorporation of DNA into the membrane of nonadherent Jurkat cells. Based on the complementarity of the nucleic acids, highly specific DNA-assisted immobilization of the cells on the nanohydrogels with tunable cell densities was possible. Addressability of the DNA cell-to-surface anchor was demonstrated with a competitive oligonucleotide probe, resulting in a rapid release of 75-95% of cells. In addition, we developed a photolithography-based patterning of arbitrarily shaped microwells, which served to spatially define the formation of the nanohydrogels. After detaching the photoresist and PEG-blocking of the surface, DNA-assisted immobilization of the Jurkat cells on the nanohydrogel microstructures was achieved with high fidelity.
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Affiliation(s)
- Christina Heinritz
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Prof.-Rüdiger-Bormann.Str. 1, 95447 Bayreuth, Germany
| | - Zan Lamberger
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Prof.-Rüdiger-Bormann.Str. 1, 95447 Bayreuth, Germany
| | - Karolína Kocourková
- Department of Physics and Materials Engineering, Tomas Bata University in Zlín, Vavrečkova 275, 76001 Zlín, Czech Republic
| | - Antonín Minařík
- Centre of Polymer Systems, Tomas Bata University in Zlín, Třída Tomáše Bati 5678, 76001 Zlín, Czech Republic
- Department of Physics and Materials Engineering, Tomas Bata University in Zlín, Vavrečkova 275, 76001 Zlín, Czech Republic
| | - Martin Humenik
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Prof.-Rüdiger-Bormann.Str. 1, 95447 Bayreuth, Germany
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5
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Molecularly Imprinted Polymer-Amyloid Fibril-Based Electrochemical Biosensor for Ultrasensitive Detection of Tryptophan. BIOSENSORS 2022; 12:bios12050291. [PMID: 35624592 PMCID: PMC9139163 DOI: 10.3390/bios12050291] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 12/03/2022]
Abstract
A tryptophan (Trp) sensor was investigated based on electrochemical impedance spectroscopy (EIS) of a molecularly imprinted polymer on a lysozyme amyloid fibril (MIP-AF). The MIP-AF was composed of aniline as a monomer chemically polymerized in the presence of a Trp template molecule onto the AF surface. After extracting the template molecule, the MIP-AF had cavities with a high affinity for the Trp molecules. The obtained MIP-AF demonstrated rapid Trp adsorption and substantial binding capacity (50 µM mg−1). Trp determination was studied using non-Faradaic EIS by drop drying the MIP-AF on the working electrode of a screen-printed electrode. The MIP-AF provided a large linear range (10 pM–80 µM), a low detection limit (8 pM), and high selectivity for Trp determination. Furthermore, the proposed method also indicates that the MIP-AF can be used to determine Trp in real samples such as milk and cancer cell media.
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6
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Chan NJ, Lentz S, Gurr PA, Scheibel T, Qiao GG. Mimicry of silk utilizing synthetic polypeptides. Prog Polym Sci 2022. [DOI: 10.1016/j.progpolymsci.2022.101557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Zein HF, Alam I, Asanithi P, Sutthibutpong T. Molecular dynamics study on the effects of charged amino acid distribution under low pH condition to the unfolding of hen egg white lysozyme and formation of beta strands. PLoS One 2022; 17:e0249742. [PMID: 35324907 PMCID: PMC8946743 DOI: 10.1371/journal.pone.0249742] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 02/23/2022] [Indexed: 11/19/2022] Open
Abstract
Aggregation of unfolded or misfolded proteins into amyloid fibrils can cause various diseases in humans. However, the fibrils synthesized in vitro can be developed toward useful biomaterials under some physicochemical conditions. In this study, atomistic molecular dynamics simulations were performed to address the mechanism of beta-sheet formation of the unfolded hen egg-white lysozyme (HEWL) under a high temperature and low pH. Simulations of the protonated HEWL at pH 2 and the non-protonated HEWL at pH 7 were performed at the highly elevated temperature of 450 K to accelerate the unfolding, followed by the 333 K temperature to emulate some previous in vitro studies. The simulations showed that HEWL unfolded faster, and higher beta-strand contents were observed at pH 2. In addition, one of the simulation replicas at pH 2 showed that the beta-strand forming sequence was consistent with the 'K-peptide', proposed as the core region for amyloidosis in previous experimental studies. Beta-strand formation mechanisms at the earlier stage of amyloidosis were explained in terms of the radial distribution of the amino acids. The separation between groups of positively charged sidechains from the hydrophobic core corresponded to the clustering of the hydrophobic residues and beta-strand formation.
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Affiliation(s)
- Husnul Fuad Zein
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Department of Physics, Theoretical and Computational Physics Group, KMUTT, Thung Khru, Bangkok, Thailand
- Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Ibrar Alam
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Piyapong Asanithi
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Thana Sutthibutpong
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Department of Physics, Theoretical and Computational Physics Group, KMUTT, Thung Khru, Bangkok, Thailand
- Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
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8
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Hadar D, Strugach DS, Amiram M. Conjugates of Recombinant Protein‐Based Polymers: Combining Precision with Chemical Diversity. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202100142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Dagan Hadar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
| | - Daniela S. Strugach
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
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9
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Yao S, Liao Y, Pan R, Zhu W, Xu Y, Yang Y, Qian X. Programmed co-assembly of DNA-peptide hybrid microdroplets by phase separation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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Lendel C, Solin N. Protein nanofibrils and their use as building blocks of sustainable materials. RSC Adv 2021; 11:39188-39215. [PMID: 35492452 PMCID: PMC9044473 DOI: 10.1039/d1ra06878d] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/25/2021] [Indexed: 12/21/2022] Open
Abstract
The development towards a sustainable society requires a radical change of many of the materials we currently use. Besides the replacement of plastics, derived from petrochemical sources, with renewable alternatives, we will also need functional materials for applications in areas ranging from green energy and environmental remediation to smart foods. Proteins could, with their intriguing ability of self-assembly into various forms, play important roles in all these fields. To achieve that, the code for how to assemble hierarchically ordered structures similar to the protein materials found in nature must be cracked. During the last decade it has been demonstrated that amyloid-like protein nanofibrils (PNFs) could be a steppingstone for this task. PNFs are formed by self-assembly in water from a range of proteins, including plant resources and industrial side streams. The nanofibrils display distinct functional features and can be further assembled into larger structures. PNFs thus provide a framework for creating ordered, functional structures from the atomic level up to the macroscale. This review address how industrial scale protein resources could be transformed into PNFs and further assembled into materials with specific mechanical and functional properties. We describe what is required from a protein to form PNFs and how the structural properties at different length scales determine the material properties. We also discuss potential chemical routes to modify the properties of the fibrils and to assemble them into macroscopic structures.
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Affiliation(s)
- Christofer Lendel
- Department of Chemistry, KTH Royal Institute of Technology Teknikringen 30 SE-100 44 Stockholm Sweden
| | - Niclas Solin
- Department of Physics, Chemistry, and Biology, Electronic and Photonic Materials, Biomolecular and Organic Electronics, Linköping University Linköping 581 83 Sweden
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11
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Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks. Proc Natl Acad Sci U S A 2021; 118:2015285118. [PMID: 33622789 DOI: 10.1073/pnas.2015285118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.
