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Electrochemical DNA Sensors
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Electrochemical DNA Sensors

A special issue of Sensors (ISSN 1424-8220). This special issue belongs to the section "Biosensors".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 19544

Special Issue Editors

Prof. Dr. Tibor Hianik

E-Mail Website
Guest Editor
Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48 Bratislava, Slovakia
Interests: biosensors; DNA aptamers; electrochemistry; molecular acoustics; model membranes; nanomaterials; nanoparticles
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Gennady Evtugyn

E-Mail Website
Guest Editor
Analytical Chemistry Department, Kazan Federal University, Kazan 420008, Russian
Interests: electrochemical sensors; biosensors based on electroplymerized materials; supramolecular receptors

Special Issue Information

Dear Colleagues,

This Special Issue is focused on recent achievements in the development of DNA sensors in various fields of medicine, environmental and food safety. First, DNA as a probe can be used for the detection of specific genes in order to detect various diseases, food-borne pathogens or genetically modified organisms. Second, DNA as receptor is rather useful for the detection of various important molecules such as chemotherapeutics that interact with nucleic acids. In addition, DNA is the target of various pharmacologically important molecules, pesticides, herbicides, heavy metals and other molecules that are crucial for medicine, environmental monitoring and for the determination of food quality and safety. Third, DNA aptamers are rather useful receptors that can determine various small molecules, macromolecules and cells with high specificity.

Prof. Dr. Tibor Hianik
Prof. Dr. Gennady Evtugyn
Guest Editors

Manuscript Submission Information

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Keywords

  • DNA hybridization
  • DNA–drug interactions
  • DNA aptamers
  • Immobilization of nucleic acids on a solid support
  • Nanomaterials
  • Nanoparticles

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Published Papers (5 papers)

