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.

Autor: Suprun EV; 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. Electronic address: lenasuprun@mail.ru., Khmeleva SA; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia., Duskaev IF; 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., Ptitsyn KG; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia., Kurbatov LK; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia., Shershov VE; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia., Kuznetsova VE; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia., Lapa SA; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia., Chudinov AV; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia., Radko SP; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia.
Jazyk: angličtina
Zdroj: Talanta [Talanta] 2024 Jun 01; Vol. 273, pp. 125841. Date of Electronic Publication: 2024 Feb 29.
DOI: 10.1016/j.talanta.2024.125841
Abstrakt: 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 'I p , 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.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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