1
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Gras M, Adler P, Smietana M. A Catalytic Approach for the Synthesis of Peptide-Oligonucleotides Conjugates in Aqueous Solution or On-Column. Chemistry 2024; 30:e202401069. [PMID: 38709711 DOI: 10.1002/chem.202401069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
Peptide-oligonucleotide conjugates (POCs) are covalent architectures composed of a DNA or RNA molecules linked to a peptide. These constructs have found widespread applications ranging from hybrid nanomaterials to gene-targeted therapies. Considering the important role of POCs, a new catalytic approach for their preparation is reported here, that could be applied either on solid support in anhydrous media, or post-synthetically in aqueous buffer. Single amino acids, peptides and cell penetrating peptides (CPPs) were conjugated to various oligo(ribo)nucleotides with high conversions and good isolated yields. The applicability of the method was demonstrated on more than 35 examples including an analogue of a commercial therapeutic oligonucleotide. Other conjugation partners, such as deoxycholic acid and biotin were also successfully conjugated to oligonucleotides. To highlight the potential of this catalytic approach, these conditions have been applied to iterative processes, which is of high interest for the development of DNA-Encoded Libraries.
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Affiliation(s)
- Marion Gras
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Pauline Adler
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Michael Smietana
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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2
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Daly ML, Nishi K, Klawa SJ, Hinton KY, Gao Y, Freeman R. Designer peptide-DNA cytoskeletons regulate the function of synthetic cells. Nat Chem 2024:10.1038/s41557-024-01509-w. [PMID: 38654104 DOI: 10.1038/s41557-024-01509-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/15/2024] [Indexed: 04/25/2024]
Abstract
The bottom-up engineering of artificial cells requires a reconfigurable cytoskeleton that can organize at distinct locations and dynamically modulate its structural and mechanical properties. Here, inspired by the vast array of actin-binding proteins and their ability to reversibly crosslink or bundle filaments, we have designed a library of peptide-DNA crosslinkers varying in length, valency and geometry. Peptide filaments conjoint through DNA hybridization give rise to tactoid-shaped bundles with tunable aspect ratios and mechanics. When confined in cell-sized water-in-oil droplets, the DNA crosslinker design guides the localization of cytoskeletal structures at the cortex or within the lumen of the synthetic cells. The tunable spatial arrangement regulates the passive diffusion of payloads within the droplets and complementary DNA handles allow for the reversible recruitment and release of payloads on and off the cytoskeleton. Heat-induced reconfiguration of peptide-DNA architectures triggers shape deformations of droplets, regulated by DNA melting temperatures. Altogether, the modular design of peptide-DNA architectures is a powerful strategy towards the bottom-up assembly of synthetic cells.
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Affiliation(s)
- Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kengo Nishi
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kameryn Y Hinton
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuan Gao
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA.
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3
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Gong T, Liao L, Jiang B, Yuan R, Xiang Y. Ag +-stabilized DNA triplex coupled with catalytic hairpin assembly and CRISPR/Cas12a amplifications for sensitive metallothionein assay. Talanta 2024; 268:125392. [PMID: 37948952 DOI: 10.1016/j.talanta.2023.125392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Metallothionein (MT) is a protein biomarker secreted by liver in response to the treatment for heavy metal toxicity and oncological diseases. On the basis of a new Ag+-stabilized DNA triplex probe (Ag+-SDTP), we establish a fluorescent biosensing system for high sensitivity detection of MT by combining catalytic hairpin assembly (CHA) and the CRISPR/Cas12a signal enhancements. The MT analyte complexes with Ag+ in Ag+-SDTP to disrupt the triplex structure and to release the ssDNA strands, which trigger subsequent CHA formation of many protospacer adjacent motif (PAM)-containing dsDNAs from two hairpins. Cas12a/crRNA further recognizes these PAM sequences to activate its trans-catalytic activity to cyclically cleave the fluorescently quenched ssDNA reporters to recovery drastically amplified fluorescence for detecting MT down to 0.34 nM within the dynamic range of 1∼800 nM. Moreover, the sensing method is able to selectively discriminate MT from other non-specific molecules and can realize low level detection of MT in diluted human serums, manifesting its potentiality for monitoring the disease-specific MT biomarker at trace levels.
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Affiliation(s)
- Tingting Gong
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Lei Liao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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4
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Perez AR, Lee Y, Colvin ME, Merg AD. Interhelical E@g-N@a interactions modulate coiled coil stability within a de novo set of orthogonal peptide heterodimers. J Pept Sci 2024; 30:e3540. [PMID: 37690796 DOI: 10.1002/psc.3540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023]
Abstract
The designability of orthogonal coiled coil (CC) dimers, which draw on well-established design rules, plays a pivotal role in fueling the development of CCs as synthetically versatile assembly-directing motifs for the fabrication of bionanomaterials. Here, we aim to expand the synthetic CC toolkit through establishing a "minimalistic" set of orthogonal, de novo CC peptides that comprise 3.5 heptads in length and a single buried Asn to prescribe dimer formation. The designed sequences display excellent partner fidelity, confirmed via circular dichroism (CD) spectroscopy and Ni-NTA binding assays, and are corroborated in silico using molecular dynamics (MD) simulation. Detailed analysis of the MD conformational data highlights the importance of interhelical E@g-N@a interactions in coordinating an extensive 6-residue hydrogen bonding network that "locks" the interchain Asn-Asn' contact in place. The enhanced stability imparted to the Asn-Asn' bond elicits an increase in thermal stability of CCs up to ~15°C and accounts for significant differences in stability within the collection of similarly designed orthogonal CC pairs. The presented work underlines the utility of MD simulation as a tool for constructing de novo, orthogonal CCs, and presents an alternative handle for modulating the stability of orthogonal CCs via tuning the number of interhelical E@g-N@a contacts. Expansion of CC design rules is a key ingredient for guiding the design and assembly of more complex, intricate CC-based architectures for tackling a variety of challenges within the fields of nanomedicine and bionanotechnology.
