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Suprun EV, Khmeleva SA, Duskaev IF, Ptitsyn KG, Kurbatov LK, Shershov VE, Kuznetsova VE, Lapa SA, Chudinov AV, Radko SP. Combining recombinase polymerase amplification with tyrosine modified 2'-deoxyuridine-5'-triphosphate for direct voltammetric detection of double-stranded DNA: Application to potato pathogen Dickeya solani. Talanta 2024; 273:125841. [PMID: 38460421 DOI: 10.1016/j.talanta.2024.125841] [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: 11/09/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024]
Abstract
The approach based on a combination of isothermal recombinase polymerase amplification (RPA), 2'-deoxyuridine-5'-triphosphate modified with tyrosine aromatic group (dUTP-Y1), and direct voltammetric detection of RPA product carrying electroactive labels was successfully applied to the potato pathogen Dickeya solani. The artificial nucleotide dUTP-Y1 demonstrated a good compatibility with RPA, enabling by targeting a section of D. solani genome with a unique sequence to produce the full-size modified products at high levels of substitution of dTTP by dUTP-Y1 (up to 80-90 %) in the reaction mixture. The optimized procedure of square wave voltammetry allowed to reliably detect the product generated by RPA at 80 % substitution of dTTP by dUTP-Y1 (dsDNA-Y1) in microliter sample volumes on the surface of disposable carbon screen printed electrodes at the potential of about 0.6 V. The calibration curve for the amplicon detection was linear in coordinates 'Ip, A vs. Log (c, M)' within the 0.05-1 μM concentration range. The limit of detection for dsDNA-Y1 was estimated as 8 nM. The sensitivity of the established electrochemical approach allowed to detect amplicons generated in a single standard 50 μL RPA reaction after their purification with silica-coated magnetic beads. The overall detectability of D. solani with the suggested combination of RPA and voltammetric registration of dsDNA-Y1 can be as low as a few copies of bacterial genome per standard reaction. In total, amplification, purification, and electrochemical detection take about 120-150 min. Considering the potential of direct electrochemical analysis for miniaturization, as well as compliance with low-cost and low-power requirements, the findings provide grounds for future development of microfluidic devices integrating isothermal amplification, amplicon purification and detection based on the tyrosine modified nucleotide for the purpose of 'on-site' detection of various pathogens.
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Affiliation(s)
- Elena V Suprun
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow, 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia.
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Insaf F Duskaev
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow, 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Konstantin G Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Leonid K Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
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2
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Suprun EV, Khmeleva SA, Duskaev IF, Kurbatov LK, Kuznetsova VE, Shershov VE, Chudinov AV, Radko SP. Polymerase incorporation of 4-nitrophenyl modified 2'-deoxyuridine-5'-triphosphates into double-stranded DNA for direct electrochemical detection. J Pharm Biomed Anal 2024; 241:115977. [PMID: 38241909 DOI: 10.1016/j.jpba.2024.115977] [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: 10/23/2023] [Revised: 12/23/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
Three novel 2'-deoxyuridine-5'-triphosphates modified with 4-nitrophenyl groups via various linkers (dUTP-N1, dUTP-N2, and dUTP-N3) were tested as bearers of reducible electroactive labels as well as substrates suitable for enzymes used in polymerase chain reaction (PCR) and recombinase polymerase amplification (RPA) with a potential application to direct electrochemical detection of double-stranded deoxyribonucleic acid (dsDNA). In cyclic and square wave voltammograms on carbon screen printed electrodes, the labeled dUTP have demonstrated distinct reduction peaks at potentials of -0.7 V to -0.9 V (phosphate buffer, pH 7.4). The reduction peak currents of dUTP-N derivatives were found to increase with their molar concentrations. The dUTP-N3 with a double bond in the linker had the lowest reduction potential (about 100 mV less negative) among the derivatives studied. Further, dUTP-N nucleotides were tested as substrates in PCR and RPA to incorporate the electroactive labels into 90, 210, or 206 base pair long dsDNA amplicons. However, only a dUTP-N1 derivative with a shorter linker without the double bond demonstrated satisfactory compatibility with both PCR and RPA, though with a low reaction output of modified dsDNA amplicons (at 100% substitution of dTTP). The dsDNA amplicons produced by PCR with 85% substitution of dTTP by the dUTP-N1 in the reaction mixture were successfully detected by square wave voltammetry at micromolar concentrations at high square wave frequency.
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Affiliation(s)
- Elena V Suprun
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia.