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12
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Steiner D, Winkler S, Heltmann-Meyer S, Trossmann VT, Fey T, Scheibel T, Horch RE, Arkudas A. Enhanced vascularization and de novotissue formation in hydrogels made of engineered RGD-tagged spider silk proteins in the arteriovenous loop model. Biofabrication 2021; 13. [PMID: 34157687 DOI: 10.1088/1758-5090/ac0d9b] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022]
Abstract
Due to its low immunogenic potential and the possibility to fine-tune their properties, materials made of recombinant engineered spider silks are promising candidates for tissue engineering applications. However, vascularization of silk-based scaffolds is one critical step for the generation of bioartificial tissues and consequently for clinical application. To circumvent insufficient vascularization, the surgically induced angiogenesis by means of arteriovenous loops (AVL) represents a highly effective methodology. Here, previously established hydrogels consisting of nano-fibrillary recombinant eADF4(C16) were transferred into Teflon isolation chambers and vascularized in the rat AVL model over 4 weeks. To improve vascularization, also RGD-tagged eADF4(C16) hydrogels were implanted in the AVL model over 2 and 4 weeks. Thereafter, the specimen were explanted and analyzed using histology and microcomputed tomography. We were able to confirm biocompatibility and tissue formation over time. Functionalizing eADF4(C16) with RGD-motifs improved hydrogel stability and enhanced vascularization even outperforming other hydrogels, such as fibrin. This study demonstrates that the scaffold ultrastructure as well as biofunctionalization with RGD-motifs are powerful tools to optimize silk-based biomaterials for tissue engineering applications.
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Affiliation(s)
- Dominik Steiner
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sophie Winkler
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Stefanie Heltmann-Meyer
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Vanessa T Trossmann
- Faculty of Engineering, Department for Biomaterials, University of Bayreuth, 95447 Bayreuth, Germany
| | - Tobias Fey
- Department of Materials Science and Engineering, Institute of Glass and Ceramics, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany.,Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Thomas Scheibel
- Faculty of Engineering, Department for Biomaterials, University of Bayreuth, 95447 Bayreuth, Germany.,Bayreuth Center for Colloids and Interfaces (BZKG), University of Bayreuth, 95447 Bayreuth, Germany.,Bayreuth Center for Molecular Biosciences (BZMB), University of Bayreuth, 95447 Bayreuth, Germany.,Center for Material Science and Engineering (BayMAT), University of Bayreuth, 95447 Bayreuth, Germany.,Bavarian Polymer Institute (BPI), University of Bayreuth, 95447 Bayreuth, Germany
| | - Raymund E Horch
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andreas Arkudas
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
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13
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Humenik M, Winkler A, Scheibel T. Patterning of protein-based materials. Biopolymers 2020; 112:e23412. [PMID: 33283876 DOI: 10.1002/bip.23412] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/03/2023]
Abstract
Micro- and nanopatterning of proteins on surfaces allows to develop for example high-throughput biosensors in biomedical diagnostics and in general advances the understanding of cell-material interactions in tissue engineering. Today, many techniques are available to generate protein pattern, ranging from technically simple ones, such as micro-contact printing, to highly tunable optical lithography or even technically sophisticated scanning probe lithography. Here, one focus is on the progress made in the development of protein-based materials as positive or negative photoresists allowing micro- to nanostructured scaffolds for biocompatible photonic, electronic and tissue engineering applications. The second one is on approaches, which allow a controlled spatiotemporal positioning of a single protein on surfaces, enabled by the recent developments in immobilization techniques coherent with the sensitive nature of proteins, defined protein orientation and maintenance of the protein activity at interfaces. The third one is on progress in photolithography-based methods, which allow to control the formation of protein-repellant/adhesive polymer brushes.
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Affiliation(s)
- Martin Humenik
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany
| | - Anika Winkler
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany
| | - Thomas Scheibel
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Colloids and Interfaces (BZKG), Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Molecular Biosciences (BZMB), Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Material Science (BayMAT), Universität Bayreuth, Bayreuth, Germany.,Bavarian Polymer Institute (BPI), Universität Bayreuth, Bayreuth, Germany
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14
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Albert SK, Golla M, Krishnan N, Perumal D, Varghese R. DNA-π Amphiphiles: A Unique Building Block for the Crafting of DNA-Decorated Unilamellar Nanostructures. Acc Chem Res 2020; 53:2668-2679. [PMID: 33052654 DOI: 10.1021/acs.accounts.0c00492] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The unparalleled ability of DNA to recognize its complementary strand through Watson and Crick base pairing is one of the most reliable molecular recognition events found in natural systems. This highly specific sequence information encoded in DNA enables it to be a versatile building block for bottom-up self-assembly. Hence, the decoration of functional nanostructures with information-rich DNA is extremely important as this allows the integration of other functional molecules onto the surface of the nanostructures through DNA hybridization in a highly predictable manner. DNA amphiphiles are a class of molecular hybrids where a short hydrophilic DNA is conjugated to a hydrophobic moiety. Since DNA amphiphiles comprise DNA as the hydrophilic segment, their self-assembly in aqueous medium always results in the formation of nanostructures with shell made of DNA. This clearly suggests that self-assembly of DNA amphiphiles is a straightforward strategy for the ultradense decoration of a nanostructure with DNA. However, initial attempts toward the design of DNA amphiphiles were primarily focused on long flexible hydrocarbon chains as the hydrophobic moiety, and it has been demonstrated in several examples that they typically self-assemble into DNA-decorated micelles (spherical or cylindrical). Hence, molecular level control over the self-assembly of DNA amphiphiles and achieving diverse morphologies was extremely challenging and unrealized until recently.In this Account, we summarize our recent efforts in the area of self-assembly of DNA amphiphiles and narrate the remarkable effect of the incorporation of a large π-surface as the hydrophobic domain in the self-assembly of DNA amphiphiles. Self-assembly of DNA amphiphiles with flexible hydrocarbon chains as the hydrophobic moiety is primarily driven by the hydrophobic effect. The morphology of such nanostructures is typically predicted based on the volume ratio of hydrophobic to hydrophilic segments. However, control over the self-assembly and prediction of the morphology become increasingly challenging when the hydrophobic moieties can interact with each other through other noncovalent interactions. In this Account, the unique self-assembly behaviors of DNA-π amphiphiles, where a large π-surface acts as the hydrophobe, are described. Due to the extremely strong π-π stacking in aqueous medium, the assembly of the amphiphile is found to preferably proceed in a lamellar fashion (bilayer) and hence the morphology of the nanostructures can easily be tuned by the structural modification of the π-surface. Design principles for crafting various DNA-decorated lamellar nanostructures including unilamellar vesicles, two-dimensional (2D) nanosheets, and helically twisted nanoribbons by selecting suitable π-surfaces are discussed. Unilamellar vesicular nanostructures were achieved by using linear oligo(phenylene ethynylene) (OPE) as the hydrophobic segment, where lamellar assembly undergoes folding to form unilamellar vesicles. The replacement of OPE with a strongly π-stacking hydrophobe such as hexabenzocoronene (HBC) or tetraphenylethylene (TPE) provides extremely strong π-stacking compared to OPE, which efficiently directed the 2D growth for the lamellar assembly and led to the formation of 2D nanosheets. A helical twist in the lamella was achieved by the replacement of HBC with hexaphenylbenzene (HPB), which is the twisted analogue of HBC, directing the assembly into helically twisted nanoribbons. The most beneficial structural feature of this kind of nanostructure is the extremely dense decoration of their surface with ssDNA, which can further be used for DNA-directed organization of other functional nanomaterials. By exploring this, their potential as a nanoscaffold for predefined assembly of plasmonic nanomaterials into various plasmonic 1D, 2D, and 3D nanostructures through DNA hybridization is discussed. Moreover, the design of pH-responsive DNA-based vesicles and their application as a nanocarrier for payload delivery is also demonstrated.