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Affiliation(s)
- Anthony R Perez
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Yumie Lee
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Michael E Colvin
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Andrea D Merg
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
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5
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Aldulaijan S. In-silico selection of peptides for the recognition of imidacloprid. PLoS One 2023; 18:e0295619. [PMID: 38085733 PMCID: PMC10715655 DOI: 10.1371/journal.pone.0295619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The sensitive detection of pesticides using low-cost receptors designed from peptides can widen their uses in the environmental surveillance for emerging pollutants. In-silico selection of peptides can help accelerate the design of receptor sequence banks for a given target of interest. In this work, we started from Lymnaea stagnalis acetylcholine-binding protein Q55R mutant receptor-imidacloprid complex, available in the PDB databank, to select three primary short peptides (YSP09, DMR12, WQW13 respectively having 9, 12 and 13 amino acids (AA) in length) from the pesticide interacting zones with the A, B and C chains of the nicotinic receptor. Using molecular docking and molecular dynamics (MD) simulations, we showed that the three peptides can form complexes with the target imidacloprid, having energies close to that obtained from a reference RNR12 peptide. Combination of these peptides allowed preparing a new set of longer peptides (YSM21, PSM22, PSW31 and WQA34) that have higher stability and affinity as shown by the MM-PBSA calculations. In particular, the WQA34 peptide displayed an average binding free energy of -6.44±0.27 kcal/mol, which is three times higher than that of the reference RNR12 peptide (-2.29±0.25 kcal/mol) and formed a stable complex with imidacloprid. Furthermore, the dissociation constants (Kd), calculated from the binding free energy, showed that WQA32 (40 μM) has three orders of magnitude lower Kd than the reference RNR12 peptide (3.4 × 104 μM). Docking and RMSD scores showed that the WQA34 peptide is potentially selective to the target imidacloprid with respect to acetamiprid and clothianidin. Therefore, this peptide can be used in wet-lab experiments to prepare a biosensor to selectively detect imidacloprid.
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Affiliation(s)
- Sarah Aldulaijan
- Chemistry Department, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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6
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Freitag JS, Möser C, Belay R, Altattan B, Grasse N, Pothineni BK, Schnauß J, Smith DM. Integration of functional peptides into nucleic acid-based nanostructures. NANOSCALE 2023; 15:7608-7624. [PMID: 37042085 DOI: 10.1039/d2nr05429a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In many applications such as diagnostics and therapy development, small peptide fragments consisting of only a few amino acids are often attractive alternatives to bulky proteins. This is due to factors such as the ease of scalable chemical synthesis and numerous methods for their discovery. One drawback of using peptides is that their activity can often be negatively impacted by the lack of a rigid, 3D stabilizing structure provided by the rest of the protein. In many cases, this can be alleviated by different methods of rational templating onto nanomaterials, which provides additional possibilities to use concepts of multivalence or rational nano-engineering to enhance or even create new types of function or structure. In recent years, nanostructures made from the self-assembly of DNA strands have been used as scaffolds to create functional arrangements of peptides, often leading to greatly enhanced biological activity or new material properties. This review will give an overview of nano-templating approaches based on the combination of DNA nanotechnology and peptides. This will include both bioengineering strategies to control interactions with cells or other biological systems, as well as examples where the combination of DNA and peptides has been leveraged for the rational design of new functional materials.
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Affiliation(s)
- Jessica S Freitag
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Christin Möser
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Robel Belay
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Basma Altattan
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Nico Grasse
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | | | - Jörg Schnauß
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
- Unconventional Computing Lab, UWE, Bristol, BS16 1QY, UK
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany
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7
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Menon D, Singh R, Joshi KB, Gupta S, Bhatia D. Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems. Chembiochem 2023; 24:e202200580. [PMID: 36468492 DOI: 10.1002/cbic.202200580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/07/2022]
Abstract
The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.
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Affiliation(s)
- Dhruv Menon
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Kashti B Joshi
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
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8
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Sugiura S, Shintani Y, Mori D, Higashi SL, Shibata A, Kitamura Y, Kawano SI, Hirosawa KM, Suzuki KGN, Ikeda M. Design of supramolecular hybrid nanomaterials comprising peptide-based supramolecular nanofibers and in situ generated DNA nanoflowers through rolling circle amplification. NANOSCALE 2023; 15:1024-1031. [PMID: 36444534 DOI: 10.1039/d2nr04556g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The artificial construction of multicomponent supramolecular materials comprising plural supramolecular architectures that are assembled orthogonally from their constituent molecules has attracted growing attention. Here, we describe the design and development of multicomponent supramolecular materials by combining peptide-based self-assembled fibrous nanostructures with globular DNA nanoflowers constructed by the rolling circle amplification reaction. The orthogonally constructed architectures were dissected by fluorescence imaging using the selective fluorescence staining procedures adapted to this study. The present, unique hybrid materials developed by taking advantage of each supramolecular architecture based on their peptide and DNA functions may offer distinct opportunities to explore their bioapplications as a soft matrix.
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Affiliation(s)
- Shintaro Sugiura
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Yuki Shintani
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Daisuke Mori
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Sayuri L Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Aya Shibata
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Yoshiaki Kitamura
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Shin-Ichiro Kawano
- Department of Chemistry, Faculty of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Koichiro M Hirosawa
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kenichi G N Suzuki
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masato Ikeda
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
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9
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Taylor ER, Sato A, Jones I, Gudeangadi PG, Beal DM, Hopper JA, Xue WF, Reithofer MR, Serpell CJ. Tuning dynamic DNA- and peptide-driven self-assembly in DNA-peptide conjugates. Chem Sci 2022; 14:196-202. [PMID: 36605750 PMCID: PMC9769108 DOI: 10.1039/d2sc02482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
DNA-peptide conjugates offer an opportunity to marry the benefits of both biomolecular classes, combining the high level of programmability found with DNA, with the chemical diversity of peptides. These hybrid systems offer potential in fields such as therapeutics, nanotechnology, and robotics. Using the first DNA-β-turn peptide conjugate, we present three studies investigating the self-assembly of DNA-peptide conjugates over a period of 28 days. Time-course studies, such as these have not been previously conducted for DNA-peptide conjugates, although they are common in pure peptide assembly, for example in amyloid research. By using aging studies to assess the structures produced, we gain insights into the dynamic nature of these systems. The first study explores the influence varying amounts of DNA-peptide conjugates have on the self-assembly of our parent peptide. Study 2 explores how DNA and peptide can work together to change the structures observed during aging. Study 3 investigates the presence of orthogonality within our system by switching the DNA and peptide control on and off independently. These results show that two orthogonal self-assemblies can be combined and operated independently or in tandem within a single macromolecule, with both spatial and temporal effects upon the resultant nanostructures.