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Insaf F Duskaev
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Leonid K Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow 119991, Russia
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow 119991, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow 119991, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
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3
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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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4
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Gao Y, Peng L, Zhao C. MYH7 in cardiomyopathy and skeletal muscle myopathy. Mol Cell Biochem 2024; 479:393-417. [PMID: 37079208 DOI: 10.1007/s11010-023-04735-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/07/2023] [Indexed: 04/21/2023]
Abstract
Myosin heavy chain gene 7 (MYH7), a sarcomeric gene encoding the myosin heavy chain (myosin-7), has attracted considerable interest as a result of its fundamental functions in cardiac and skeletal muscle contraction and numerous nucleotide variations of MYH7 are closely related to cardiomyopathy and skeletal muscle myopathy. These disorders display significantly inter- and intra-familial variability, sometimes developing complex phenotypes, including both cardiomyopathy and skeletal myopathy. Here, we review the current understanding on MYH7 with the aim to better clarify how mutations in MYH7 affect the structure and physiologic function of sarcomere, thus resulting in cardiomyopathy and skeletal muscle myopathy. Importantly, the latest advances on diagnosis, research models in vivo and in vitro and therapy for precise clinical application have made great progress and have epoch-making significance. All the great advance is discussed here.
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Affiliation(s)
- Yuan Gao
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Lu Peng
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Cuifen Zhao
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, 250012, China.
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5
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Suprun EV, Khmeleva SA, Bibik KV, Ptitsyn KG, Kurbatov LK, Radko SP. Polymerase incorporation of fluorescein or rhodamine modified 2'-deoxyuridine-5'-triphosphates into double-stranded DNA for direct electrochemical detection. J Pharm Biomed Anal 2023; 236:115737. [PMID: 37774487 DOI: 10.1016/j.jpba.2023.115737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
The 2'-deoxyuridine-5'-triphosphates modified with fluorescein (dUTP-Fl) or rhodamine (dUTP-Rh) were tested as bearers of electroactive labels and as proper substrates for polymerases used in polymerase chain reaction (PCR) and isothermal recombinase polymerase amplification (RPA) with the aim of electrochemical detection of double-stranded DNA (dsDNA) amplification products. For this purpose, electrochemical behavior of free fluorescein and rhodamine as well as the modified nucleotides, dUTP-Fl and dUTP-Rh, was studied by cyclic (CV) and square wave (SWV) voltammetry on carbon screen printed electrodes. Both free fluorescein and dUTP-Fl underwent a two-step oxidation at the peak potentials (Ep) of 0.6-0.7 V and 0.8-0.9 V (phosphate buffer, pH 7.4). The reduction peaks of fluorescein and dUTP-Fl were registered between -0.9 V and -1 V, but they did not depend on concentration. The free rhodamine and dUTP-Rh have demonstrated the well-defined oxidation peaks at 0.8-0.9 V. In addition, the distinct reduction peaks at Ep between -0.8 V and -0.9 V were registered for both rhodamine and dUTP-Rh. The dUTP-Fl and dUTP-Rh were further tested as substrates to incorporate an electroactive label into 210 or 206 base pair long dsDNA amplicons generated either by PCR or RPA. Among two dUTP derivatives tested, dUTP-Fl revealed significantly better compatibility with PCR and RPA, producing the full-size amplicons at 50-90% substitution of dTTP in the reaction mixture. In the PCR, the best compromise between amplicon output and labeling was achieved at the dUTP-Fl : dTTP and dUTP-Rh : dTTP molar ratios of 70% : 30% and 20% : 80% in the PCR mixture, respectively, allowing the direct electrochemical detection of amplicons at micromolar concentrations. Alongside with fluorescence DNA assays, the fluorescein and rhodamine modified dUTP appear as promising electroactive labels to develop direct electrochemical DNA assays for detecting PCR and RPA products.
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Affiliation(s)
- Elena V Suprun
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia.
