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Vishnubhotla R, Montgomery CB, Steffens KL, Semancik S. Conformational Changes of Immobilized Polythymine due to External Stressors Studied with Temperature-Controlled Electrochemical Microdevices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:2607-2618. [PMID: 33595321 PMCID: PMC9278808 DOI: 10.1021/acs.langmuir.0c03219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Conformational changes of single-stranded DNA (ssDNA) play an important role in a DNA strand's ability to bind to target ligands. A variety of factors can influence conformation, including temperature, ionic strength, pH, buffer cation valency, strand length, and sequence. To better understand the effects of these factors on immobilized DNA structures, we employ temperature-controlled electrochemical microsensors to study the effects of salt concentration and temperature variation on the conformation and motion of polythymine (polyT) strands of varying lengths (10, 20, 50 nucleotides). PolyT strands were tethered to a gold working electrode at the proximal end through a thiol linker via covalent bonding between the Au electrode and sulfur link, which can tend to decompose between a temperature range of 60 and 90 °C. The strands were also modified with an electrochemically active methylene blue (MB) moiety at the distal end. Electron transfer (eT) was measured by square wave voltammetry (SWV) and used to infer information pertaining to the average distance between the MB and the working electrode. We observe changes in DNA flexibility due to varying ionic strength, while the effects of increased DNA thermal motion are tracked for elevated temperatures. This work elucidates the behavior of ssDNA in the presence of a phosphate-buffered saline at NaCl concentrations ranging from 20 to 1000 mmol/L through a temperature range of 10-50 °C in 1° increments, well below the decomposition temperature range. The results lay the groundwork for studies on more complex DNA strands in conjunction with different chemical and physical conditions.
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Ligand-Based Stability Changes in Duplex DNA Measured with a Microscale Electrochemical Platform. BIOSENSORS-BASEL 2019; 9:bios9020054. [PMID: 31013753 PMCID: PMC6628196 DOI: 10.3390/bios9020054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/03/2019] [Accepted: 04/09/2019] [Indexed: 01/20/2023]
Abstract
Development of technologies for rapid screening of DNA secondary structure thermal stability and the effects on stability for binding of small molecule drugs is important to the drug discovery process. In this report, we describe the capabilities of an electrochemical, microdevice-based approach for determining the melting temperatures (Tm) of electrode-bound duplex DNA structures. We also highlight new features of the technology that are compatible with array development and adaptation for high-throughput screening. As a foundational study to exhibit device performance and capabilities, melting-curve analyses were performed on 12-mer DNA duplexes in the presence/absence of two binding ligands: diminazene aceturate (DMZ) and proflavine. By measuring electrochemical current as a function of temperature, our measurement platform has the ability to determine the effect of binding ligands on Tm values with high signal-to-noise ratios and good reproducibility. We also demonstrate that heating our three-electrode cell with either an embedded microheater or a thermoelectric module produces similar results. The ΔTm values we report show the stabilizing ability of DMZ and proflavine when bound to duplex DNA structures. These initial proof-of-concept studies highlight the operating characteristics of the microdevice platform and the potential for future application toward other immobilized samples.
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Amplified detection of single base mismatches with the competing-strand assay reveals complex kinetic and thermodynamic behavior of strand displacement at the electrode surface. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.07.188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Wu SH, Zhang B, Wang FF, Mi ZZ, Sun JJ. Heating enhanced sensitive and selective electrochemical detection of Hg 2+ based on T-Hg 2+ -T structure and exonuclease III-assisted target recycling amplification strategy at heated gold disk electrode. Biosens Bioelectron 2018; 104:145-151. [DOI: 10.1016/j.bios.2018.01.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/15/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
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Rizzi G, Dufva M, Hansen MF. Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor. LAB ON A CHIP 2017; 17:2256-2263. [PMID: 28593203 DOI: 10.1039/c7lc00485k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a microfluidic system and its use to measure DNA denaturation curves by varying the temperature or salt (Na+) concentration. The readout is based on real-time measurements of DNA hybridization using magnetoresistive sensors and magnetic nanoparticles (MNPs) as labels. We report the first melting curves of DNA hybrids measured as a function of continuously decreasing salt concentration at fixed temperature and compare them to the corresponding curves obtained vs. temperature at fixed salt concentration. The magnetoresistive sensor platform provided reliable results under varying temperature as well as salt concentration. The salt concentration melting curves were found to be more reliable than temperature melting curves. We performed a two-dimensional mapping of the melting profiles of a target to probes targeting its wild type (WT) and mutant type (MT) variants in the temperature-salt concentration plane. This map clearly showed a region of optimum ability to differentiate between the two variants. We finally demonstrated single nucleotide polymorphysm (SNP) genotyping using both denaturation methods on both separate sensors but also using a differential measurement on a single sensor. The results demonstrate that concentration melting provides an attractive alternative to temperature melting in on-chip DNA denaturation experiments and further show that the magnetoresistive platform is attractive due to its low cross-sensitivity to temperature and liquid composition.