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Affiliation(s)
- Emerald R. Taylor
- School of Chemistry and Forensic Science, University of KentIngram BuildingCanterburyKentCT2 7NHUK
| | - Akiko Sato
- School of Chemistry and Forensic Science, University of KentIngram BuildingCanterburyKentCT2 7NHUK
| | - Isobel Jones
- School of Chemistry and Forensic Science, University of KentIngram BuildingCanterburyKentCT2 7NHUK
| | - Prashant G. Gudeangadi
- School of Chemistry and Forensic Science, University of KentIngram BuildingCanterburyKentCT2 7NHUK
| | - David M. Beal
- School of Biosciences, University of KentStacey BuildingCanterburyKentCT2 7NJUK
| | - James A. Hopper
- School of Chemistry and Forensic Science, University of KentIngram BuildingCanterburyKentCT2 7NHUK
| | - Wei-Feng Xue
- School of Biosciences, University of KentStacey BuildingCanterburyKentCT2 7NJUK
| | - Michael R. Reithofer
- Department of Inorganic Chemistry, University of ViennaWähringer Straße. 421090ViennaAustria
| | - Christopher J. Serpell
- School of Chemistry and Forensic Science, University of KentIngram BuildingCanterburyKentCT2 7NHUK
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10
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Buchberger A, Riker K, Bernal-Chanchavac J, Narayanan RP, Simmons CR, Fahmi NE, Freeman R, Stephanopoulos N. Bioactive Fibronectin-III 10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading. ACS APPLIED BIO MATERIALS 2022; 5:10.1021/acsabm.2c00303. [PMID: 36108278 PMCID: PMC10014493 DOI: 10.1021/acsabm.2c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The integration of proteins with DNA nanotechnology would enable materials with diverse applications in biology, medicine, and engineering. Here, we describe a method for the incorporation of bioactive fibronectin domain proteins with DNA nanostructures using two orthogonal coiled-coil peptides. One peptide from each coiled-coil pair is attached to a DNA origami cuboid in a multivalent fashion by attaching the peptides to DNA handles. These structures can then be assembled into one-dimensional arrays through the addition of a fibronectin domain linker genetically fused with the complementary peptides to those on the origami. We validate array formation using two different self-assembly protocols and characterize the fibers by atomic force and electron microscopy. Finally, we demonstrate that surfaces coated with the protein-DNA nanofibers can serve as biomaterial substrates for fibroblast adhesion and spreading with the nanofibers showing enhanced bioactivity compared to that of the monomeric protein.
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Affiliation(s)
- Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Kyle Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Chad R Simmons
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Nour Eddine Fahmi
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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11
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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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12
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Xu M, Zhou B, Ding Y, Du S, Su M, Liu H. Programmable Oligonucleotide-Peptide Complexes: Synthesis and Applications. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-021-1265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Cornier PG, Delpiccolo CM, Martiren NL, Mata EG, Mendez L, Permingeat Squizatto C, Pizzio MG. Transition Metal‐Catalyzed Reactions and Solid‐Phase Synthesis: A Convenient Blend. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Patricia G. Cornier
- Instituto de Química Rosario: Instituto de Quimica Rosario Organic Chemistry Suipacha 531 2000 Rosario ARGENTINA
| | - Carina M.L. Delpiccolo
- Instituto de Química Rosario: Instituto de Quimica Rosario Organic Chemistry Suipacha 531 2000 Rosario ARGENTINA
| | - Nadia L. Martiren
- Instituto de Química Rosario: Instituto de Quimica Rosario Organic Chemistry Suipacha 531 S2000 Rosario ARGENTINA
| | - Ernesto G Mata
- Instituto de Química Rosario Chemistry Suipacha 531 2000 Rosario ARGENTINA
| | - Luciana Mendez
- Instituto de Química Rosario: Instituto de Quimica Rosario Organic Chemistry Suipacha 531 S2000 ROSARIO ARGENTINA
| | | | - Marianela G. Pizzio
- Instituto de Química Rosario: Instituto de Quimica Rosario Organic Chemistry Suipacha 531 S2000 Rosario ARGENTINA
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14
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Rothenbühler S, Gonzalez A, Iacovache I, Langenegger SM, Zuber B, Häner R. Tetraphenylethylene-DNA conjugates: influence of sticky ends and DNA sequence length on the supramolecular assembly of AIE-active vesicles. Org Biomol Chem 2022; 20:3703-3707. [PMID: 35262542 PMCID: PMC9092531 DOI: 10.1039/d2ob00357k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The supramolecular assembly of DNA conjugates, functionalized with tetraphenylethylene (TPE) sticky ends, into vesicular structures is described. The aggregation-induced emission (AIE) active TPE units allow monitoring the assembly process by fluorescence spectroscopy. The number of TPE modifications in the overhangs of the conjugates influences the supramolecular assembly behavior. A minimum of two TPE residues on each end are required to ensure a well-defined assembly process. The design of the presented DNA-based nanostructures offers tailored functionalization with applications in DNA nanotechnology. The supramolecular assembly of tetraphenylethylene (TPE)–DNA conjugates is presented. The length of the TPE sticky ends exerts a pronounced effect on the formation of aggregation-induced emission (AIE)-active vesicles.![]()
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Affiliation(s)
- Simon Rothenbühler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Adrian Gonzalez
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Ioan Iacovache
- Institute of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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15
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Mastouri M, Baachaoui S, Mosbah A, Raouafi N. In silico screening for oligopeptides useful as capture and reporting probes for interleukin-6 biosensing. RSC Adv 2022; 12:13003-13013. [PMID: 35497015 PMCID: PMC9049833 DOI: 10.1039/d2ra01496c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/24/2022] [Indexed: 11/21/2022] Open
Abstract
IL-6 is an important interleukin associated with inflammation and several diseases such as cancer. Evaluation of its levels in human blood sera is a critical step for an accurate diagnosis of the diseases. Our goal is to design peptides that can selectively bind in different poses with good affinities to IL-6. For this purpose, we started from the crystal structures of different IL-6/protein complexes available in the Protein Data Bank (PDB) to select short peptides in the interaction zones, in which we intentionally introduced point mutations to increase their stability and affinity. To examine their usefulness as capture and reporting probes for the IL-6 biosensing, the five peptides and their interaction with IL-6 were studied in saline aqueous solution. Molecular docking, MD, and MM-PBSA were used to investigate the affinity and stability of these complexes. The conformational changes, the distance between the mass centers, the gyration radii, and the numbers of hydrogen bonds were analyzed to select the most suitable candidates. Three peptides, namely CTE17, CAY15 and CSE25, have the highest affinities presenting significant numbers of residues that have contact frequencies greater than 50% of simulation run time and are the most promising candidates. CTE17 and CSE25 showed they can form a stable sandwich with the target protein. For sake of comparison, we examined the previously known peptides (FND20, INL19 and CEK17) having affinity to IL-6 and the affinity of the lead i.e. CSE25 to two other interleukin family members (IL-4 and to IL-10). In silico design by docking and molecular dynamics of short peptides that can selectively recognize IL-6 for biosensing purposes.![]()