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Konstantin V Bibik
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Konstantin G Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Leonid K Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
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6
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Yenice C, Chahin N, Jauset-Rubio M, Hall M, Biggs P, Dimai HP, Obermayer-Pietsch B, Ortiz M, O’Sullivan CK. Semiautomated Electrochemical Melting Curve Analysis Device for the Detection of an Osteoporosis Associated Single Nucleotide Polymorphism in Blood. Anal Chem 2023; 95:14192-14202. [PMID: 37713191 PMCID: PMC10534999 DOI: 10.1021/acs.analchem.3c01668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
The detection of single nucleotide polymorphisms (SNPs) is of increasing importance in many areas including clinical diagnostics, patient stratification for pharmacogenomics, and advanced forensic analysis. In the work reported, we apply a semiautomated system for solid-phase electrochemical melting curve analysis (éMCA) for the identification of the allele present at a specific SNP site associated with an increased risk of bone fracture and predisposition to osteoporosis. Asymmetric isothermal recombinase polymerase amplification using ferrocene labeled forward primers was employed to generate single stranded redox labeled amplicons. In a first approach to demonstrate the proof of concept of combining asymmetric RPA with solid-phase éMCA, a simplified system housing a multielectrode array within a polymeric microsystem, sandwiched between two aluminum plates of a heater device, was used. Sample manipulation through the microfluidic channel was controlled by a syringe pump, and an external Ag/AgCl reference electrode was employed. Individual electrodes of the array were functionalized with four different oligonucleotide probes, each probe equivalent in design with the exception of the middle nucleotide. The isothermally generated amplicons were allowed to hybridize to the surface-tethered probes and subsequently subjected to a controlled temperature ramp, and the melting of the duplex was monitored electrochemically. A clear difference between the fully complementary and a single mismatch was observed. Having demonstrated the proof-of-concept, a device for automated éMCA with increased flexibility to house diverse electrode arrays with internal quasi-gold reference electrodes, higher resolution, and broader melting temperature range was developed and exploited for the detection of SNP hetero/homozygosity. Using the optimized conditions, the system was applied to the identification of the allele present at an osteoporosis associated SNP site, rs2741856, in 10 real fingerprick/venous blood samples, with results validated using Sanger sequencing.
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Affiliation(s)
- Cansu
Pinar Yenice
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Nassif Chahin
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Miriam Jauset-Rubio
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Matthew Hall
- Labman
Automation Ltd., Seamer Hill, Stokesley, North Yorkshire TS9 5NQ, U.K.
| | - Phil Biggs
- Labman
Automation Ltd., Seamer Hill, Stokesley, North Yorkshire TS9 5NQ, U.K.
| | - Hans-Peter Dimai
- Division
of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Barbara Obermayer-Pietsch
- Division
of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Mayreli Ortiz
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Ciara K. O’Sullivan
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Institució
Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
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7
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Campuzano S, Pingarrón JM. Electrochemical Affinity Biosensors: Pervasive Devices with Exciting Alliances and Horizons Ahead. ACS Sens 2023; 8:3276-3293. [PMID: 37534629 PMCID: PMC10521145 DOI: 10.1021/acssensors.3c01172] [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: 06/12/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
Electrochemical affinity biosensors are evolving at breakneck speed, strengthening and colonizing more and more niches and drawing unimaginable roadmaps that increasingly make them protagonists of our daily lives. They achieve this by combining their intrinsic attributes with those acquired by leveraging the significant advances that occurred in (nano)materials technology, bio(nano)materials and nature-inspired receptors, gene editing and amplification technologies, and signal detection and processing techniques. The aim of this Perspective is to provide, with the support of recent representative and illustrative literature, an updated and critical view of the repertoire of opportunities, innovations, and applications offered by electrochemical affinity biosensors fueled by the key alliances indicated. In addition, the imminent challenges that these biodevices must face and the new directions in which they are envisioned as key players are discussed.
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Affiliation(s)
- Susana Campuzano
- Departamento de Química Analítica,
Facultad de Ciencias Químicas, Universidad
Complutense de Madrid, 28040 Madrid, España
| | - José M. Pingarrón
- Departamento de Química Analítica,
Facultad de Ciencias Químicas, Universidad
Complutense de Madrid, 28040 Madrid, España
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8
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Warmt C, Broweleit LM, Fenzel CK, Henkel J. An experimental comparison between primer and nucleotide labelling to produce RPA-amplicons used for multiplex detection of antibiotic resistance genes. Sci Rep 2023; 13:15734. [PMID: 37735542 PMCID: PMC10514322 DOI: 10.1038/s41598-023-42830-7] [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: 05/18/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023] Open
Abstract
Direct labelling of amplification products using isothermal amplification is currently done most frequently by incorporating previously labelled primer. Although this method is well proven and widely used, it is not a universal solution due to some weaknesses. Alternatively, labelled nucleotides could be used, whose application and functionality have been already partially demonstrated. It remains to be determined how this method performs in comparison to traditional labelling, in particular combined with isothermal amplification methods. In this work, we show a detailed analysis of the labelling efficiency under different conditions and compare the results with the traditional primer-labelling method in the context of RPA amplification. Impressively, our results showed that using Cy5-labelled dUTPs can achieve much more efficient labelling for fragments above 200 bp, while using them for smaller fragments does not bring any relevant disadvantages, but also no major benefit. Furthermore, this work successfully demonstrate for the first time a quadruplex microarray for the detection of resistance genes using RPA and direct labelling with Cy5-dUTP as a potential application scenario. The sensitivities achieved here extend to SNP discovery for the detection of the proper blaKPC variant.