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Research

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10 pages, 1942 KiB  
Article
Thrombin Aptamer-Modified Metal–Organic Framework Nanoparticles: Functional Nanostructures for Sensing Thrombin and the Triggered Controlled Release of Anti-Blood Clotting Drugs
by Wei-Hai Chen, Ola Karmi, Bilha Willner, Rachel Nechushtai and Itamar Willner
Sensors 2019, 19(23), 5260; https://doi.org/10.3390/s19235260 - 29 Nov 2019
Cited by 18 | Viewed by 3901
Abstract
This paper features the synthesis of thrombin-responsive, nucleic acid-gated, UiO-68 metal–organic framework nanoparticles (NMOFs) loaded with the drug Apixaban or rhodamine 6G as a drug model. Apixaban acts as an inhibitor of blood clots formation. The loads in the NMOFs are locked by [...] Read more.
This paper features the synthesis of thrombin-responsive, nucleic acid-gated, UiO-68 metal–organic framework nanoparticles (NMOFs) loaded with the drug Apixaban or rhodamine 6G as a drug model. Apixaban acts as an inhibitor of blood clots formation. The loads in the NMOFs are locked by duplex nucleic acids that are composed of anchor nucleic acids linked to the NMOFs that are hybridized with the anti-thrombin aptamer. In the presence of thrombin, the duplex gating units are separated through the formation of thrombin–aptamer complexes. The unlocking of the NMOFs releases the drug (or the drug model). The release of the drug is controlled by the concentration of thrombin. The Apixaban-loaded NMOFs revealed improved inhibition, as compared to free Apixaban, toward blood clot formation. This is reflected by their longer time intervals for inducing clot formation and the decreased doses of the drug required to affect clots formation. The beneficial effects of the Apixaban-loaded NMOFs are attributed to the slow-release mechanism induced by the NMOFs carriers, where the inhibition of factor Xa in the blood clotting cycle retards the formation of thrombin, which slows down the release of the drug. Full article
(This article belongs to the Special Issue Electrochemical DNA Sensors)
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16 pages, 1333 KiB  
Article
Detection of Marker miRNAs, Associated with Prostate Cancer, in Plasma Using SOI-NW Biosensor in Direct and Inversion Modes
by Yuri Ivanov, Tatyana Pleshakova, Kristina Malsagova, Leonid Kurbatov, Vladimir Popov, Alexander Glukhov, Alexander Smirnov, Dmitry Enikeev, Natalia Potoldykova, Boris Alekseev, Daniyar Dolotkazin, Andrey Kaprin, Vadim Ziborov, Oleg Petrov and Alexander Archakov
Sensors 2019, 19(23), 5248; https://doi.org/10.3390/s19235248 - 29 Nov 2019
Cited by 22 | Viewed by 3123
Abstract
Information about the characteristics of measuring chips according to their storage conditions is of great importance for clinical diagnosis. In our present work, we have studied the capability of chips to detect nanowire biosensors when they are either freshly prepared or have been [...] Read more.
Information about the characteristics of measuring chips according to their storage conditions is of great importance for clinical diagnosis. In our present work, we have studied the capability of chips to detect nanowire biosensors when they are either freshly prepared or have been stored for either one or two years in a clean room. Potential to detect DNA oligonucleotides (oDNAs)—synthetic analogues of microRNAs (miRNAs) 198 and 429 that are associated with the development of prostate cancer (PCa)—in buffer solution was demonstrated using a nanowire biosensor based on silicon-on-insulator structures (SOI-NW biosensor). To provide biospecific detection, nanowire surfaces were sensitized with oligonucleotide probes (oDNA probes) complimentary to the known sequences of miRNA 183 and 484. In this study it is demonstrated that freshly prepared SOI-NW biosensor chips with n-type conductance and immobilized oDNA probes exhibit responses to the addition of complimentary oDNAs in buffer, leading to decreases in chips’ conductance at a concentration of 3.3 × 10−16 M. The influence of storage time on the characteristics of SOI-NW biosensor chips is also studied herein. It is shown that a two-year storage of the chips leads to significant changes in their characteristics, resulting in “inverse” sensitivity toward negatively charged oDNA probes (i.e., through an increase in chips’ conductance). It is concluded that the surface layer makes the main contribution to conductance of the biosensor chip. Our results indicate that the detection of target nucleic acid molecules can be carried out with high sensitivity using sensor chips after long-term storage, but that changes in their surface properties, which lead to inversed detection signals, must be taken into account. Examples of the applications of such chips for the detection of cancer-associated microRNAs in plasma samples of patients with diagnosed prostate cancer are given. The results obtained herein are useful for the development of highly sensitive nanowire-based diagnostic systems for the revelation of (prostate) cancer-associated microRNAs in human plasma. Full article
(This article belongs to the Special Issue Electrochemical DNA Sensors)
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16 pages, 3436 KiB  
Article
DNA-Polylactide Modified Biosensor for Electrochemical Determination of the DNA-Drugs and Aptamer-Aflatoxin M1 Interactions
by Veronika Stepanova, Vladimir Smolko, Vladimir Gorbatchuk, Ivan Stoikov, Gennady Evtugyn and Tibor Hianik
Sensors 2019, 19(22), 4962; https://doi.org/10.3390/s19224962 - 14 Nov 2019
Cited by 18 | Viewed by 3036
Abstract
DNA sensors were assembled by consecutive deposition of thiacalix[4]arenes bearing oligolactic fragments, poly(ethylene imine), and DNA onto the glassy carbon electrode. The assembling of the layers was monitored with scanning electron microscopy, cyclic voltammetry and electrochemical impedance spectroscopy. The configuration of the thiacalix[4]arene [...] Read more.
DNA sensors were assembled by consecutive deposition of thiacalix[4]arenes bearing oligolactic fragments, poly(ethylene imine), and DNA onto the glassy carbon electrode. The assembling of the layers was monitored with scanning electron microscopy, cyclic voltammetry and electrochemical impedance spectroscopy. The configuration of the thiacalix[4]arene core determined self-assembling of the polymeric species to the nano/micro particles with a size of 70–350 nm. Depending on the granulation, the coatings show the accumulation of a variety of DNA quantities, charges, and internal pore volumes. These parameters were used to optimize the DNA sensors based on these coatings. Thus, doxorubicin was determined to have limits of detection of 0.01 nM (cone configuration), 0.05 nM (partial cone configuration), and 0.10 nM (1,3-alternate configuration of the macrocycle core). Substitution of native DNA with aptamer specific to aflatoxin M1 resulted in the detection of the toxin in the range of 20 to 200 ng/L (limit of detection 5 ng/L). The aptasensor was tested in spiked milk samples and showed a recovery of 80 and 85% for 20 and 50 ng/L of the aflatoxin M1, respectively. Full article
(This article belongs to the Special Issue Electrochemical DNA Sensors)
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14 pages, 2480 KiB  
Article
DNA Biosensor Based on Double-Layer Discharge for the Detection of HPV Type 16
by José R. Espinosa, Marisol Galván, Arturo S. Quiñones, Jorge L. Ayala and Sergio M. Durón
Sensors 2019, 19(18), 3956; https://doi.org/10.3390/s19183956 - 13 Sep 2019
Cited by 16 | Viewed by 4111
Abstract
DNA electrochemical biosensors represent a feasible alternative for the diagnosis of different pathologies. In this work, the development of an electrochemical method for Human Papillomavirus-16 (HPV-16) sensing is reported based on potential relaxation measurements related to the discharge of a complex double layer [...] Read more.
DNA electrochemical biosensors represent a feasible alternative for the diagnosis of different pathologies. In this work, the development of an electrochemical method for Human Papillomavirus-16 (HPV-16) sensing is reported based on potential relaxation measurements related to the discharge of a complex double layer of a DNA-modified gold electrode. The method used allows us to propose an equivalent circuit (EC) for a DNA/Au electrode, which was corroborated by electrochemical impedance spectroscopy (EIS) measurement. This model differs from the Randles circuit that is commonly used in double-layer simulations. The change in the potential relaxation and associated charge transfer resistance were used for sensing the DNA hybridization by using the redox pair Fe(CN)64-/Fe(CN)63+ as an electrochemical indicator. In order to determinate only the potential relaxation of the composed double layer, the faradic and double-layer current contributions were separated using a rectifier diode arrangement. A detection limit of 0.38 nM was obtained for the target HPV-16 DNA sequences. The biosensor showed a qualitative discrimination between a single-base mismatched sequence and the fully complementary HPV-16 DNA target. The results indicate that the discharge of the double-layer detection method can be used to develop an HPV DNA biosensor. Full article
(This article belongs to the Special Issue Electrochemical DNA Sensors)
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Review