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Affiliation(s)
- Mohamed Mastouri
- Sensors and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Sabrine Baachaoui
- Sensors and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Amor Mosbah
- BVBGR Laboratory (LR11ES31), ISBST, Biotechnopole Sidi Thabet, University of Manouba Ariana 2020 Tunisia
| | - Noureddine Raouafi
- Sensors and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
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16
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Giraud T, Hoschtettler P, Pickaert G, Averlant-Petit MC, Stefan L. Emerging low-molecular weight nucleopeptide-based hydrogels: state of the art, applications, challenges and perspectives. NANOSCALE 2022; 14:4908-4921. [PMID: 35319034 DOI: 10.1039/d1nr06131c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Over the last twenty years, low-molecular weight gelators and, in particular, peptide-based hydrogels, have drawn great attention from scientists thanks to both their inherent advantages in terms of properties and their high modularity (e.g., number and nature of the amino acids). These supramolecular hydrogels originate from specific peptide self-assembly processes that can be driven, modulated and optimized via specific chemical modifications brought to the peptide sequence. Among them, the incorporation of nucleobases, another class of biomolecules well-known for their abilities to self-assemble, has recently appeared as a new promising and burgeoning approach to finely design supramolecular hydrogels. In this minireview, we would like to highlight the interest, high potential, applications and perspectives of these innovative and emerging low-molecular weight nucleopeptide-based hydrogels.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
| | | | | | | | - Loic Stefan
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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17
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MacCulloch T, Novacek A, Stephanopoulos N. Proximity-enhanced synthesis of DNA-peptide-DNA triblock molecules. Chem Commun (Camb) 2022; 58:4044-4047. [PMID: 35260875 DOI: 10.1039/d1cc04970d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a proximity-enhanced method to synthesize a peptide flanked by two different oligonucleotide handles. Our method relies on sequential bioorthogonal reactions, and partial hybridization of the second handle to the first. We demonstrate the synthesis of a protease-responsive DNA "latch" and a cyclic bioactive peptide using this method.
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Affiliation(s)
- Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Alexandra Novacek
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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18
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Chen X, Cui W, Liu Z, Ma W, Yang X, Tian T, Yang Y, Xie Y, Liu Y, Lin Y. Positive Neuroplastic Effect of DNA Framework Nucleic Acids on Neuropsychiatric Diseases. ACS MATERIALS LETTERS 2022. [DOI: 10.1021/acsmaterialslett.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xingyu Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Weitong Cui
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zhiqiang Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xiao Yang
- Psychiatric Laboratory and Mental Health Centre, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yuting Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yu Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yuhao Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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19
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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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20
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Masaki Y, Maruyama A, Yoshida K, Tomori T, Kishimura T, Seio K. Oligodeoxynucleotides Modified with 2'- O-(Cysteinylaminobutyl)carbamoylethylribothymidine Residues for Native Chemical Ligation with Peptide at Internal Positions. Bioconjug Chem 2022; 33:272-278. [PMID: 35129971 DOI: 10.1021/acs.bioconjchem.1c00575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We used native chemical ligation (NCL) to synthesize a 2'-O-{N-[N-(S-tert-butylthiocysteinyl)aminobutyl]carbamoylethyl} (CysBCE) ribothymidine-derived oligonucleotide to expand the variety of peptide conjugation sites, allowing the incorporation of peptides at the 2'-hydroxy group when the oligonucleotide forms a duplex with the complementary strand. The NCL reaction with a peptide thioester and the modified oligonucleotide proceeded smoothly even when the CysBCE modification was in the middle of the oligonucleotide sequence. In addition, we incorporated two CysBCEs into an oligonucleotide to conjugate two peptides to one oligonucleotide. The results indicated that the tandem NCL reactions proceeded efficiently when the oligonucleotide hybridized to the complementary strand to avoid intramolecular disulfide formation between the two CysBCE groups. This method could be useful for peptide conjugation on the 2'-position.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Keita Yoshida
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Takahito Tomori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Tomohiro Kishimura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
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21
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Gatto E, Toniolo C, Venanzi M. Peptide Self-Assembled Nanostructures: From Models to Therapeutic Peptides. NANOMATERIALS 2022; 12:nano12030466. [PMID: 35159810 PMCID: PMC8838750 DOI: 10.3390/nano12030466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/25/2022]
Abstract
Self-assembly is the most suitable approach to obtaining peptide-based materials on the nano- and mesoscopic scales. Applications span from peptide drugs for personalized therapy to light harvesting and electron conductive media for solar energy production and bioelectronics, respectively. In this study, we will discuss the self-assembly of selected model and bioactive peptides, in particular reviewing our recent work on the formation of peptide architectures of nano- and mesoscopic size in solution and on solid substrates. The hierarchical and cooperative characters of peptide self-assembly will be highlighted, focusing on the structural and dynamical properties of the peptide building blocks and on the nature of the intermolecular interactions driving the aggregation phenomena in a given environment. These results will pave the way for the understanding of the still-debated mechanism of action of an antimicrobial peptide (trichogin GA IV) and the pharmacokinetic properties of a peptide drug (semaglutide) currently in use for the therapy of type-II diabetes.