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Affiliation(s)
- Giovanni Rizzi
- Department of Micro- and Nanotechnology, DTU Nanotech, Building 345B, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
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Sequence Detection of Unlabeled DNA Using the Sandwich Assay: Strand-Displacement, Hybridization Efficiency, and Probe- Conformation Considerations for the Tethered Surface. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.10.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Biala K, Sedova A, Flechsig GU. Sequence and Temperature Influence on Kinetics of DNA Strand Displacement at Gold Electrode Surfaces. ACS APPLIED MATERIALS & INTERFACES 2015; 7:19948-19959. [PMID: 26302819 DOI: 10.1021/acsami.5b04435] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Understanding complex contributions of surface environment to tethered nucleic acid sensing experiments has proven challenging, yet it is important because it is essential for interpretation and calibration of indispensable methods, such as microarrays. We investigate the effects of DNA sequence and solution temperature gradients on the kinetics of strand displacement at heated gold wire electrodes, and at gold disc electrodes in a heated solution. Addition of a terminal double mismatch (toehold) provides a reduction in strand displacement energy barriers sufficient to probe the secondary mechanisms involved in the hybridization process. In four different DNA capture probe sequences (relevant for the identification of genetically modified maize MON810), all but one revealed a high activation energy up to 200 kJ/mol during hybridization, that we attribute to displacement of protective strands by capture probes. Protective strands contain 4 to 5 mismatches to ease their displacement by the surface-confined probes at the gold electrodes. A low activation energy (30 kJ/mol) was observed for the sequence whose protective strand contained a toehold and one central mismatch, its kinetic curves displayed significantly different shapes, and we observed a reduced maximum signal intensity as compared to other sequences. These findings point to potential sequence-related contributions to oligonucleotide diffusion influencing kinetics. Additionally, for all sequences studied with heated wire electrodes, we observed a 23 K lower optimal hybridization temperature in comparison with disc electrodes in heated solution, and greatly reduced voltammetric signals after taking into account electrode surface area. We propose that thermodiffusion due to temperature gradients may influence both hybridization and strand displacement kinetics at heated microelectrodes, an explanation supported by computational fluid dynamics. DNA assays with surface-confined capture probes and temperature gradients should not neglect potential influences of thermodiffusion as well as sequence-related effects. Furthermore, studies attempting to characterize surface-tethered environments should consider thermodiffusion if temperature gradients are involved.
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Affiliation(s)
- Katarzyna Biala
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
- Department of Chemistry, University of Rostock , A.-Einstein-Str. 3a, D-18059 Rostock, Germany
| | - Ada Sedova
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Gerd-Uwe Flechsig
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
- Department of Chemistry, University of Rostock , A.-Einstein-Str. 3a, D-18059 Rostock, Germany
- Gensoric GmbH, Schillingallee 68, D-18057 Rostock, Germany
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Papadopoulou E, Meneghello M, Marafini P, Johnson RP, Brown T, Bartlett PN. The effect of temperature on electrochemically driven denaturation monitored by SERS. Bioelectrochemistry 2015; 106:353-8. [PMID: 26145815 DOI: 10.1016/j.bioelechem.2015.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/11/2015] [Accepted: 06/21/2015] [Indexed: 10/23/2022]
Abstract
Scanning the electrochemical potential negative results in the gradual denaturation of dsDNA immobilised at a nanostructure gold electrode, the DNA melting is monitored by SERS. We demonstrate the effect of the experimental temperature on the electrochemically driven melting (E-melting) by carrying out experiments between 10 and 28 °C using two DNA duplexes (20 and 21 base pairs). Significant temperature dependence for both the melting potentials, Em, and the steepness of the melting curves was found over the range 10 to 18 °C. Above 18 °C the results were found to be independent of temperature. The relative temperature insensitivity of the melting potentials above 18 °C is advantageous for the application of the electrochemically driven melting technique because precise temperature control is not necessary for measurements that are carried out around room temperature. Conversely temperature dependence below 18 °C offers a way to improve discrimination for highly similar DNA sequences.
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Affiliation(s)
| | - Marta Meneghello
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Pietro Marafini
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK
| | - Robert P Johnson
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK
| | - Philip N Bartlett
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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A novel morphine electrochemical biosensor based on intercalative and electrostatic interaction of morphine with double strand DNA immobilized onto a modified Au electrode. Talanta 2015; 131:460-6. [DOI: 10.1016/j.talanta.2014.08.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/03/2014] [Accepted: 08/04/2014] [Indexed: 11/17/2022]
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Rapid nucleic acid melting analyses using a microfabricated electrochemical platform. Anal Chim Acta 2014; 853:265-270. [PMID: 25467468 DOI: 10.1016/j.aca.2014.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/10/2014] [Accepted: 10/15/2014] [Indexed: 11/24/2022]
Abstract
Microfabrication methods have been used to fabricate a new microscale platform that integrates thermal control and multi-electrode components to enable rapid, temperature-dependent electrochemical measurements on small-volume fluid samples. A wide range of biochemical phenomena can be characterized with the device, for example, when monitoring interactions at the working electrode between probe and target species which include an electroactive moiety. Employing square wave voltammetry, we have demonstrated the utility and reproducibility of the microplatform in melting studies on full-match, single-mismatch, and double-mismatch DNA structures of relevance to single-nucleotide polymorphism (SNP) discrimination. As shown, the small size of the reported device, low volume for the samples it can interrogate (∼10 μL), individual addressing of platform components and fast localized heating (settling times ∼5 s) combine to allow for efficient sample analyses. In addition, a straight-forward route exists, involving replication into array formats and integration with microfluidics, for extending the technology toward eventual high throughput work on drug discovery and medical diagnostics.