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20 pages, 4307 KiB  
Review
Opportunities, Challenges, and Prospects in Electrochemical Biosensing of Circulating Tumor DNA and Its Specific Features
by Susana Campuzano, Verónica Serafín, Maria Gamella, María Pedrero, Paloma Yáñez-Sedeño and José M. Pingarrón
Sensors 2019, 19(17), 3762; https://doi.org/10.3390/s19173762 - 30 Aug 2019
Cited by 22 | Viewed by 4525
Abstract
Nowadays, analyzing circulating tumor DNA (ctDNA), a very small part of circulating free DNA (cfDNA) carried by blood, is considered to be an interesting alternative to conventional single-site tumor tissue biopsies, both to assess tumor burden and provide a more comprehensive snapshot of [...] Read more.
Nowadays, analyzing circulating tumor DNA (ctDNA), a very small part of circulating free DNA (cfDNA) carried by blood, is considered to be an interesting alternative to conventional single-site tumor tissue biopsies, both to assess tumor burden and provide a more comprehensive snapshot of the time-related and spatial heterogeneity of cancer genetic/epigenetic scenery. The determination of ctDNA and/or mapping its characteristic features, including tumor-specific mutations, chromosomal aberrations, microsatellite alterations, and epigenetic changes, are minimally invasive, powerful and credible biomarkers for early diagnosis, follow-up, prediction of therapy response/resistance, relapse monitoring, and tracking the rise of new mutant subclones, leading to improved cancer outcomes This review provides an outline of advances published in the last five years in electrochemical biosensing of ctDNA and surrogate markers. It emphasizes those strategies that have been successfully applied to real clinical samples. It highlights the unique opportunities they offer to shift the focus of cancer patient management methods from actual decision making, based on clinic-pathological features, to biomarker-driven treatment strategies, based on genotypes and customized targeted therapies. Also highlighted are the unmet hurdles and future key points to guide these devices in the development of liquid biopsy cornerstone tools in routine clinical practice for the diagnosis, prognosis, and therapy response monitoring in cancer patients. Full article
(This article belongs to the Special Issue Electrochemical DNA Sensors)
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