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Affiliation(s)
- Emanuela Gatto
- PEPSA-LAB, Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy;
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padua, 35131 Padua, Italy;
| | - Mariano Venanzi
- PEPSA-LAB, Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy;
- Correspondence: ; Tel.: +39-06-7259-4468
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22
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Bernal-Chanchavac J, Al-Amin M, Stephanopoulos N. Nanoscale structures and materials from the self-assembly of polypeptides and DNA. Curr Top Med Chem 2021; 22:699-712. [PMID: 34911426 DOI: 10.2174/1568026621666211215142916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/22/2022]
Abstract
The use of biological molecules with programmable self-assembly properties is an attractive route to functional nanomaterials. Proteins and peptides have been used extensively for these systems due to their biological relevance and large number of supramolecular motifs, but it is still difficult to build highly anisotropic and programmable nanostructures due to their high complexity. Oligonucleotides, by contrast, have the advantage of programmability and reliable assembly, but lack biological and chemical diversity. In this review, we discuss systems that merge protein or peptide self-assembly with the addressability of DNA. We outline the various self-assembly motifs used, the chemistry for linking polypeptides with DNA, and the resulting nanostructures that can be formed by the interplay of these two molecules. Finally, we close by suggesting some interesting future directions in hybrid polypeptide-DNA nanomaterials, and potential applications for these exciting hybrids.
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Affiliation(s)
- Julio Bernal-Chanchavac
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
| | - Md Al-Amin
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
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23
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Advances in the synthesis and application of self-assembling biomaterials. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:46-62. [PMID: 34329646 DOI: 10.1016/j.pbiomolbio.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 02/08/2023]
Abstract
The present study scrutinized some of the crucial advancements in the synthesis and functionalisation of self-assembling biomaterials for application in biomedicine. The basic concept of self-organization was discussed along with the mechanisms and methods involved in its implementation with biomaterials. Further, several recent applications of this technology in the biological and medical domain, and the avenues for future research and development were presented. This study brought to focus the vast potential of basic and applied research involved, especially in the context of hybrids and composites, as well as the difference in pace of new developments for different types of biomolecular materials. As nanobiotechnology matures, the tools and techniques available for developing and controlling self-assembled biomaterials as well as studying their interaction with biological tissue, will grow exponentially. Presently, self-assembly remains a potent tool for the synthesis of functional biomaterials.
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24
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McLoughlin NM, Kuepper A, Neubacher S, Grossmann TN. Synergistic DNA- and Protein-Based Recognition Promote an RNA-Templated Bio-orthogonal Reaction. Chemistry 2021; 27:10477-10483. [PMID: 33914384 PMCID: PMC8362040 DOI: 10.1002/chem.202101103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 12/28/2022]
Abstract
Biomolecular assemblies composed of proteins and oligonucleotides play a central role in biological processes. While in nature, oligonucleotides and proteins usually assemble via non-covalent interactions, synthetic conjugates have been developed which covalently link both modalities. The resulting peptide-oligonucleotide conjugates have facilitated novel biological applications as well as the design of functional supramolecular systems and materials. However, despite the importance of concerted protein/oligonucleotide recognition in nature, conjugation approaches have barely utilized the synergistic recognition abilities of such complexes. Herein, the structure-based design of peptide-DNA conjugates that bind RNA through Watson-Crick base pairing combined with peptide-mediated major groove recognition is reported. Two distinct conjugate families with tunable binding characteristics have been designed to adjacently bind a particular RNA sequence. In the resulting ternary complex, their peptide elements are located in proximity, a feature that was used to enable an RNA-templated click reaction. The introduced structure-based design approach opens the door to novel functional biomolecular assemblies.
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Affiliation(s)
- Niall M. McLoughlin
- Department of Chemistry and Pharmaceutical SciencesVrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck SocietyDortmund44227Germany
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical SciencesVrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical SciencesVrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
- Chemical Genomics Centre of the Max Planck SocietyDortmund44227Germany
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25
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Muramatsu W, Hattori T, Yamamoto H. Amide bond formation: beyond the dilemma between activation and racemisation. Chem Commun (Camb) 2021; 57:6346-6359. [PMID: 34121110 DOI: 10.1039/d1cc01795k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of methods for amide bond formation without recourse to typical condensation reagents has become an emerging research area and has been actively explored in the past quarter century. Inspired by the structure of vitamin B12, we have developed a metal-templated macrolactamisation that generates a new wave towards classical macrolactam synthesis. Further, distinct from the extensively used methods with condensation reagents or catalysts based on catalyst/reagent control our metal-catalysed methods based on substrate control can effectively address long-standing challenges such as racemisation in the field of peptide chemistry. In addition, the substrate-controlled strategy demonstrates the feasibility of "remote" peptide bond-forming reaction catalysed by a metal-ligand complex. Moreover, an originally designed hydrosilane/aminosilane system can avoid not only racemisation but also unnecessary waste production. This feature article documents our discovery and application of our original approaches in amide bond formation.
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Affiliation(s)
- Wataru Muramatsu
- Molecular Catalyst Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan.
| | - Tomohiro Hattori
- Molecular Catalyst Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan.
| | - Hisashi Yamamoto
- Molecular Catalyst Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan.
