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Muslihati A, Septiani NLW, Gumilar G, Nugraha N, Wasisto HS, Yuliarto B. Peptide-Based Flavivirus Biosensors: From Cell Structure to Virological and Serological Detection Methods. ACS Biomater Sci Eng 2024; 10:2041-2061. [PMID: 38526408 DOI: 10.1021/acsbiomaterials.3c01965] [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] [Indexed: 03/26/2024]
Abstract
In tropical and developing countries, mosquito-borne diseases by flaviviruses pose a serious threat to public health. Early detection is critical for preventing their spread, but conventional methods are time-consuming and require skilled technicians. Biosensors have been developed to address this issue, but cross-reactivity with other flaviviruses remains a challenge. Peptides are essentially biomaterials used in diagnostics that allow virological and serological techniques to identify flavivirus selectively. This biomaterial originated as a small protein consisting of two to 50 amino acid chains. They offer flexibility in chemical modification and can be easily synthesized and applied to living cells in the engineering process. Peptides could potentially be developed as robust, low-cost, sensitive, and selective receptors for detecting flaviviruses. However, modification and selection of the receptor agents are crucial to determine the effectiveness of binding between the targets and the receptors. This paper addresses two potential peptide nucleic acids (PNAs) and affinity peptides that can detect flavivirus from another target-based biosensor as well as the potential peptide behaviors of flaviviruses. The PNAs detect flaviviruses based on the nucleotide base sequence of the target's virological profile via Watson-Crick base pairing, while the affinity peptides sense the epitope or immunological profile of the targets. Recent developments in the functionalization of peptides for flavivirus biosensors are explored in this Review by division into electrochemical, optical, and other detection methods.
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Affiliation(s)
- Atqiya Muslihati
- Doctoral Program of Engineering Physics, Faculty of Industrial Technology, Institut Teknologi Bandung, Ganesha 10, Bandung 40132, Indonesia
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- PT Biostark Analitika Inovasi, Bandung 40375, Indonesia
| | - Ni Luh Wulan Septiani
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanotechnology Systems, National Research and Innovation Agency (BRIN), Kawasan Puspiptek, South Tangerang 15134, Indonesia
| | - Gilang Gumilar
- Research Center for Electronics, National Research and Innovation Agency (BRIN), Bandung 40135, Indonesia
| | - Nugraha Nugraha
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanosciences and Nanotechnology (RCNN), Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
| | | | - Brian Yuliarto
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanosciences and Nanotechnology (RCNN), Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
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Sarkar S. Recent advancements in bionanomaterial applications of peptide nucleic acid assemblies. Biopolymers 2024; 115:e23567. [PMID: 37792292 DOI: 10.1002/bip.23567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/02/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
Peptide nucleic acid (PNA) is a unique combination of peptides and nucleic acids. PNA can exhibit hydrogen bonding interactions with complementary nucleobases like DNA/RNA. Also, its polyamide backbone allows easy incorporation of biomolecules like peptides and proteins to build hybrid molecular constructs. Because of chimeric structural properties, PNA has lots of potential to build diverse nanostructures. However, progress in the PNA material field is still immature compared with its massive applications in antisense oligonucleotide research. Examples of well-defined molecular assemblies have been reported with PNA amphiphiles, self-assembling guanine-PNA monomers/dimers, and PNA-decorated nucleic acids/ polymers/ peptides. All these works indicate the great potential of PNA to be used as bionanomaterials. The review summarizes the recent reports on PNA-based nanostructures and their versatile applications. Additionally, this review shares a perspective to promote a better understanding of controlling molecular assembly by the systematic structural modifications of PNA monomers.