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Affiliation(s)
- Shine K. Albert
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551 Kerala, India
| | - Murali Golla
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551 Kerala, India
| | - Nthiyanandan Krishnan
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551 Kerala, India
| | - Devanathan Perumal
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551 Kerala, India
| | - Reji Varghese
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551 Kerala, India
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15
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Kye M, Zhang Z, Lim Y. Self‐assembling cyclic peptide‐oligonucleotide conjugates: Synthetic strategies and the effect of cyclic topology on self‐assembly and base pairing. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mahnseok Kye
- Department of Materials Science & Engineering Yonsei University Seoul South Korea
| | - Zhihao Zhang
- Department of Materials Science & Engineering Yonsei University Seoul South Korea
| | - Yong‐beom Lim
- Department of Materials Science & Engineering Yonsei University Seoul South Korea
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16
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Lefevre M, Flammang P, Aranko AS, Linder MB, Scheibel T, Humenik M, Leclercq M, Surin M, Tafforeau L, Wattiez R, Leclère P, Hennebert E. Sea star-inspired recombinant adhesive proteins self-assemble and adsorb on surfaces in aqueous environments to form cytocompatible coatings. Acta Biomater 2020; 112:62-74. [PMID: 32502634 DOI: 10.1016/j.actbio.2020.05.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
Sea stars adhere to various underwater substrata using an efficient protein-based adhesive secretion. The protein Sfp1 is a major component of this secretion. In the natural glue, it is cleaved into four subunits (Sfp1 Alpha, Beta, Delta and Gamma) displaying specific domains which mediate protein-protein or protein-carbohydrate interactions. In this study, we used the bacterium E. coli to produce recombinantly two fragments of Sfp1 comprising most of its functional domains: the C-terminal part of the Beta subunit (rSfp1 Beta C-term) and the Delta subunit (rSfp1 Delta). Using native polyacrylamide gel electrophoresis and size exclusion chromatography, we show that the proteins self-assemble and form oligomers and aggregates in the presence of NaCl. Moreover, they adsorb onto glass and polystyrene upon addition of Na+ and/or Ca2+ ions, forming homogeneous coatings or irregular meshworks, depending on the cation species and concentration. We show that coatings made of each of the two proteins have no cytotoxic effects on HeLa cells and even increase their proliferation. We propose that the Sfp1 recombinant protein coatings are valuable new materials with potential for cell culture or biomedical applications. STATEMENT OF SIGNIFICANCE: Biological adhesives offer impressive performance in their natural context and, therewith, the potential to inspire the development of advanced biomaterials for an increasing variety of applications in medicine or in material sciences. To date, most marine adhesive proteins that have been produced recombinantly in order to develop bio-inspired adhesives are small proteins from mussels and barnacles. Here, we produced two multi-modular proteins based on the sequence of Sfp1, a major protein from sea star adhesive secretion. These two proteins comprise most of Sfp1 functional domains which mediate protein-protein and protein-carbohydrate interactions. We characterized the two recombinant proteins with an emphasis on functional characteristics such as self-assembly, adsorption and cytocompatibility. We discuss their potential as biomaterials.
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Affiliation(s)
- Mathilde Lefevre
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium; Laboratory for Chemistry of Novel Materials, Research Institute for Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-02150 Espoo, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-02150 Espoo, Finland
| | - Thomas Scheibel
- Department of Biomaterials, Faculty of Engineering Science, University of Bayreuth, Prof.-Rüdiger-Bormann Str.1, 95447 Bayreuth, Germany
| | - Martin Humenik
- Department of Biomaterials, Faculty of Engineering Science, University of Bayreuth, Prof.-Rüdiger-Bormann Str.1, 95447 Bayreuth, Germany
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel Materials, Research Institute for Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Research Institute for Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Lionel Tafforeau
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Philippe Leclère
- Laboratory for Chemistry of Novel Materials, Research Institute for Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium.
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17
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Kelnar I, Zhigunov A, Kaprálková L, Krejčíková S, Dybal J. Synergistic effects in Methylcellulose/Hydroxyethylcellulose blend: Influence of components ratio and graphene oxide. Carbohydr Polym 2020; 236:116077. [PMID: 32172890 DOI: 10.1016/j.carbpol.2020.116077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
A specific feature of water-soluble polysaccharides is formation of organized structures in solutions. This study deals with an unexpected effect of 2-hydroxyethylcellulose (HEC) on structure and mechanical performance of methylcellulose (MC) films. The values of modulus with 5 and 10 % HEC content exceed those of the linear model, which indicates synergistic effect consisting in formation of ordered structures. However, higher content of HEC leads to worse properties corresponding to contribution of its lower parameters. The structural transformations are confirmed by XRD and polarized-light microscopy. Ability of HEC to support formation of ordered structures in MC solutions is indicated by rheology. Important fact is that low graphene oxide (GO) content has a high reinforcing effect on neat MC or HEC, but its presence in blends is accompanied by elimination of HEC-induced structural transformations. The results confirm complex effect of blending and GO on structure and properties of the MC/HEC system.
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Affiliation(s)
- Ivan Kelnar
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Praha, Czech Republic.
| | - Alexander Zhigunov
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Praha, Czech Republic
| | - Ludmila Kaprálková
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Praha, Czech Republic
| | - Sabina Krejčíková
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Praha, Czech Republic
| | - Jiří Dybal
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Praha, Czech Republic
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18
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Lou C, Boesen JT, Christensen NJ, Sørensen KK, Thulstrup PW, Pedersen MN, Giralt E, Jensen KJ, Wengel J. Self‐Assembly of DNA–Peptide Supermolecules: Coiled‐Coil Peptide Structures Templated by
d
‐DNA and
l
‐DNA Triplexes Exhibit Chirality‐Independent but Orientation‐Dependent Stabilizing Cooperativity. Chemistry 2020; 26:5676-5684. [DOI: 10.1002/chem.201905636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/31/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Chenguang Lou
- Biomolecular Nanoscale Engineering CenterDepartment of Physics, Chemistry and PharmacyUniversity of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Josephine Tuborg Boesen
- Biomolecular Nanoscale Engineering CenterDepartment of ChemistryUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering CenterDepartment of ChemistryUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Kasper K. Sørensen
- Biomolecular Nanoscale Engineering CenterDepartment of ChemistryUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Peter W. Thulstrup
- Department of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Ø Denmark
| | - Martin Nors Pedersen
- X-ray and Neutron ScienceNiels Bohr InstituteUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Ø Denmark
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
- Department of Inorganic and Organic ChemistryUniversity of Barcelona Martí i Franquès 1–11 Barcelona 08028 Spain
| | - Knud J. Jensen
- Biomolecular Nanoscale Engineering CenterDepartment of ChemistryUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering CenterDepartment of Physics, Chemistry and PharmacyUniversity of Southern Denmark Campusvej 55 5230 Odense M Denmark
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19
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Humenik M, Preiß T, Gödrich S, Papastavrou G, Scheibel T. Functionalized DNA-spider silk nanohydrogels for controlled protein binding and release. Mater Today Bio 2020; 6:100045. [PMID: 32259099 PMCID: PMC7096766 DOI: 10.1016/j.mtbio.2020.100045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
Hydrogels are excellent scaffolds to accommodate sensitive enzymes in a protective environment. However, the lack of suitable immobilization techniques on substrates and the lack of selectivity to anchor a biocatalyst are major drawbacks preventing the use of hydrogels in bioanalytical devices. Here, nanofilm coatings on surfaces were made of a recombinant spider silk protein (rssp) to induce rssp self-assembly and thus the formation of fibril-based nanohydrogels. To functionalize spider silk nanohydrogels for bioselective binding of proteins, two different antithrombin aptamers were chemically conjugated with the rssp, thereby integrating the target-binding function into the nanohydrogel network. Human thrombin was selected as a sensitive model target, in which the structural integrity determines its activity. The chosen aptamers, which bind various exosites of thrombin, enabled selective and cooperative embedding of the protein into the nanohydrogels. The change of the aptamer secondary structure using complementary DNA sequences led to the release of active thrombin and confirmed the addressable functionalization of spider silk nanohydrogels.