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26
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Giraud T, Bouguet-Bonnet S, Stébé MJ, Richaudeau L, Pickaert G, Averlant-Petit MC, Stefan L. Co-assembly and multicomponent hydrogel formation upon mixing nucleobase-containing peptides. NANOSCALE 2021; 13:10566-10578. [PMID: 34100504 DOI: 10.1039/d1nr02417e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peptide-based hydrogels are physical gels formed through specific supramolecular self-assembling processes, leading to ordered nanostructures which constitute the water entrapping scaffold of the soft material. Thanks to the inherent properties of peptides, these hydrogels are highly considered in the biomedical domain and open new horizons in terms of application in advanced therapies and biotechnologies. The use of one, and only one, native peptide to formulate a gel is by far the most reported approach to design such materials, but suffers from several limitations, including in terms of mechanical properties. To improve peptide-based hydrogels interest and give rise to innovative properties, several strategies have been proposed in the recent years, and the development of multicomponent peptide-based hydrogels appears as a promising and relevant strategy. Indeed, mixing two or more compounds to develop new materials is a much-used approach that has proven its effectiveness in a wide variety of domains, including polymers, composites and alloys. While still limited to a handful of examples, we would like to report herein on the formulation and the comprehensive study of multicomponent hybrid DNA-nucleobase/peptide-based hydrogels using a multiscale approach based on a large panel of analytical techniques (i.e., rheometry, proton relaxometry, SAXS, electronic microscopy, infrared, circular dichroism, fluorescence, Thioflavin T assays). Among the six multicomponent systems studied, the results highlight the synergistic role of the presence of the two complementary DNA-nucleobases (i.e., adenine/thymine and guanine/cytosine) on the co-assembling process from structural (e.g., morphology of the nanoobjects) to physicochemical (e.g., kinetics of formation, fluorescence properties) and mechanical (e.g., stiffness, resistance to external stress) properties. All the data confirm the relevance of the multicomponent peptide-based approach in the design of innovative hydrogels and bring another brick in the wall of the understanding of these complex and promising systems.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
| | | | | | | | | | | | - Loic Stefan
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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27
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Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
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Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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28
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Tan DJY, Cheong VV, Lim KW, Phan AT. A modular approach to enzymatic ligation of peptides and proteins with oligonucleotides. Chem Commun (Camb) 2021; 57:5507-5510. [PMID: 34036975 DOI: 10.1039/d1cc01348c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Joining peptides and oligonucleotides offers potential benefits, but current methods remain laborious. Here we present a novel approach towards enzymatic ligation of the two modalities through the development of tag phosphoramidites as adaptors that can be readily incorporated onto oligonucleotides. This simple and highly efficient approach paves the way towards streamlined development and production of peptide/protein-oligonucleotide conjugates.
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Affiliation(s)
- Derrick Jing Yang Tan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
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29
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Wang B, Pan R, Zhu W, Xu Y, Tian Y, Endo M, Sugiyama H, Yang Y, Qian X. Short intrinsically disordered polypeptide-oligonucleotide conjugates for programmed self-assembly of nanospheres with temperature-dependent size controllability. SOFT MATTER 2021; 17:1184-1188. [PMID: 33527954 DOI: 10.1039/d0sm01817a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A series of short intrinsically disordered polypeptide conjugated oligonucleotides (IDPOCs) were rationally developed and assembled into well-defined nanospheres. The nanospheres exhibited excellent reversible thermoresponsive regulation of their contraction and expansion. Furthermore, the nanospheres showed biocompatibility, drug encapsulation and effective cellular uptake.
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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.
| | - Rizhao Pan
- 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.
| | - Ye Tian
- College of Engineering and Applied Science, Nanjing University, Nanjing, 210093, China
| | - Masayuki Endo
- Department of Chemistry, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502, Kyoto, Japan
| | - 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. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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30
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Hivare P, Panda C, Gupta S, Bhatia D. Programmable DNA Nanodevices for Applications in Neuroscience. ACS Chem Neurosci 2021; 12:363-377. [PMID: 33433192 DOI: 10.1021/acschemneuro.0c00723] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The broad area of neuroscience has witnessed an increasing exploitation of a variety of synthetic biomaterials with controlled nanosized features. Different bionanomaterials offer very peculiar physicochemical and biochemcial properties contributing to the development of novel imaging devices toward imaging the brain, or as smartly functionalized scaffolds, or diverse tools contributing toward a better understanding of nervous tissue and its functions. DNA nanotechnology-based devices and scaffolds have emerged as ideal materials for cellular and tissue engineering due to their very biocompatible properties, robust adaptation with diverse biological systems, and biosafety in terms of reduced immune response triggering. Here we present technologies with respect to DNA nanodevices that are designed to better interact with nervous systems like neural cells, advanced molecular imaging technologies for imaging brain, biomaterials in neural regeneration, neuroprotection, and targeted delivery of drugs and small molecules across the blood-brain barrier. Along with comments regarding the progress of DNA nanotechnology in neuroscience, we also present a perspective on challenges and opportunities for applying DNA nanotechnology in applications pertaining to neurosciences.
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Affiliation(s)
- Pravin Hivare
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Chinmaya Panda
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Sharad Gupta
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Dhiraj Bhatia
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
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31
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Honcharenko D, Druceikaite K, Honcharenko M, Bollmark M, Tedebark U, Strömberg R. New Alkyne and Amine Linkers for Versatile Multiple Conjugation of Oligonucleotides. ACS OMEGA 2021; 6:579-593. [PMID: 33458510 PMCID: PMC7807750 DOI: 10.1021/acsomega.0c05075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/08/2020] [Indexed: 05/08/2023]
Abstract
Oligonucleotide (ON) conjugates are increasingly important tools for various molecular diagnostics, nanotechnological applications, and for the development of nucleic acid-based therapies. Multiple labeling of ONs can further equip ON-conjugates and provide improved or additional tailored properties. Typically, the preparation of ON multiconjugates involves additional synthetic steps and/or manipulations in post-ON assembly. This report describes the simplified methodology allowing for multiple labeling of ONs on a solid support and is compatible with phosphodiester as well as phosphorothioate (PS) ONs. The current approach utilizes two novel alkyne- and amino-functionalized linker phosphoramidites that can be readily synthesized from a common aminodiol intermediate in three steps. The combination of new linkers provides orthogonal functionalities, which allow for multiple attachments of similar or varied moieties. The linkers are incorporated into ONs during automated solid-phase ON synthesis, and the conjugation with functional entities is achieved by either amide bond formation or by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The versatility of the approach is demonstrated by the synthesis of 5'-site ON multiconjugates with small molecules, peptides, and fatty acids as well as in the preparation of an internal peptide-ON conjugate.
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Affiliation(s)
- Dmytro Honcharenko
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
| | - Kristina Druceikaite
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | | | - Martin Bollmark
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | - Ulf Tedebark
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | - Roger Strömberg
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
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32
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Chernikova EY, Berdnikova DV. Cucurbiturils in nucleic acids research. Chem Commun (Camb) 2020; 56:15360-15376. [PMID: 33206072 DOI: 10.1039/d0cc06583h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During the past ten years, the importance of cucurbiturils (CB[n]) as macrocyclic hosts in supramolecular assemblies with various types of natural and synthetic nucleic acids (NAs) has increased explosively. As a component of such systems, CB[n] macrocycles can play a wide spectrum of roles from drug and gene delivery vehicles to catalysts/inhibitors of biochemical reactions and even building blocks for NA-based materials. The aim of this highlight article is to describe the development of the CB[n] applications in nucleic acids research and to outline the current situation and perspectives of this fascinating synergistic combination of supramolecular chemistry of CB[n] and NAs.
