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Su M, Yang S, Xu M, Du S, Zheng L, Wang X, Qu C, Liu H. Intrinsic SERS Fingerprints of Aptamer-Peptide Conjugates for Direct High-Specific Profiling Abnormal Protein Levels in Cancer Patients. Anal Chem 2023; 95:12398-12405. [PMID: 37559187 DOI: 10.1021/acs.analchem.3c01988] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) with ultrasensitive vibrational fingerprints enables quick identification and trace detection of various kinds of molecules. But proteins usually have low Raman cross sections and are difficult to generate recognizable signals in direct SERS detection. Recently, nucleic acid-peptide conjugates are emerging with great potential in structuring, assembling, catalyzing, sensing, etc., and the coupling of aptamers further enables superior biological recognition and programmability. Here, we develop the aptamer-peptide conjugates as a new kind of SERS probe for direct high-specific profiling abnormal protein levels in cancer patients. The aptamer conjugated with glutathione (GSH) functions as both the recognition element and the SERS reporters that can simultaneously generate SERS fingerprints of both peptides and nucleic acids. This kind of biocompatible probe appears to have excellent performance in high-salt environments and realizes rapid, simple, and multisignal detection of thrombin (TB). Data-driven soft independent modeling of class analogy (DD-SIMCA) is used to distinguish SERS profiles of actual blood samples and realize the identification and classification of cancer patients. Furthermore, the effect of low-temperature storage time on blood samples is analyzed by tracking the changes of SERS profiles; the results hint that plasma samples stored under 4 °C for more than 2 days could generate false negative results due to TB hydrolysis, which has important implications for clinical sample analysis. This kind of nucleic acid-peptide conjugate provides new ideas for SERS sensing strategy in the future.
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Affiliation(s)
- Mengke Su
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China
| | - Shixuan Yang
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
| | - Min Xu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
| | - Shanshan Du
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
| | - Liqin Zheng
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
| | - Xian Wang
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
| | - Cheng Qu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
| | - Honglin Liu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
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2
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Grelska J, Jurkiewicz K, Nowok A, Pawlus S. Computer simulations as an effective way to distinguish supramolecular nanostructure in cyclic and phenyl alcohols. Phys Rev E 2023; 108:024603. [PMID: 37723707 DOI: 10.1103/physreve.108.024603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 07/02/2023] [Indexed: 09/20/2023]
Abstract
Molecular dynamics simulations supported by x-ray-diffraction experimental data were utilized to demonstrate how replacing the cyclic ring with the phenyl one in molecules of alcohols significantly differentiates their nanostructure by reducing the number of H-bonded clusters. Besides, molecules in the phenyl alcohols associate themselves in clusters via phenyl ring organization which likely is the result of OH⋯π and π⋯π interactions. Thus, at room temperature, the supramolecular structure of phenyl alcohols is more heterogeneous and governed by the formation of various clusters arising due to three types of interactions, while in cyclic alcohols, the H bonding controls the association of molecules. We believe that our methodology could be applied to better understand the fundamental process of association via H bonding and the competitive aggregation caused by phenyl rings.
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Affiliation(s)
- Joanna Grelska
- A. Chełkowski Institute of Physics, University of Silesia in Katowice, 75 Pułku Piechoty 1, 41-500 Chorzów, Poland
| | - Karolina Jurkiewicz
- A. Chełkowski Institute of Physics, University of Silesia in Katowice, 75 Pułku Piechoty 1, 41-500 Chorzów, Poland
| | - Andrzej Nowok
- Department of Experimental Physics, Wrocław University of Science and Technology, Wybrzeże Stanisława Wyspiańskiego 27, 50-370 Wrocław, Poland
- Laboratoire National des Champs Magnétiques Intenses, UPR 3228, CNRS-UGA-UPS-INSA, Grenoble and Toulouse, France
| | - Sebastian Pawlus
- A. Chełkowski Institute of Physics, University of Silesia in Katowice, 75 Pułku Piechoty 1, 41-500 Chorzów, Poland
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3
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Brown TM, Fakih HH, Saliba D, Asohan J, Sleiman HF. Stabilization of Functional DNA Structures with Mild Photochemical Methods. J Am Chem Soc 2023; 145:2142-2151. [PMID: 36651186 DOI: 10.1021/jacs.2c08808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A significant barrier to biological applications of DNA structures is their instability to nucleases. UV-mediated thymine dimerization can crosslink and stabilize DNA nanostructures, but its effect on DNA strand hybridization fidelity and function is unclear. In this work, we first compare a number of methods for DNA irradiation with different wavelengths of light and different photosensitizers. We demonstrate that all approaches can achieve nuclease protection; however, the levels of DNA off-target crosslinking and damage vary. We then describe mild irradiation conditions intended to safeguard DNA against nuclease degradation. We demonstrate up to 25× increase in serum stability while minimizing off-target damage and maintaining functions such as hybridization efficiency, gene silencing, aptamer binding, and DNA nanostructure formation. Our methodology requires no complex instruments beyond a UV light source and no synthetic modification of the DNA itself, allowing for applications in numerous areas of nucleic acid therapy and nanotechnology.