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Affiliation(s)
- Martin Humenik
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Prof.-Rüdiger-Bormann.Str. 1, 95447 Bayreuth, Germany
| | - Tamara Preiß
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Prof.-Rüdiger-Bormann.Str. 1, 95447 Bayreuth, Germany
| | - Sebastian Gödrich
- Department of Physical Chemistry II, Faculty of Biology, Chemistry & Earth Sciences, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Georg Papastavrou
- Department of Physical Chemistry II, Faculty of Biology, Chemistry & Earth Sciences, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Bayreuth Center for Colloids and Interfaces (BZKG), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Bavarian Polymer Institute (BPI), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Thomas Scheibel
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Prof.-Rüdiger-Bormann.Str. 1, 95447 Bayreuth, Germany
- Bayreuth Center for Colloids and Interfaces (BZKG), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Bayreuth Center for Molecular Biosciences (BZMB), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Bayreuth Center for Material Science (BayMAT), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Bavarian Polymer Institute (BPI), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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20
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Albert SK, Hu X, Park SJ. Dynamic Nanostructures from DNA-Coupled Molecules, Polymers, and Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900504. [PMID: 30985085 DOI: 10.1002/smll.201900504] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/28/2019] [Indexed: 05/20/2023]
Abstract
Dynamic and reconfigurable systems that can sense and react to physical and chemical signals are ubiquitous in nature and are of great interest in diverse areas of science and technology. DNA is a powerful tool for fabricating such smart materials and devices due to its programmable and responsive molecular recognition properties. For the past couple of decades, DNA-based self-assembly is actively explored to fabricate various DNA-organic and DNA-inorganic hybrid nanostructures with high-precision structural control. Building upon past development, researchers have recently begun to design and assemble dynamic nanostructures that can undergo an on-demand transformation in the structure, properties, and motion in response to various external stimuli. In this Review, recent advances in dynamic DNA nanostructures, focusing on hybrid structures fabricated from DNA-conjugated molecules, polymers, and nanoparticles, are introduced, and their potential applications and future perspectives are discussed.
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Affiliation(s)
- Shine K Albert
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Xiaole Hu
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - So-Jung Park
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
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21
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Hajiraissi R, Hanke M, Gonzalez Orive A, Duderija B, Hofmann U, Zhang Y, Grundmeier G, Keller A. Effect of Terminal Modifications on the Adsorption and Assembly of hIAPP(20-29). ACS OMEGA 2019; 4:2649-2660. [PMID: 31459500 PMCID: PMC6649277 DOI: 10.1021/acsomega.8b03028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/22/2019] [Indexed: 06/10/2023]
Abstract
The assembly of peptides and proteins into nanoscale amyloid fibrils via formation of intermolecular β-sheets not only plays an important role in the development of degenerative diseases but also represents a promising approach for the synthesis of functional nanomaterials. In many biological and technological settings, peptide assembly occurs in the presence of organic and inorganic interfaces with different physicochemical properties. In an attempt to dissect the relative contributions of the different molecular interactions governing amyloid assembly at interfaces, we here present a systematic study of the effects of terminal modifications on the adsorption and assembly of the human islet amyloid polypeptide fragment hIAPP(20-29) at organic self-assembled monolayers (SAMs) presenting different functional groups (cationic, anionic, polar, or hydrophobic). Using a selection of complementary in situ and ex situ analytical techniques, we find that even this well-defined and comparatively simple model system is governed by a rather complex interplay of electrostatic interactions, hydrophobic interactions, and hydrogen bonding, resulting in a plethora of observations and dependencies, some of which are rather counterintuitive. In particular, our results demonstrate that terminal modifications can have tremendous effects on peptide adsorption and assembly dynamics, as well as aggregate morphology and molecular structure. The effects exerted by the terminal modifications can furthermore be modulated in nontrivial ways by the physicochemical properties of the SAM surface. Therefore, terminal modifications are an important factor to consider when conducting and comparing peptide adsorption and aggregation studies and may represent an additional parameter for guiding the assembly of peptide-based nanomaterials.
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Affiliation(s)
- Roozbeh Hajiraissi
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Marcel Hanke
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Alejandro Gonzalez Orive
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Belma Duderija
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Ulrike Hofmann
- B
CUBE—Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Yixin Zhang
- B
CUBE—Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Guido Grundmeier
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Adrian Keller
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
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22
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Zha RH, Delparastan P, Fink TD, Bauer J, Scheibel T, Messersmith PB. Universal nanothin silk coatings via controlled spidroin self-assembly. Biomater Sci 2019; 7:683-695. [PMID: 30628598 PMCID: PMC6459601 DOI: 10.1039/c8bm01186a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Robust, biocompatible, and facile coatings are promising for improving the in vivo performance of medical implants and devices. Here, we demonstrate the formation of nanothin silk coatings by leveraging the biomimetic self-assembly of eADF4(C16), an amphiphilic recombinant protein based on the Araneus diadematus dragline spidroin ADF4. These coatings result from concurrent adsorption and supramolecular assembly of eADF4(C16) induced by KH2PO4, thereby providing a mild one-pot coating strategy in which the coating rate can be controlled by protein and KH2PO4 concentration. The thickness of the coatings ranges from 2-30 nm depending on the time immersed in the aqueous coating solution. Coatings can be formed on hydrophobic and hydrophilic substrates regardless of surface chemistry and without requiring specialized surface activation. Moreover, coatings appear to be stable through vigorous rinsing and prolonged agitation in water. Grazing incidence wide angle X-ray scattering, single-molecule force spectroscopy, and Congo red staining techniques confirm the formation of β-sheet nanocrystals within the eADF4(C16) coating, which contributes to the cohesive and adhesive stability of the material. Coatings are exceptionally smooth in the dry state and are hydrophilic regardless of substrate hydrophobicity. Under aqueous conditions, nanothin silk coatings exhibit the properties of a hydrogel material.