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Affiliation(s)
- Ekaterina Y Chernikova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, Russia.
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Giraud T, Bouguet-Bonnet S, Marchal P, Pickaert G, Averlant-Petit MC, Stefan L. Improving and fine-tuning the properties of peptide-based hydrogels via incorporation of peptide nucleic acids. NANOSCALE 2020; 12:19905-19917. [PMID: 32985645 DOI: 10.1039/d0nr03483e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Peptide self-assemblies have attracted intense research interest over the last few decades thanks to their implications in key biological processes (e.g., amyloid formation) and their use in biotechnological and (bio)material fields. In particular, peptide-based hydrogels have been highly considered as high potential supramolecular materials in the biomedical domain and open new horizons in terms of applications. To further understand their self-assembly mechanisms and to optimize their properties, several strategies have been proposed with the modification of the constituting amino acid chains via, per se, the introduction of d-amino acids, halogenated amino acids, pseudopeptide bonds, or other chemical moieties. In this context, we report herein on the incorporation of DNA-nucleobases into their peptide nucleic acid (PNA) forms to develop a new series of hybrid nucleopeptides. Thus, depending on the nature of the nucleobase (i.e., thymine, cytosine, adenine or guanine), the physicochemical and mechanical properties of the resulting hydrogels can be significantly improved and fine-tuned with, for instance, drastic enhancements of both the gel stiffness (up to 70-fold) and the gel resistance to external stress (up to 40-fold), and the generation of both thermo-reversible and uncommon red-edge excitation shift (REES) properties. To decipher the actual role of each PNA moiety in the self-assembly processes, the induced modifications from the molecular to the macroscopic scales are studied thanks to the multiscale approach based on a large panel of analytical techniques (i.e., rheology, NMR relaxometry, TEM, thioflavin T assays, FTIR, CD, fluorescence, NMR chemical shift index). Thus, such a strategy provides new opportunities to adapt and fit hydrogel properties to the intended ones and pushes back the limits of supramolecular materials.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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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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Abstract
Abstract
Site-specific protein conjugation is a critical step in the generation of unique protein analogs for a range of basic research and therapeutic developments. Protein transformations must target a precise residue in the presence of a plethora of functional groups to obtain a well-characterized homogeneous product. Competing reactive residues on natural proteins render rapid and selective conjugation a challenging task. Organometallic reagents have recently emerged as a powerful strategy to achieve site-specific labeling of a diverse set of biopolymers, due to advances in water-soluble ligand design, high reaction rate, and selectivity. The thiophilic nature of various transition metals, especially soft metals, makes cysteine an ideal target for these reagents. The distinctive reactivity and selectivity of organometallic-based reactions, along with the unique reactivity and abundancy of cysteine within the human proteome, provide a powerful platform to modify native proteins in aqueous media. These reactions often provide the modified proteins with a stable linkage made from irreversible cross-coupling steps. Additionally, transition metal reagents have recently been applied for the decaging of cysteine residues in the context of chemical protein synthesis. Orthogonal cysteine protecting groups and functional tags are often necessary for the synthesis of challenging proteins, and organometallic reagents are powerful tools for selective, rapid, and water-compatible removal of those moieties. This review examines transition metal-based reactions of cysteine residues for the synthesis and modification of natural peptides and proteins.
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Affiliation(s)
- Muhammad Jbara
- Massachusetts Institute of Technology , Department of Chemistry , 77 Massachusetts Avenue , Cambridge , MA , 02139, USA
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36
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Ni M, Tresset G, Iliescu C, Hauser CAE. Ultrashort Peptide Theranostic Nanoparticles by Microfluidic-Assisted Rapid Solvent Exchange. IEEE Trans Nanobioscience 2020; 19:627-632. [PMID: 32746332 DOI: 10.1109/tnb.2020.3007103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ultrashort peptides (USPs), composed of three to seven amino acids, can self-assemble into nanofibers in pure water. Here, using hydrodynamic focusing and a solvent exchange method on a microfluidic setup, we convert these nanofibers into globular nanoparticles with excellent dimensional control and polydispersity. Thanks to USP nanocarriers' structure, different drugs can be loaded. We used Curcumin as a model drug to evaluate the performance of USP nanocarriers as a novel drug delivery vehicle. These nanoparticles can efficiently cross the cell membrane and possess nonlinear optical properties. Therefore, we envisage USP nanoparticles as promising future theranostic nanocarriers.
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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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38
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Lombardo D, Calandra P, Pasqua L, Magazù S. Self-assembly of Organic Nanomaterials and Biomaterials: The Bottom-Up Approach for Functional Nanostructures Formation and Advanced Applications. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E1048. [PMID: 32110877 PMCID: PMC7084717 DOI: 10.3390/ma13051048] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 12/11/2022]
Abstract
In this paper, we survey recent advances in the self-assembly processes of novel functional platforms for nanomaterials and biomaterials applications. We provide an organized overview, by analyzing the main factors that influence the formation of organic nanostructured systems, while putting into evidence the main challenges, limitations and emerging approaches in the various fields of nanotechology and biotechnology. We outline how the building blocks properties, the mutual and cooperative interactions, as well as the initial spatial configuration (and environment conditions) play a fundamental role in the construction of efficient nanostructured materials with desired functional properties. The insertion of functional endgroups (such as polymers, peptides or DNA) within the nanostructured units has enormously increased the complexity of morphologies and functions that can be designed in the fabrication of bio-inspired materials capable of mimicking biological activity. However, unwanted or uncontrollable effects originating from unexpected thermodynamic perturbations or complex cooperative interactions interfere at the molecular level with the designed assembly process. Correction and harmonization of unwanted processes is one of the major challenges of the next decades and requires a deeper knowledge and understanding of the key factors that drive the formation of nanomaterials. Self-assembly of nanomaterials still remains a central topic of current research located at the interface between material science and engineering, biotechnology and nanomedicine, and it will continue to stimulate the renewed interest of biologist, physicists and materials engineers by combining the principles of molecular self-assembly with the concept of supramolecular chemistry.
