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Kim JE, Kang JH, Kwon WH, Lee I, Park SJ, Kim CH, Jeong WJ, Choi JS, Kim K. Self-assembling biomolecules for biosensor applications. Biomater Res 2023; 27:127. [PMID: 38053161 PMCID: PMC10696764 DOI: 10.1186/s40824-023-00466-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Abstract
Molecular self-assembly has received considerable attention in biomedical fields as a simple and effective method for developing biomolecular nanostructures. Self-assembled nanostructures can exhibit high binding affinity and selectivity by displaying multiple ligands/receptors on their surface. In addition, the use of supramolecular structure change upon binding is an intriguing approach to generate binding signal. Therefore, many self-assembled nanostructure-based biosensors have been developed over the past decades, using various biomolecules (e.g., peptides, DNA, RNA, lipids) and their combinations with non-biological substances. In this review, we provide an overview of recent developments in the design and fabrication of self-assembling biomolecules for biosensing. Furthermore, we discuss representative electrochemical biosensing platforms which convert the biochemical reactions of those biomolecules into electrical signals (e.g., voltage, ampere, potential difference, impedance) to contribute to detect targets. This paper also highlights the successful outcomes of self-assembling biomolecules in biosensor applications and discusses the challenges that this promising technology needs to overcome for more widespread use.
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Affiliation(s)
- Ji-Eun Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea
| | - Jeon Hyeong Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Woo Hyun Kwon
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Inseo Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Sang Jun Park
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Chun-Ho Kim
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Woo-Jin Jeong
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
- Department of Biological Engineering, Inha University, Incheon, 22212, Republic of Korea.
| | - Jun Shik Choi
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea.
| | - Kyobum Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea.
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Adedeji Olulana AF, Choi D, Inverso V, Redhu SK, Vidonis M, Crevatin L, Nicholson AW, Castronovo M. Noncanonical DNA Cleavage by BamHI Endonuclease in Laterally Confined DNA Monolayers Is a Step Function of DNA Density and Sequence. Molecules 2022; 27:5262. [PMID: 36014501 PMCID: PMC9416302 DOI: 10.3390/molecules27165262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Cleavage of DNA at noncanonical recognition sequences by restriction endonucleases (star activity) in bulk solution can be promoted by global experimental parameters, including enzyme or substrate concentration, temperature, pH, or buffer composition. To study the effect of nanoscale confinement on the noncanonical behaviour of BamHI, which cleaves a single unique sequence of 6 bp, we used AFM nanografting to generate laterally confined DNA monolayers (LCDM) at different densities, either in the form of small patches, several microns in width, or complete monolayers of thiol-modified DNA on a gold surface. We focused on two 44-bp DNAs, each containing a noncanonical BamHI site differing by 2 bp from the cognate recognition sequence. Topographic AFM imaging was used to monitor end-point reactions by measuring the decrease in the LCDM height with respect to the surrounding reference surface. At low DNA densities, BamHI efficiently cleaves only its cognate sequence while at intermediate DNA densities, noncanonical sequence cleavage occurs, and can be controlled in a stepwise (on/off) fashion by varying the DNA density and restriction site sequence. This study shows that endonuclease action on noncanonical sites in confined nanoarchitectures can be modulated by varying local physical parameters, independent of global chemical parameters.
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Affiliation(s)
- Abimbola F. Adedeji Olulana
- Department of Physics, PhD School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Regional Centre for Rare Diseases, University Hospital Udine, 33100 Udine, Italy
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Dianne Choi
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Vincent Inverso
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Shiv K. Redhu
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Marco Vidonis
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Department of Chemistry, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Luca Crevatin
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Allen W. Nicholson
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Matteo Castronovo
- Department of Physics, PhD School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Regional Centre for Rare Diseases, University Hospital Udine, 33100 Udine, Italy
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
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Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors. Int J Mol Sci 2021; 22:ijms22020812. [PMID: 33467468 PMCID: PMC7831021 DOI: 10.3390/ijms22020812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/17/2022] Open
Abstract
The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA-peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide's spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface-liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.
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Nicholson AW. Ribonuclease III mechanisms of double-stranded RNA cleavage. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:31-48. [PMID: 24124076 PMCID: PMC3867540 DOI: 10.1002/wrna.1195] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/09/2013] [Accepted: 08/10/2013] [Indexed: 12/22/2022]
Abstract
Double-stranded(ds) RNA has diverse roles in gene expression and regulation, host defense, and genome surveillance in bacterial and eukaryotic cells. A central aspect of dsRNA function is its selective recognition and cleavage by members of the ribonuclease III (RNase III) family of divalent-metal-ion-dependent phosphodiesterases. The processing of dsRNA by RNase III family members is an essential step in the maturation and decay of coding and noncoding RNAs, including miRNAs and siRNAs. RNase III, as first purified from Escherichia coli, has served as a biochemically well-characterized prototype, and other bacterial orthologs provided the first structural information. RNase III family members share a unique fold (RNase III domain) that can dimerize to form a structure that binds dsRNA and cleaves phosphodiesters on each strand, providing the characteristic 2 nt, 3′-overhang product ends. Ongoing studies are uncovering the functions of additional domains, including, inter alia, the dsRNA-binding and PAZ domains that cooperate with the RNase III domain to select target sites, regulate activity, confer processivity, and support the recognition of structurally diverse substrates. RNase III enzymes function in multicomponent assemblies that are regulated by diverse inputs, and at least one RNase III-related polypeptide can function as a noncatalytic, dsRNA-binding protein. This review summarizes the current knowledge of the mechanisms of catalysis and target site selection of RNase III family members, and also addresses less well understood aspects of these enzymes and their interactions with dsRNA. WIREs RNA 2014, 5:31–48. doi: 10.1002/wrna.1195
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Affiliation(s)
- Allen W Nicholson
- Department of Biology and Chemistry, College of Science & Technology, Temple University, Philadelphia, PA, USA
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