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Affiliation(s)
- Christian Warmt
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany.
| | - Lisa-Marie Broweleit
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Carolin Kornelia Fenzel
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Jörg Henkel
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
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9
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Ortiz M, Jauset-Rubio M, Trummer O, Foessl I, Kodr D, Acero JL, Botero ML, Biggs P, Lenartowicz D, Trajanoska K, Rivadeneira F, Hocek M, Obermayer-Pietsch B, O’Sullivan CK. Generic Platform for the Multiplexed Targeted Electrochemical Detection of Osteoporosis-Associated Single Nucleotide Polymorphisms Using Recombinase Polymerase Solid-Phase Primer Elongation and Ferrocene-Modified Nucleoside Triphosphates. ACS CENTRAL SCIENCE 2023; 9:1591-1602. [PMID: 37637735 PMCID: PMC10450878 DOI: 10.1021/acscentsci.3c00243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Indexed: 08/29/2023]
Abstract
Osteoporosis is a multifactorial disease influenced by genetic and environmental factors, which contributes to an increased risk of bone fracture, but early diagnosis of this disease cannot be achieved using current techniques. We describe a generic platform for the targeted electrochemical genotyping of SNPs identified by genome-wide association studies to be associated with a genetic predisposition to osteoporosis. The platform exploits isothermal solid-phase primer elongation with ferrocene-labeled nucleoside triphosphates. Thiolated reverse primers designed for each SNP were immobilized on individual gold electrodes of an array. These primers are designed to hybridize to the SNP site at their 3'OH terminal, and primer elongation occurs only where there is 100% complementarity, facilitating the identification and heterozygosity of each SNP under interrogation. The platform was applied to real blood samples, which were thermally lysed and directly used without the need for DNA extraction or purification. The results were validated using Taqman SNP genotyping assays and Sanger sequencing. The assay is complete in just 15 min with a total cost of 0.3€ per electrode. The platform is completely generic and has immense potential for deployment at the point of need in an automated device for targeted SNP genotyping with the only required end-user intervention being sample addition.
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Affiliation(s)
- Mayreli Ortiz
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Miriam Jauset-Rubio
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Olivia Trummer
- Division
of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Ines Foessl
- Division
of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - David Kodr
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo namesti 2, CZ 16610 Prague 6, Czech Republic
| | - Josep Lluís Acero
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Mary Luz Botero
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Phil Biggs
- Labman
Automation
Ltd., Seamer Hill, Stokesley, North Yorkshire, TS9 5NQ U.K.
| | - Daniel Lenartowicz
- Labman
Automation
Ltd., Seamer Hill, Stokesley, North Yorkshire, TS9 5NQ U.K.
| | - Katerina Trajanoska
- Department
of Internal Medicine, Erasmus MC, 40 3015 Rotterdam, The Netherlands
| | | | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo namesti 2, CZ 16610 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Barbara Obermayer-Pietsch
- Division
of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Ciara K. O’Sullivan
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Institució
Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
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10
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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11
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Electrochemical biosensors for analysis of DNA point mutations in cancer research. Anal Bioanal Chem 2023; 415:1065-1085. [PMID: 36289102 DOI: 10.1007/s00216-022-04388-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 02/07/2023]
Abstract
Cancer is a genetic disease induced by mutations in DNA, in particular point mutations in important driver genes that lead to protein malfunctioning and ultimately to tumorigenesis. Screening for the most common DNA point mutations, especially in such genes as TP53, BRCA1 and BRCA2, EGFR, KRAS, or BRAF, is crucial to determine predisposition risk for cancer or to predict response to therapy. In this review, we briefly depict how these genes are involved in cancer, followed by a description of the most common techniques routinely applied for their analysis, including high-throughput next-generation sequencing technology and less expensive low-throughput options, such as real-time PCR, restriction fragment length polymorphism, or high resolution melting analysis. We then introduce benefits of electrochemical biosensors as interesting alternatives to the standard methods in terms of cost, speed, and simplicity. We describe most common strategies involved in electrochemical biosensing of point mutations, relying mostly on PCR or isothermal amplification techniques, and critically discuss major challenges and obstacles that, until now, prevented their more widespread application in clinical settings.