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Affiliation(s)
- Domenico Lombardo
- Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici, 98158 Messina, Italy
| | - Pietro Calandra
- Consiglio Nazionale delle Ricerche, Istituto Studio Materiali Nanostrutturati, 00015 Roma, Italy;
| | - Luigi Pasqua
- Department of Environmental and Chemical Engineering, University of Calabria, 87036 Rende, Italy;
| | - Salvatore Magazù
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, 98166 Messina, Italy;
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40
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Abd-Elsalam KA. Multifunctional hybrid nanomaterials for sustainable agri-food and ecosystems: A note from the editor. MULTIFUNCTIONAL HYBRID NANOMATERIALS FOR SUSTAINABLE AGRI-FOOD AND ECOSYSTEMS 2020:1-19. [DOI: 10.1016/b978-0-12-821354-4.00001-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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41
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Meschaninova MI, Novopashina DS, Semikolenova OA, Silnikov VN, Venyaminova AG. Novel Convenient Approach to the Solid-Phase Synthesis of Oligonucleotide Conjugates. Molecules 2019; 24:E4266. [PMID: 31771111 PMCID: PMC6930482 DOI: 10.3390/molecules24234266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/03/2023] Open
Abstract
A novel and convenient approach for the solid-phase 5'-functionalization of oligonucleotides is proposed in this article. The approach is based on the activation of free 5'-hydroxyl of polymer support-bound protected oligonucleotides by N,N'-disuccinimidyl carbonate followed by interaction with amino-containing ligands. Novel amino-containing derivatives of closo-dodecaborate, estrone, cholesterol, and α-tocopherol were specially prepared. A wide range of oligonucleotide conjugates bearing closo-dodecaborate, short peptide, pyrene, lipophilic residues (cholesterol, α-tocopherol, folate, estrone), aliphatic diamines, and propargylamine were synthesized and characterized to demonstrate the versatility of the approach. The developed method is suitable for the conjugate synthesis of oligonucleotides of different types (ribo-, deoxyribo-, 2'-O-methylribo-, and others).
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Affiliation(s)
- Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Olga A. Semikolenova
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
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Dovgan I, Koniev O, Kolodych S, Wagner A. Antibody-Oligonucleotide Conjugates as Therapeutic, Imaging, and Detection Agents. Bioconjug Chem 2019; 30:2483-2501. [PMID: 31339691 DOI: 10.1021/acs.bioconjchem.9b00306] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibody-oligonucleotide conjugates (AOCs) are a novel class of synthetic chimeric biomolecules that has been continually gaining traction in different fields of modern biotechnology. This is mainly due to the unique combination of the properties of their two constituents, exceptional targeting abilities and antibody biodistribution profiles, in addition to an extensive scope of oligonucleotide functional and structural roles. Combining these two classes of biomolecules in one chimeric construct has therefore become an important milestone in the development of numerous biotechnological applications, including imaging (DNA-PAINT), detection (PLA, PEA), and therapeutics (targeted siRNA/antisense delivery). Numerous synthetic approaches have been developed to access AOCs ranging from stochastic chemical bioconjugation to site-specific conjugation with reactive handles, introduced into antibody sequences through protein engineering. This Review gives a general overview of the current status of AOC applications with a specific emphasis on the synthetic methods used for their preparation. The reported synthetic techniques are discussed in terms of their practical aspects and limitations. The importance of the development of novel methods for the facile generation of AOCs possessing a defined constitution is highlighted as a priority in AOC research to ensure the advance of their new applications.
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Affiliation(s)
- Igor Dovgan
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis , University of Strasbourg , 74 Route du Rhin , 67400 Illkirch-Graffenstaden , France
| | - Oleksandr Koniev
- Syndivia SAS , 650 Boulevard Gonthier d'Andernach , 67400 Illkirch-Graffenstaden , France
| | - Sergii Kolodych
- Syndivia SAS , 650 Boulevard Gonthier d'Andernach , 67400 Illkirch-Graffenstaden , France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis , University of Strasbourg , 74 Route du Rhin , 67400 Illkirch-Graffenstaden , France
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43
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Stephanopoulos N. Peptide-Oligonucleotide Hybrid Molecules for Bioactive Nanomaterials. Bioconjug Chem 2019; 30:1915-1922. [PMID: 31082220 DOI: 10.1021/acs.bioconjchem.9b00259] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peptides and oligonucleotides are two of the most interesting molecular platforms for making bioactive materials. Peptides provide bioactivity that can mimic that of proteins, whereas oligonucleotides like DNA can be used as scaffolds to immobilize other molecules with nanoscale precision. In this Topical Review, we discuss covalent conjugates of peptides and DNA for creating bioactive materials that can interface with cells. In particular, we focus on two areas. The first is multivalent presentation of peptides on a DNA scaffold, both linear assemblies and more complex nanostructures. The second is the reversible tuning of the extracellular environment-like ligand presentation, stiffness, and hierarchical morphology-in peptide-DNA biomaterials. These examples highlight the potential for creating highly potent materials with benefits not possible with either molecule alone, and we outline a number of future directions and applications for peptide-DNA conjugates.
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Abstract
Template assistance allows organic reactions to occur under highly dilute conditions-where intermolecular reactions often fail to proceed-by bringing reactants into close spatial proximity. This strategy has been elegantly applied to numerous systems, but always with the retention of at least one of the templating groups in the product. In this report, we describe a traceless, templated amide-forming ligation that proceeds at low micromolar concentration under aqueous conditions in the presence of biomolecules. We utilized the unique features of an acylboronate-hydroxylamine ligation, in which covalent bonds are broken in each of the reactants as the new amide bond is formed. By using streptavidin as a template and acylboronates and O-acylhydroxylamines bearing desthiobiotins that are cleaved upon amide formation, we demonstrate that traceless, templated ligation occurs rapidly even at submicromolar concentrations. The requirement for a close spatial orientation of the functional groups-achieved upon binding to streptavidin-is critical for the observed enhancement in the rate and quantity of product formed.
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Affiliation(s)
- Alberto Osuna Gálvez
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
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