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Affiliation(s)
- R Helen Zha
- Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY 12180, USA.
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23
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Nanostructured, Self-Assembled Spider Silk Materials for Biomedical Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:187-221. [PMID: 31713200 DOI: 10.1007/978-981-13-9791-2_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The extraordinary mechanical properties of spider silk fibers result from the interplay of composition, structure and self-assembly of spider silk proteins (spidroins). Genetic approaches enabled the biotechnological production of recombinant spidroins which have been employed to unravel the self-assembly and spinning process. Various processing conditions allowed to explore non-natural morphologies including nanofibrils, particles, capsules, hydrogels, films or foams. Recombinant spider silk proteins and materials made thereof can be utilized for biomedical applications, such as drug delivery, tissue engineering or 3D-biomanufacturing.
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24
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Molina A, Scheibel T, Humenik M. Nanoscale Patterning of Surfaces via DNA Directed Spider Silk Assembly. Biomacromolecules 2018; 20:347-352. [DOI: 10.1021/acs.biomac.8b01333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Krishnan N, Golla M, Thelu HVP, Albert SK, Atchimnaidu S, Perumal D, Varghese R. Self-assembly of DNA-tetraphenylethylene amphiphiles into DNA-grafted nanosheets as a support for the immobilization of gold nanoparticles: a recyclable catalyst with enhanced activity. NANOSCALE 2018; 10:17174-17181. [PMID: 30187067 DOI: 10.1039/c8nr03746a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Preventing the aggregation of NPs and their recovery are the two major hurdles in NP based catalysis. Immobilization of NPs on a support has proven to be a promising strategy to overcome these difficulties. Herein we report the design of high aspect ratio two-dimensional (2D) crystalline DNA nanosheets formed from the amphiphilicity-driven self-assembly of DNA-tetraphenylethylene amphiphiles and also demonstrate the potential of DNA nanosheets for the immobilization of catalytically active NPs. The most remarkable feature of this approach is the high loading of NPs in a non-aggregated manner, and hence exhibiting enhanced catalytic activity. Recycling of NP loaded nanosheets for several cycles without reduction in catalytic efficiency by simple ultrafiltration is also demonstrated.
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Affiliation(s)
- Nithiyanandan Krishnan
- School of Chemistry, Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM), Vithura, Trivandrum-695551, India.
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26
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Kye M, Lim YB. Synthesis and purification of self-assembling peptide-oligonucleotide conjugates by solid-phase peptide fragment condensation. J Pept Sci 2018; 24:e3092. [PMID: 29920844 DOI: 10.1002/psc.3092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
Abstract
Peptide-oligonucleotide conjugates (POCs) are interesting molecules as they covalently combine 2 of the most important biomacromolecules. Sometimes, the synthesis of POCs involves unexpected difficulties; however, POCs with self-assembling propensity are even harder to synthesize and purify. Here, we show that solid-phase peptide fragment condensation combined with thiol-maleimide or copper-catalyzed azide-alkyne cycloaddition click chemistries is useful for the syntheses of self-assembling POCs. We describe guidelines for the selection of reactive functional groups and their placement during the conjugation reaction and consider the cost-effectiveness of the reaction. Purification is another important challenge during the preparation of POCs. Our results show that polyacrylamide gel electrophoresis under denaturing conditions is most suitable to recover a high yield of self-assembling POCs. This report provides the first comprehensive study of the preparation of self-assembling POCs, which will lay a foundation for the development of elegant and sophisticated molecular assemblies.
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Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
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27
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Merg AD, Thaner RV, Mokashi-Punekar S, Nguyen ST, Rosi NL. Triblock peptide-oligonucleotide chimeras (POCs): programmable biomolecules for the assembly of morphologically tunable and responsive hybrid materials. Chem Commun (Camb) 2018; 53:12221-12224. [PMID: 29082986 DOI: 10.1039/c7cc07708d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Triblock peptide-oligonucleotide chimeras (POCs) consisting of peptides and oligonucleotides interlinked by an organic core are presented and their assembly behaviour is investigated. Several factors influence POC assembly, resulting in the formation of either vesicles or fibres. Design rules are introduced and used to predict and alter POC assembly morphology.
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Affiliation(s)
- Andrea D Merg
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA.
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28
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Helbing C, Deckert-Gaudig T, Firkowska-Boden I, Wei G, Deckert V, Jandt KD. Protein Handshake on the Nanoscale: How Albumin and Hemoglobin Self-Assemble into Nanohybrid Fibers. ACS NANO 2018; 12:1211-1219. [PMID: 29298383 DOI: 10.1021/acsnano.7b07196] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Creating and establishing proof of hybrid protein nanofibers (hPNFs), i.e., PNFs that contain more than one protein, is a currently unsolved challenge in bioinspired materials science. Such hPNFs could serve as universal building blocks for the bottom-up preparation of functional materials with bespoke properties. Here, inspired by the protein assemblies occurring in nature, we introduce hPNFs created via a facile self-assembly route and composed of human serum albumin (HSA) and human hemoglobin (HGB) proteins. Our circular dichroism results shed light on the mechanism of the proteins' self-assembly into hybrid nanofibers, which is driven by electrostatic/hydrophobic interactions between similar amino acid sequences (protein handshake) exposed to ethanol-triggered protein denaturation. Based on nanoscale characterization with tip-enhanced Raman spectroscopy (TERS) and immunogold labeling, our results demonstrate the existence and heterogenic nature of the hPNFs and reveal the high HSA/HGB composition ratio, which is attributed to the fast self-assembling kinetics of HSA. The self-assembled hPNFs with a high aspect ratio of over 100 can potentially serve as biocompatible units to create larger bioactive structures, devices, and sensors.