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Affiliation(s)
- Tyler M Brown
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
| | - Hassan H Fakih
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
| | - Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
| | - Jathavan Asohan
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
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4
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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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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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6
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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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7
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Ariga K. Biomimetic and Biological Nanoarchitectonics. Int J Mol Sci 2022; 23:3577. [PMID: 35408937 PMCID: PMC8998553 DOI: 10.3390/ijms23073577] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
A post-nanotechnology concept has been assigned to an emerging concept, nanoarchitectonics. Nanoarchitectonics aims to establish a discipline in which functional materials are fabricated from nano-scale components such as atoms, molecules, and nanomaterials using various techniques. Nanoarchitectonics opens ways to form a more unified paradigm by integrating nanotechnology with organic chemistry, supramolecular chemistry, material chemistry, microfabrication technology, and biotechnology. On the other hand, biological systems consist of rational organization of constituent molecules. Their structures have highly asymmetric and hierarchical features that allow for chained functional coordination, signal amplification, and vector-like energy and signal flow. The process of nanoarchitectonics is based on the premise of combining several different processes, which makes it easier to obtain a hierarchical structure. Therefore, nanoarchitectonics is a more suitable methodology for creating highly functional systems based on structural asymmetry and hierarchy like biosystems. The creation of functional materials by nanoarchitectonics is somewhat similar to the creation of functional systems in biological systems. It can be said that the goal of nanoarchitectonics is to create highly functional systems similar to those found in biological systems. This review article summarizes the synthesis of biomimetic and biological molecules and their functional structure formation from various viewpoints, from the molecular level to the cellular level. Several recent examples are arranged and categorized to illustrate such a trend with sections of (i) synthetic nanoarchitectonics for bio-related units, (ii) self-assembly nanoarchitectonics with bio-related units, (iii) nanoarchitectonics with nucleic acids, (iv) nanoarchitectonics with peptides, (v) nanoarchitectonics with proteins, and (vi) bio-related nanoarchitectonics in conjugation with materials.
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Affiliation(s)
- Katsuhiko Ariga
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan;
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
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8
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Rajak A, Das A. Programmed Macromolecular Assembly by Dipole-Dipole Interactions with Aggregation-Induced Enhanced Emission in Aqueous Medium. ACS POLYMERS AU 2022; 2:223-231. [PMID: 36855564 PMCID: PMC9954255 DOI: 10.1021/acspolymersau.1c00054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-assembling polymers by bioinspired directional supramolecular interactions currently hold great scientific and technological interests. Herein, we report an unorthodox strategy based on a dipole-dipole interaction-mediated extended antiparallel dipolar assembly of a model merocyanine (MC) dye for maneuvering the self-assembly of a highly water-soluble MC-functionalized block copolymer (P2). Unlike traditional amphiphilic block copolymers featuring distinct hydrophobic segments (flexible aliphatic hydrocarbon chains or rigid nonpolar aromatic scaffolds), P2 comprises polyethylene glycol monomethyl ether (PEG) as a hydrophilic block and an unconventional structure-directing acrylate block functionalized with polar MC-dyes in the side chains of every repeat unit. In the absence of any additional hydrophobic assistance, P2 spontaneously self-assembles in water through the continuous opposite alignment of its pendant MCs by multiple dipole-dipole interactions to cancel out their ground state dipole moments, which initially generates an H-aggregated species with ill-defined morphology (Aggregate 1). Upon thermal annealing, Aggregate 1 reorganizes into higher-order core-shell nanodisc-like structures (Aggregate 2) driven by the orthogonal π-stacking interactions of the rigid aromatic framework derived from the extended cofacial MC-stacks. The aromatic interiors of the nanodiscs gain colloidal stability from the externally decorated hydrophilic PEG chains. While the initially formed Aggregate 1, predominantly by dipole-dipole interactions, showed remarkable thermal stability due to the cooperative effect of the polymer chain, the hierarchical assembly guided by relatively weaker dispersion forces of the MC-stacked π-surfaces could be tailored by dilution or thermal treatment. Such organized packing of pendant MCs by the dual effect of dipole-dipole interactions and π-stacking conferred several exciting properties to the P2 assembly in water. Long-range ordered antiparallel stacking of the pendant MCs rendered outstanding aggregation-induced enhanced emission (AIEE) properties to the resultant nanostructures in water with increased fluorescence lifetime, quantum yield, and Stokes shift compared to nonaggregating P2 in CHCl3. The remarkable thermal and kinetic stability of the nanodiscs, their guest loading ability, and very low critical aggregation concentration (CAC) were demonstrated by Förster resonance energy transfer (FRET) studies with an encapsulated donor-acceptor dye pair.
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Rozhin P, Charitidis C, Marchesan S. Self-Assembling Peptides and Carbon Nanomaterials Join Forces for Innovative Biomedical Applications. Molecules 2021; 26:4084. [PMID: 34279424 PMCID: PMC8271590 DOI: 10.3390/molecules26134084] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023] Open
Abstract
Self-assembling peptides and carbon nanomaterials have attracted great interest for their respective potential to bring innovation in the biomedical field. Combination of these two types of building blocks is not trivial in light of their very different physico-chemical properties, yet great progress has been made over the years at the interface between these two research areas. This concise review will analyze the latest developments at the forefront of research that combines self-assembling peptides with carbon nanostructures for biological use. Applications span from tissue regeneration, to biosensing and imaging, and bioelectronics.
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Affiliation(s)
- Petr Rozhin
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy;
| | - Costas Charitidis
- School of Chemical Engineering, National Technical University of Athens, Iroon Polytechneiou 9, Zografou, 157 80 Athens, Greece;
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy;
- INSTM, Unit of Trieste, 34127 Trieste, Italy
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