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Affiliation(s)
- Srijani Sarkar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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Liu C, Guan C, Li Y, Li Z, Wang Y, Han G. Advances in Electrochemical Biosensors for the Detection of Common Oral Diseases. Crit Rev Anal Chem 2024:1-21. [PMID: 38366356 DOI: 10.1080/10408347.2024.2315112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
Limiting and preventing oral diseases remains a major challenge to the health of populations around the world, so finding ways to detect early-stage diseases (e.g., caries, periodontal disease, and oral cancer) and aiding in their prevention has always been an important clinical treatment concept. The development and application of electrochemical detection technology can provide important support for the early detection and non-invasive diagnosis of oral diseases and make up for the shortcomings of traditional diagnostic methods, which are highly sensitive, non-invasive, cost-effective, and less labor-intensive. It detects specific disease markers in body fluids through electrochemical reactions, discovers early warning signals of diseases, and realizes rapid and reliable diagnosis. This paper comprehensively summarizes the development and application of electrochemical biosensors in the detection and diagnosis of common oral diseases in terms of application platforms, sensing types, and disease detection, and discusses the challenges faced by electrochemical biosensors in the detection of oral diseases as well as the great prospects for future applications, in the hope of providing important insights for the future development of electrochemical biosensors for the early detection of oral diseases.
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Affiliation(s)
- Chaoran Liu
- Department of Oral Geriatrics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Changjun Guan
- School of Electrical and Electronic Engineering, Changchun University of Technology, Changchun, China
| | - Yanan Li
- Department of Oral Geriatrics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Ze Li
- Department of Oral Geriatrics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Yanchun Wang
- Department of Oral Geriatrics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Guanghong Han
- Department of Oral Geriatrics, Hospital of Stomatology, Jilin University, Changchun, China
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Sakar S, Anderson CF, Schneider JP. The Design of a Participatory Peptide Nucleic Acid Duplex Crosslinker to Enhance the Stiffness of Self-Assembled Peptide Gels. Angew Chem Int Ed Engl 2024; 63:e202313507. [PMID: 38057633 PMCID: PMC10872331 DOI: 10.1002/anie.202313507] [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: 09/11/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/08/2023]
Abstract
Herein, peptide nucleic acids (PNAs) are employed in the design of a participatory duplex PNA-peptide crosslinking agent. Biophysical and mechanical studies show that crosslinkers present during peptide assembly leading to hydrogelation participate in the formation of fibrils while simultaneously installing crosslinks into the higher-order network that constitutes the peptide gel. The addition of 2 mol % crosslinker into the assembling system results in a ~100 % increase in mechanical stiffness without affecting the rate of peptide assembly or the local morphology of fibrils within the gel network. Stiffness enhancement is realized by only affecting change in the elastic component of the viscoelastic gel. A synthesis of the PNA-peptide duplex crosslinkers is provided that allows facile variation in peptide composition and addresses the notorious hydrophobic content of PNAs. This crosslinking system represents a new tool for modulating the mechanical properties of peptide-based hydrogels.
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Affiliation(s)
- Srijani Sakar
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD 21702, USA
| | - Caleb F Anderson
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD 21702, USA
| | - Joel P Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD 21702, USA
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Lomae A, Preechakasedkit P, Hanpanich O, Ozer T, Henry CS, Maruyama A, Pasomsub E, Phuphuakrat A, Rengpipat S, Vilaivan T, Chailapakul O, Ruecha N, Ngamrojanavanich N. Label free electrochemical DNA biosensor for COVID-19 diagnosis. Talanta 2023; 253:123992. [PMID: 36228554 PMCID: PMC9546783 DOI: 10.1016/j.talanta.2022.123992] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/31/2022] [Accepted: 10/02/2022] [Indexed: 11/07/2022]
Abstract
The COVID-19 pandemic has significantly increased the development of the development of point-of-care (POC) diagnostic tools because they can serve as useful tools for detecting and controlling spread of the disease. Most current methods require sophisticated laboratory instruments and specialists to provide reliable, cost-effective, specific, and sensitive POC testing for COVID-19 diagnosis. Here, a smartphone-assisted Sensit Smart potentiostat (PalmSens) was integrated with a paper-based electrochemical sensor to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A disposable paper-based device was fabricated, and the working electrode directly modified with a pyrrolidinyl peptide nucleic acid (acpcPNA) as the biological recognition element to capture the target complementary DNA (cDNA). In the presence of the target cDNA, hybridization with acpcPNA probe blocks the redox conversion of a redox reporter, leading to a decrease in electrochemical response correlating to SARS-CoV-2 concentration. Under optimal conditions, a linear range from 0.1 to 200 nM and a detection limit of 1.0 pM were obtained. The PNA-based electrochemical paper-based analytical device (PNA-based ePAD) offers high specificity toward SARS-CoV-2 N gene because of the highly selective PNA-DNA binding. The developed sensor was used for amplification-free SARS-CoV-2 detection in 10 nasopharyngeal swab samples (7 SARS-CoV-2 positive and 3 SARS-CoV-2 negative), giving a 100% agreement result with RT-PCR.