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Affiliation(s)
- Christian Helbing
- Chair of Materials Science (CMS), Otto Schott Institute of Materials Research, Faculty of Physics and Astronomy, Friedrich Schiller University Jena , Löbdergraben 32, 07743 Jena, Germany
| | - Tanja Deckert-Gaudig
- Leibnitz Institute of Photonic Technology IPHT , Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Izabela Firkowska-Boden
- Chair of Materials Science (CMS), Otto Schott Institute of Materials Research, Faculty of Physics and Astronomy, Friedrich Schiller University Jena , Löbdergraben 32, 07743 Jena, Germany
| | - Gang Wei
- Faculty of Production Engineering, University of Bremen , Am Fallturm 1, 28359 Bremen, Germany
| | - Volker Deckert
- Leibnitz Institute of Photonic Technology IPHT , Albert-Einstein-Strasse 9, 07745 Jena, Germany
- Institute for Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena , Helmholtzweg 4, 07743 Jena, Germany
| | - Klaus D Jandt
- Chair of Materials Science (CMS), Otto Schott Institute of Materials Research, Faculty of Physics and Astronomy, Friedrich Schiller University Jena , Löbdergraben 32, 07743 Jena, Germany
- Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena , Humboldtstraße 10, 07743 Jena, Germany
- Jena School for Microbial Communication (JSMC), Friedrich Schiller University , 07743 Jena, Germany
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29
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Fink TD, Zha RH. Silk and Silk-Like Supramolecular Materials. Macromol Rapid Commun 2018; 39:e1700834. [DOI: 10.1002/marc.201700834] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/16/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Tanner D. Fink
- Department of Chemical and Biological Engineering; Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; 110 8th St. Troy NY 12180 USA
| | - R. Helen Zha
- Department of Chemical and Biological Engineering; Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; 110 8th St. Troy NY 12180 USA
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Humenik M, Lang G, Scheibel T. Silk nanofibril self-assembly versus electrospinning. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1509. [PMID: 29393590 DOI: 10.1002/wnan.1509] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 10/18/2017] [Accepted: 12/19/2017] [Indexed: 01/16/2023]
Abstract
Natural silk fibers represent one of the most advanced blueprints for (bio)polymer scientists, displaying highly optimized mechanical properties due to their hierarchical structures. Biotechnological production of silk proteins and implementation of advanced processing methods enabled harnessing the potential of these biopolymer not just based on the mechanical properties. In addition to fibers, diverse morphologies can be produced, such as nonwoven meshes, films, hydrogels, foams, capsules and particles. Among them, nanoscale fibrils and fibers are particularly interesting concerning medical and technical applications due to their biocompatibility, environmental and mechanical robustness as well as high surface-to-volume ratio. Therefore, we introduce here self-assembly of silk proteins into hierarchically organized structures such as supramolecular nanofibrils and fabricated materials based thereon. As an alternative to self-assembly, we also present electrospinning a technique to produce nanofibers and nanofibrous mats. Accordingly, we introduce a broad range of silk-based dopes, used in self-assembly and electrospinning: natural silk proteins originating from natural spinning glands, natural silk protein solutions reconstituted from fibers, engineered recombinant silk proteins designed from natural blueprints, genetic fusions of recombinant silk proteins with other structural or functional peptides and moieties, as well as hybrids of recombinant silk proteins chemically conjugated with nonproteinaceous biotic or abiotic molecules. We highlight the advantages but also point out drawbacks of each particular production route. The scope includes studies of the natural self-assembly mechanism during natural silk spinning, production of silk fibrils as new nanostructured non-native scaffolds allowing dynamic morphological switches, as well as studying potential applications. This article is categorized under: Biology-Inspired Nanomaterials > Peptide-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Martin Humenik
- Biomaterials, Faculty of Engineering Science, University of Bayreuth, Bayreuth, Germany
| | - Gregor Lang
- Biomaterials, Faculty of Engineering Science, University of Bayreuth, Bayreuth, Germany
| | - Thomas Scheibel
- Biomaterials, Faculty of Engineering Science, University of Bayreuth, Bayreuth, Germany.,Bayreuth Center for Colloids and Interfaces (BZKG), Research Center Bio-Macromolecules (BIOmac), Bayreuth Center for Molecular Biosciences (BZMB), Bayreuth Center for Material Science (BayMAT), Bavarian Polymer Institute (BPI), Universität Bayreuth, Bayreuth, Germany
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Humenik M, Mohrand M, Scheibel T. Self-Assembly of Spider Silk-Fusion Proteins Comprising Enzymatic and Fluorescence Activity. Bioconjug Chem 2018; 29:898-904. [DOI: 10.1021/acs.bioconjchem.7b00759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Bioinks, 3D cell culture systems which can be printed, are still in the early development stages. Currently, extensive research is going into designing printers to be more accommodating to bioinks, designing scaffolds with stiff materials as support structures for the often soft bioinks, and modifying the bioinks themselves. Recombinant spider silk proteins, a potential biomaterial component for bioinks, have high biocompatibility, can be processed into several morphologies and can be modified with cell adhesion motifs to enhance their bioactivity. In this work, thermally gelled hydrogels made from recombinant spider silk protein encapsulating mouse fibroblast cell line BALB/3T3 were prepared and characterized. The bioinks were evaluated for performance in vitro both before and after printing, and it was observed that unprinted bioinks provided a good platform for cell spreading and proliferation, while proliferation in printed scaffolds was prohibited. To improve the properties of the printed hydrogels, gelatin was given as an additive and thereby served indirectly as a plasticizer, improving the resolution of printed strands. Taken together, recombinant spider silk proteins and hydrogels made thereof show good potential as a bioink, warranting further development.
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Affiliation(s)
- Elise DeSimone
- Lehrstuhl Biomaterialien, Bayreuther Zentrum für Kolloide und Grenzflächen (BZKG), Bayreuther Zentrum für Bio-Makromoleküle (bio-mac), Bayreuther Zentrum für Molekulare Biowissenschaften (BZMB), Bayreuther Materialzentrum (BayMAT), Bayerisches Polymerinstitut (BPI) Universitätsstraße 30, Universität Bayreuth, Bayreuth D-95447, Germany
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Albert SK, Sivakumar I, Golla M, Thelu HVP, Krishnan N, K L JL, Ashish, Varghese R. DNA-Decorated Two-Dimensional Crystalline Nanosheets. J Am Chem Soc 2017; 139:17799-17802. [PMID: 29232955 DOI: 10.1021/jacs.7b09283] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Design and synthesis of high aspect ratio 2D nanosheets with surface having ultradense array of information-rich molecule such as DNA is extremely challenging. Herein, we report a universal strategy based on amphiphilicity-driven self-assembly for the crafting of high aspect ratio, 2D sheets that are densely surface-decorated with DNA. Microscopy and X-ray analyses have shown that the sheets are crystalline. The most unique feature of the sheets is DNA-directed surface addressability, which is demonstrated through the decoration of either faces of the sheet with gold nanoparticles through sequence-specific DNA hybridization. Our results suggest that this design strategy can be applied as a general approach for the synthesis of DNA decorated high aspect ratio sheets, which may find potential applications in materials science, drug delivery, and nanoelectronics.
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Affiliation(s)
- Shine K Albert
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram , Trivandrum-695551, Kerala, India
| | - Irla Sivakumar
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram , Trivandrum-695551, Kerala, India
| | - Murali Golla
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram , Trivandrum-695551, Kerala, India
| | - Hari Veera Prasad Thelu
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram , Trivandrum-695551, Kerala, India
| | - Nithiyanandan Krishnan
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram , Trivandrum-695551, Kerala, India
| | - Joseph Libin K L
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram , Trivandrum-695551, Kerala, India
| | - Ashish
- Protein Science and Engineering Division, Institute of Microbial Technology , Sector 39-A, Chandigarh-160036, India
| | - Reji Varghese
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram , Trivandrum-695551, Kerala, India
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Guttenplan APM, Young LJ, Matak-Vinkovic D, Kaminski CF, Knowles TPJ, Itzhaki LS. Nanoscale click-reactive scaffolds from peptide self-assembly. J Nanobiotechnology 2017; 15:70. [PMID: 28985740 PMCID: PMC6389178 DOI: 10.1186/s12951-017-0300-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/23/2017] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Due to their natural tendency to self-assemble, proteins and peptides are important components for organic nanotechnology. One particular class of peptides of recent interest is those that form amyloid fibrils, as this self-assembly results in extremely strong, stable quasi-one-dimensional structures which can be used to organise a wide range of cargo species including proteins and oligonucleotides. However, assembly of peptides already conjugated to proteins is limited to cargo species that do not interfere sterically with the assembly process or misfold under the harsh conditions often used for assembly. Therefore, a general method is needed to conjugate proteins and other molecules to amyloid fibrils after the fibrils have self-assembled. RESULTS Here we have designed an amyloidogenic peptide based on the TTR105-115 fragment of transthyretin to form fibrils that display an alkyne functionality, important for bioorthogonal chemical reactions, on their surface. The fibrils were formed and reacted both with an azide-containing amino acid and with an azide-functionalised dye by the Huisgen cycloaddition, one of the class of "click" reactions. Mass spectrometry and total internal reflection fluorescence optical microscopy were used to show that peptides incorporated into the fibrils reacted with the azide while maintaining the structure of the fibril. These click-functionalised amyloid fibrils have a variety of potential uses in materials and as scaffolds for bionanotechnology. DISCUSSION Although previous studies have produced peptides that can both form amyloid fibrils and undergo "click"-type reactions, this is the first example of amyloid fibrils that can undergo such a reaction after they have been formed. Our approach has the advantage that self-assembly takes place before click functionalization rather than pre-functionalised building blocks self-assembling. Therefore, the molecules used to functionalise the fibril do not themselves have to be exposed to harsh, amyloid-forming conditions. This means that a wider range of proteins can be used as ligands in this process. For instance, the fibrils can be functionalised with a green fluorescent protein that retains its fluorescence after it is attached to the fibrils, whereas this protein loses its fluorescence if it is exposed to the conditions used for aggregation.