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Zhou M, Wang H, Li C, Yan C, Qin P, Huang L. CRISPR/Cas9 mediated triple signal amplification platform for high selective and sensitive detection of single base mutations. Anal Chim Acta 2022; 1230:340421. [DOI: 10.1016/j.aca.2022.340421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/29/2022] [Accepted: 09/18/2022] [Indexed: 11/25/2022]
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Toldrà A, Ainla A, Khaliliazar S, Landin R, Chondrogiannis G, Hanze M, Réu P, Hamedi MM. Portable electroanalytical nucleic acid amplification tests using printed circuit boards and open-source electronics. Analyst 2022; 147:4249-4256. [PMID: 35993403 PMCID: PMC9511072 DOI: 10.1039/d2an00923d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/10/2022] [Indexed: 09/19/2023]
Abstract
The realization of electrochemical nucleic acid amplification tests (NAATs) at the point of care (POC) is highly desirable, but it remains a challenge given their high cost and lack of true portability/miniaturization. Here we show that mass-produced, industrial standardized, printed circuit boards (PCBs) can be repurposed to act as near-zero cost electrodes for self-assembled monolayer-based DNA biosensing, and further integration with a custom-designed and low-cost portable potentiostat. To show the analytical capability of this system, we developed a NAAT using isothermal recombinase polymerase amplification, bypassing the need of thermal cyclers, followed by an electrochemical readout relying on a sandwich hybridization assay. We used our sensor and device for analytical detection of the toxic microalgae Ostreopsis cf. ovata as a proof of concept. This work shows the potential of PCBs and open-source electronics to be used as powerful POC DNA biosensors at a low-cost.
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Affiliation(s)
- Anna Toldrà
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Alar Ainla
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Shirin Khaliliazar
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Roman Landin
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Georgios Chondrogiannis
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Martin Hanze
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Pedro Réu
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Mahiar M Hamedi
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
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Chen B, Li Y, Xu F, Yang X. Powerful CRISPR-Based Biosensing Techniques and Their Integration With Microfluidic Platforms. Front Bioeng Biotechnol 2022; 10:851712. [PMID: 35284406 PMCID: PMC8905290 DOI: 10.3389/fbioe.2022.851712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 12/20/2022] Open
Abstract
In the fight against the worldwide pandemic coronavirus disease 2019 (COVID-19), simple, rapid, and sensitive tools for nucleic acid detection are in urgent need. PCR has been a classic method for nucleic acid detection with high sensitivity and specificity. However, this method still has essential limitations due to the dependence on thermal cycling, which requires costly equipment, professional technicians, and long turnover times. Currently, clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensors have been developed as powerful tools for nucleic acid detection. Moreover, the CRISPR method can be performed at physiological temperature, meaning that it is easy to assemble into point-of-care devices. Microfluidic chips hold promises to integrate sample processing and analysis on a chip, reducing the consumption of sample and reagent and increasing the detection throughput. This review provides an overview of recent advances in the development of CRISPR-based biosensing techniques and their perfect combination with microfluidic platforms. New opportunities and challenges for the improvement of specificity and efficiency signal amplification are outlined. Furthermore, their various applications in healthcare, animal husbandry, agriculture, and forestry are discussed.
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Affiliation(s)
- Bing Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ya Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Feng Xu, ; Xiaonan Yang,
| | - Xiaonan Yang
- Institute of Intelligent Sensing, Zhengzhou University, Zhengzhou, China
- *Correspondence: Feng Xu, ; Xiaonan Yang,
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Figazzolo C, Ma Y, Tucker JHR, Hollenstein M. Ferrocene as a potential electrochemical reporting surrogate of abasic sites in DNA. Org Biomol Chem 2022; 20:8125-8135. [DOI: 10.1039/d2ob01540d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have evaluated the possibility of replacing abasic sites with ferrocene for enzymatic synthesis of canonical and modified DNA.
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Affiliation(s)
- Chiara Figazzolo
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Learning Planet Institute, 8, rue Charles V, 75004 Paris, France
| | - Yifeng Ma
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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