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Affiliation(s)
- Atchara Lomae
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Pattarachaya Preechakasedkit
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12 Phayathai Rd., Pathumwan, Bangkok, 10330, Thailand
| | - Orakan Hanpanich
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Tugba Ozer
- Department of Bioengineering, Faculty of Chemical-Metallurgical Engineering, Yildiz Technical University, 34220, Istanbul, Turkey
| | - Charles S. Henry
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12 Phayathai Rd., Pathumwan, Bangkok, 10330, Thailand,Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sirirat Rengpipat
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand,Qualified Diagnostic Development Center, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Orawon Chailapakul
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Nipapan Ruecha
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand,Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12 Phayathai Rd., Pathumwan, Bangkok, 10330, Thailand,Corresponding author. Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12 Phayathai Rd., Pathumwan, Bangkok, 10330, Thailand
| | - Nattaya Ngamrojanavanich
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand,Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, 10330, Thailand,Corresponding author. Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, 10330, Thailand
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Yokoi Y, Kawabuchi Y, Zulmajdi AA, Tanaka R, Shibata T, Muraoka T, Mori T. Cell-Penetrating Peptide-Peptide Nucleic Acid Conjugates as a Tool for Protein Functional Elucidation in the Native Bacterium. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248944. [PMID: 36558072 PMCID: PMC9788395 DOI: 10.3390/molecules27248944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Approximately 30% or more of the total proteins annotated from sequenced bacteria genomes are annotated as hypothetical or uncharacterized proteins. However, elucidation on the function of these proteins is hindered by the lack of simple and rapid screening methods, particularly with novel or hard-to-transform bacteria. In this report, we employed cell-penetrating peptide (CPP) -peptide nucleotide acid (PNA) conjugates to elucidate the function of such uncharacterized proteins in vivo within the native bacterium. Paenibacillus, a hard-to-transform bacterial genus, was used as a model. Two hypothetical genes showing amino acid sequence similarity to ι-carrageenases, termed cgiA and cgiB, were identified from the draft genome of Paenibacillus sp. strain YYML68, and CPP-PNA probes targeting the mRNA of the acyl carrier protein gene, acpP, and the two ι-carrageenase candidate genes were synthesized. Upon direct incubation of CPP-PNA targeting the mRNA of the acpP gene, we successfully observed growth inhibition of strain YYML68 in a concentration-dependent manner. Similarly, both the function of the candidate ι-carrageenases were also inhibited using our CPP-PNA probes allowing for the confirmation and characterization of these hypothetical proteins. In summary, we believe that CPP-PNA conjugates can serve as a simple and efficient alternative approach to characterize proteins in the native bacterium.
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Affiliation(s)
- Yasuhito Yokoi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Yugo Kawabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Abdullah Adham Zulmajdi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Reiji Tanaka
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya-cho, Tsu-shi 514-8507, Mie, Japan
| | - Toshiyuki Shibata
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya-cho, Tsu-shi 514-8507, Mie, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Tetsushi Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
- Correspondence:
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Magni M, Dall'Angelo S, Baldoli C, Licandro E, Falciola L, Mussini PR. Metal‐free phthalimide‐labeled peptide nucleic acids for electrochemical biosensing applications. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202100164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Mirko Magni
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
| | - Sergio Dall'Angelo
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
- Institute of Medical Sciences University of Aberdeen Aberdeen Scotland UK
| | - Clara Baldoli
- CNR‐ Institute of Chemical Sciences and Technologies (SCITEC) Milano Italy
| | - Emanuela Licandro
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
| | - Luigi Falciola
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
| | - Patrizia R. Mussini
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
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