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Affiliation(s)
- Alexander P. M. Guttenplan
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Laurence J. Young
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS UK
| | - Dijana Matak-Vinkovic
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS UK
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD UK
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Lou C, Christensen NJ, Martos-Maldonado MC, Midtgaard SR, Ejlersen M, Thulstrup PW, Sørensen KK, Jensen KJ, Wengel J. Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex. Chemistry 2017; 23:9297-9305. [PMID: 28383784 DOI: 10.1002/chem.201700971] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Indexed: 12/29/2022]
Abstract
The rational design of a well-defined protein-like tertiary structure formed by small peptide building blocks is still a formidable challenge. By using peptide-oligonucleotide conjugates (POC) as building blocks, we present the self-assembly of miniature coiled-coil α-helical peptides guided by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex under physiological pH, and to be capable of templating the three peptide sequences to constitute a small coiled-coil motif displaying remarkable α-helicity. The formed trimeric complex was characterized by ultraviolet thermal denaturation, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering (SAXS), and molecular modeling. Stabilizing cooperativity was observed between the trimeric peptide and the oligonucleotide triplex domains, and the overall molecular size (ca. 12 nm) in solution was revealed to be independent of concentration. The topological folding of the peptide moiety differed strongly from those of the individual POC strands and the unconjugated peptide, exclusively adopting the designed triple helical structure.
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Affiliation(s)
- Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Manuel C Martos-Maldonado
- Biomolecular Nanoscale Engineering Center, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Søren Roi Midtgaard
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Maria Ejlersen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Kasper K Sørensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Knud J Jensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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Valsangkar V, Chandrasekaran AR, Wang R, Haruehanroengra P, Levchenko O, Halvorsen K, Sheng J. Click-based functionalization of a 2'-O-propargyl-modified branched DNA nanostructure. J Mater Chem B 2017; 5:2074-2077. [PMID: 32263680 DOI: 10.1039/c6tb03277j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA has emerged as a versatile building block for programmable self-assembly. DNA-based nanostructures have been widely applied in biosensing, bioimaging, drug delivery, molecular computation and macromolecular scaffolding. A variety of strategies have been developed to functionalize these nanostructures. In this study, we report a facile click-based strategy to incorporate a metal chelating ligand and a fluorescent tag into a three-point-star DNA tile containing 2'-O-propargyl groups. Such a strategy opens up the possibility of functionalizing pre-assembled DNA strands to construct platforms for metal or drug delivery.
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Affiliation(s)
- Vibhav Valsangkar
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA.
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38
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Guo C, Hili R. Fidelity of the DNA Ligase-Catalyzed Scaffolding of Peptide Fragments on Nucleic Acid Polymers. Bioconjug Chem 2016; 28:314-318. [DOI: 10.1021/acs.bioconjchem.6b00647] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chun Guo
- 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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39
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Lou C, Martos-Maldonado MC, Madsen CS, Thomsen RP, Midtgaard SR, Christensen NJ, Kjems J, Thulstrup PW, Wengel J, Jensen KJ. Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic. Nat Commun 2016; 7:12294. [PMID: 27464951 PMCID: PMC4974474 DOI: 10.1038/ncomms12294] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 06/15/2016] [Indexed: 01/22/2023] Open
Abstract
Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain formation have never been realized for de novo protein design. Here, we show the applicability of peptide–oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design. Peptide and oligonucleotide systems are known to self-assemble both in nature and artificial systems. Here, the authors combine both forms of self-assembly through the synthesis of peptideoligonucleotide conjugates and show formation of a three-helix structure that dimerises at higher concentrations.
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Affiliation(s)
- Chenguang Lou
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Manuel C Martos-Maldonado
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Charlotte S Madsen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Rasmus P Thomsen
- Biomolecular Nanoscale Engineering Center and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Gustav Wieds Vej 14, Aarhus C 8000, Denmark
| | - Søren Roi Midtgaard
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen Ø 2100, Denmark
| | - Niels Johan Christensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Jørgen Kjems
- Biomolecular Nanoscale Engineering Center and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Gustav Wieds Vej 14, Aarhus C 8000, Denmark
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø 2100, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Knud J Jensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
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Piscitelli A, Pennacchio A, Longobardi S, Velotta R, Giardina P. Vmh2 hydrophobin as a tool for the development of “self-immobilizing” enzymes for biosensing. Biotechnol Bioeng 2016; 114:46-52. [DOI: 10.1002/bit.26049] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alessandra Piscitelli
- Department of Chemical Sciences; Università degli Studi di Napoli Federico II; Complesso Universitario Monte S. Angelo; via Cinthia Naples 4 80126 Italy
| | - Anna Pennacchio
- Department of Chemical Sciences; Università degli Studi di Napoli Federico II; Complesso Universitario Monte S. Angelo; via Cinthia Naples 4 80126 Italy
| | - Sara Longobardi
- Department of Chemical Sciences; Università degli Studi di Napoli Federico II; Complesso Universitario Monte S. Angelo; via Cinthia Naples 4 80126 Italy
| | - Raffaele Velotta
- Department of Physics; Università degli Studi di Napoli Federico II; Complesso Universitario Monte S. Angelo; Naples Italy
| | - Paola Giardina
- Department of Chemical Sciences; Università degli Studi di Napoli Federico II; Complesso Universitario Monte S. Angelo; via Cinthia Naples 4 80126 Italy
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41
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Zhu H, Guo Z, Liu W. Biomimetic water-collecting materials inspired by nature. Chem Commun (Camb) 2016; 52:3863-79. [PMID: 26898232 DOI: 10.1039/c5cc09867j] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nowadays, water shortage is a severe issue all over the world, especially in some arid and undeveloped areas. Interestingly, a variety of natural creatures can collect water from fog, which can provide a source of inspiration to develop novel and functional water-collecting materials. Recently, as an increasingly hot research topic, bioinspired materials with the water collection ability have captured vast scientific attention in both practical applications and fundamental research studies. In this review, we summarize the mechanisms of water collection in various natural creatures and present the fabrications, functions, applications, and new developments of bioinspired materials in recent years. The theoretical basis related to the phenomenon of water collection containing wetting behaviors and water droplet transportations is described in the beginning, i.e., the Young's equation, Wenzel model, Cassie model, surface energy gradient model and Laplace pressure equation. Then, the water collection mechanisms of three typical and widely researched natural animals and plants are discussed and their corresponding bioinspired materials are simultaneously detailed, which are cactus, spider, and desert beetles, respectively. This is followed by introducing another eight animals and plants (butterfly, shore birds, wheat awns, green bristlegrass, the Cotula fallax plant, Namib grass, green tree frogs and Australian desert lizards) that are rarely reported, exhibiting water collection properties or similar water droplet transportation. Finally, conclusions and outlook concerning the future development of bioinspired fog-collecting materials are presented.