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Yang AHJ, Hsieh K, Patterson AS, Ferguson BS, Eisenstein M, Plaxco KW, Soh HT. Accurate zygote-specific discrimination of single-nucleotide polymorphisms using microfluidic electrochemical DNA melting curves. Angew Chem Int Ed Engl 2014; 53:3163-7. [PMID: 24520069 PMCID: PMC3992926 DOI: 10.1002/anie.201310059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 01/17/2023]
Abstract
We report the first electrochemical system for the detection of single-nucleotide polymorphisms (SNPs) that can accurately discriminate homozygous and heterozygous genotypes using microfluidics technology. To achieve this, our system performs real-time melting-curve analysis of surface-immobilized hybridization probes. As an example, we used our sensor to analyze two SNPs in the apolipoprotein E (ApoE) gene, where homozygous and heterozygous mutations greatly affect the risk of late-onset Alzheimer's disease. Using probes specific for each SNP, we simultaneously acquired melting curves for probe-target duplexes at two different loci and thereby accurately distinguish all six possible ApoE allele combinations. Since the design of our device and probes can be readily adapted for targeting other loci, we believe that our method offers a modular platform for the diagnosis of SNP-based diseases and personalized medicine.
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Affiliation(s)
- Allen H. J. Yang
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
| | - Adriana S. Patterson
- Department of Chemistry and Biochemistry and Biomolecular Science and Engineering Program, University of California, Santa Barbara (USA)
| | - B. Scott Ferguson
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
| | - Michael Eisenstein
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry and Biomolecular Science and Engineering Program, University of California, Santa Barbara (USA)
| | - H. Tom Soh
- Materials Department and Department of Mechanical Engineering University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
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Yang AHJ, Hsieh K, Patterson AS, Ferguson BS, Eisenstein M, Plaxco KW, Soh HT. Accurate Zygote-Specific Discrimination of Single-Nucleotide Polymorphisms Using Microfluidic Electrochemical DNA Melting Curves. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Azam MS, Gibbs-Davis JM. Monitoring DNA Hybridization and Thermal Dissociation at the Silica/Water Interface Using Resonantly Enhanced Second Harmonic Generation Spectroscopy. Anal Chem 2013; 85:8031-8. [DOI: 10.1021/ac401009u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Md. Shafiul Azam
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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A heated pencil lead disk electrode with direct current and its preliminary application for highly sensitive detection of luteolin. Electrochem commun 2013. [DOI: 10.1016/j.elecom.2012.12.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Jacobsen M, Flechsig GU. Hybridization Detection of Osmium Tetroxide Bipyridine-Labeled DNA and RNA on Heated Gold Wire Electrodes. ELECTROANAL 2012. [DOI: 10.1002/elan.201200460] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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Flechsig GU, Walter A. Electrically Heated Electrodes: Practical Aspects and New Developments. ELECTROANAL 2011. [DOI: 10.1002/elan.201100412] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kostečka P, Havran L, Bittová M, Pivoňková H, Fojta M. Sensing mispaired thymines in DNA heteroduplexes using an electroactive osmium marker: towards electrochemical SNP probing. Anal Bioanal Chem 2011; 400:197-204. [DOI: 10.1007/s00216-011-4794-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 02/08/2011] [Accepted: 02/08/2011] [Indexed: 11/28/2022]
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19
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20
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Jacobsen M, Duwensee H, Wachholz F, Adamovski M, Flechsig GU. Directly Heated Bismuth Film Electrodes Based on Gold Microwires. ELECTROANAL 2010. [DOI: 10.1002/elan.200900486] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Nasef H, Beni V, Őzalp VC, O’Sullivan CK. Cystic fibrosis: a label-free detection approach based on thermally modulated electrochemical impedance spectroscopy. Anal Bioanal Chem 2010; 396:2565-74. [DOI: 10.1007/s00216-010-3489-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 01/03/2010] [Accepted: 01/17/2010] [Indexed: 10/19/2022]
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Wong AK, Marushchak DO, Gradinaru CC, Krull UJ. A mixed film composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) brushes to enhance selectivity for detection of single nucleotide polymorphisms. Anal Chim Acta 2010; 661:103-10. [DOI: 10.1016/j.aca.2009.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 11/29/2009] [Accepted: 12/01/2009] [Indexed: 10/20/2022]
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