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Affiliation(s)
- Hai Zhu
- Hubei Collaborative Innovation Centre for Advanced Organic Chemical Materials and Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei University, Wuhan 430062, People's Republic of China.
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Albert SK, Golla M, Thelu HVP, Krishnan N, Deepak P, Varghese R. Synthesis and self-assembly of DNA–chromophore hybrid amphiphiles. Org Biomol Chem 2016; 14:6960-9. [DOI: 10.1039/c6ob00681g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA based amphiphiles are synthesized through a modular “click” chemistry approach, and the DNA–chromophore hybrid amphiphiles undergo amphiphilicity-driven self-assembly into vesicular or micellar nanostructures having a DNA shell and functional core.
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Affiliation(s)
- Shine K. Albert
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Murali Golla
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Hari Veera Prasad Thelu
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Nithiyanandan Krishnan
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Perapaka Deepak
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Reji Varghese
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
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Pawcenis D, Syrek M, Aksamit-Koperska MA, Łojewski T, Łojewska J. Mark–Houwink–Sakurada coefficients determination for molar mass of silk fibroin from viscometric results. SEC-MALLS approach. RSC Adv 2016. [DOI: 10.1039/c6ra00871b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The results on the changes of average molar masses inBombyx morifibroin with use of size exclusion chromatography and viscometry are presented in terms of the determination of Mark–Houwink–Sakurada coefficients, which are lacking in the literature.
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Affiliation(s)
- D. Pawcenis
- Jagiellonian University
- Chemistry Department
- 30-060 Krakow
- Poland
| | - M. Syrek
- Jagiellonian University
- Chemistry Department
- 30-060 Krakow
- Poland
| | | | - T. Łojewski
- Jagiellonian University
- Chemistry Department
- 30-060 Krakow
- Poland
- AGH University of Science and Technology
| | - J. Łojewska
- Jagiellonian University
- Chemistry Department
- 30-060 Krakow
- Poland
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44
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Humenik M, Smith AM, Arndt S, Scheibel T. Ion and seed dependent fibril assembly of a spidroin core domain. J Struct Biol 2015; 191:130-8. [DOI: 10.1016/j.jsb.2015.06.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/13/2022]
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45
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Heidebrecht A, Eisoldt L, Diehl J, Schmidt A, Geffers M, Lang G, Scheibel T. Biomimetic fibers made of recombinant spidroins with the same toughness as natural spider silk. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:2189-94. [PMID: 25689835 DOI: 10.1002/adma.201404234] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/13/2015] [Indexed: 05/20/2023]
Abstract
Using a self-assembly of recombinant spidroins, biomimetic spinning dopes are produced and wet-spun into fibers. Upon varying the molecular design of the underlying recombinant spidroins, the influence of the amino- and carboxy-terminal domains, as well as the size of the repetitive core domain on fiber mechanics, is determined. Fiber toughness upon biomimetic processing equals and even slightly exceeds that of natural ones.
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Affiliation(s)
- Aniela Heidebrecht
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, 95440, Bayreuth, Germany
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46
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Meier C, Lifincev I, Welland ME. Conducting Core–Shell Nanowires by Amyloid Nanofiber Templated Polymerization. Biomacromolecules 2015; 16:558-63. [DOI: 10.1021/bm501618c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Meier
- Nanoscience
Centre, Cambridge University, 11 JJ Thomson Avenue, Cambridge, CB3 0FF United Kingdom
| | | | - Mark E. Welland
- Nanoscience
Centre, Cambridge University, 11 JJ Thomson Avenue, Cambridge, CB3 0FF United Kingdom
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Elsner MB, Herold HM, Müller-Herrmann S, Bargel H, Scheibel T. Enhanced cellular uptake of engineered spider silk particles. Biomater Sci 2015. [DOI: 10.1039/c4bm00401a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Drug delivery systems allow tissue/cell specific targeting of drugs in order to reduce total drug amounts administered to an organism and potential side effects upon systemic drug delivery.
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Affiliation(s)
- Martina B. Elsner
- Lehrstuhl Biomaterialien
- Universitätsstraße 30
- Universität Bayreuth
- Bayreuth D-95447
- Germany
| | - Heike M. Herold
- Lehrstuhl Biomaterialien
- Universitätsstraße 30
- Universität Bayreuth
- Bayreuth D-95447
- Germany
| | | | - Hendrik Bargel
- Lehrstuhl Biomaterialien
- Universitätsstraße 30
- Universität Bayreuth
- Bayreuth D-95447
- Germany
| | - Thomas Scheibel
- Lehrstuhl Biomaterialien
- Universitätsstraße 30
- Universität Bayreuth
- Bayreuth D-95447
- Germany
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Humenik M, Scheibel T. Self-assembly of nucleic acids, silk and hybrid materials thereof. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:503102. [PMID: 25419786 DOI: 10.1088/0953-8984/26/50/503102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here,we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.
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Humenik M, Drechsler M, Scheibel T. Controlled hierarchical assembly of spider silk-DNA chimeras into ribbons and raft-like morphologies. NANO LETTERS 2014; 14:3999-4004. [PMID: 24924514 DOI: 10.1021/nl501412k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Spider silk-DNA conjugates comprising the recombinant spider silk protein eADF4(C16) and short oligonucleotides were arranged in a linear antiparallel and parallel as well as in a branched manner via designed complementarity of the DNA moieties. After cross-β fibril self-assembly, temperature-induced annealing of the DNA moieties triggered fibril association into ribbons, composed of aligned nanofibrils, and rafts composed of ribbons ordered into sharply bordered, squared fibrous microstructures. The formation of the superstructures was clearly dependent on the individual silk-DNA conjugate. A combination of 5'-conjugated silk moieties via complementary nucleic acids enhanced fibril association, whereas mixing complementary 5'- and 3'-silk conjugates inhibited the formation of higher-order structures.
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Affiliation(s)
- Martin Humenik
- Biomaterials, Faculty of Engineering Science, ‡Bayreuth Institute of Macromolecular Research (BIMF) - Soft Matter Electron Microscopy, and §Bayreuth Center for Colloids and Interfaces (BZKG), Research Center Bio-Macromolecules (BIOmac), Bayreuth Center for Molecular Biosciences (BZMB), and Bayreuth Center for Material Science (BayMAT), University of Bayreuth , D-95440 Bayreuth, Germany
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Humenik M, Magdeburg M, Scheibel T. Influence of repeat numbers on self-assembly rates of repetitive recombinant spider silk proteins. J Struct Biol 2014; 186:431-7. [DOI: 10.1016/j.jsb.2014.03.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 12/11/2022]
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