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Estimating Detection Limits of Potentiometric DNA sensors Using Surface Plasmon Resonance Analyses
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.ORCID iD: 0000-0003-3843-7198
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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2020 (English)In: ACS Sensors, E-ISSN 2379-3694, Vol. 5, no 1, p. 217-224Article in journal (Refereed) Published
Abstract [en]

As the signals of potentiometric-based DNA ion-selective field effect transistor (ISFET) sensors differ largely from report to report, a systematic revisit to this method is needed. Herein, the hybridization of the target and the probe DNA on the sensor surface and its dependence on the surface probe DNA coverage and the ionic strength were systematically investigated by surface plasmon resonance (SPR). The maximum potentiometric DNA hybridization signal that could be registered by an ISFET sensor was estimated based on the SPR measurements, without considering buffering effects from any side interaction on the sensing electrode. We found that under physiological solutions (200 to 300 mM ionic strength), the ISFET sensor could not register the DNA hybridization events on the sensor surface due to Debye screening. Lowering the salt concentration to enlarge the Debye length would at the same time reduce the surface hybridization efficiency, thus suppressing the signal. This adverse effect of low salt concentration on the hybridization efficiency was also found to be more significant on the surface with higher probe coverage due to steric hindrance. With the method of diluting buffer, the maximum potentiometric signal generated by the DNA hybridization was estimated to be only around 120 mV with the lowest detection limit of 30 nM, occurring on a surface with optimized probe coverage and in the tris buffer with 10 mM NaCl. An alternative method would be to achieve high-efficiency hybridization in the buffer with high salt concentration (1 M NaCl) and then to perform potentiometric measurements in the buffer with low salt concentration (1 mM NaCl). Based on the characterization of the stability of the hybridized DNA duplexes on the sensor surface in low salt concentration buffer solutions, the estimated maximum potentiometric signal could be significantly higher using the alternative method. The lowest detection limit for this alternative method was estimated to be around 0.6 nM. This work can serve as an important quantitative reference for potentiometric DNA sensors.

Place, publisher, year, edition, pages
2020. Vol. 5, no 1, p. 217-224
National Category
Electrical Engineering, Electronic Engineering, Information Engineering Physical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-397806DOI: 10.1021/acssensors.9b02086ISI: 000510079300029PubMedID: 31833355OAI: oai:DiVA.org:uu-397806DiVA, id: diva2:1372952
Funder
Swedish Foundation for Strategic Research , ICA 12-0047Swedish Foundation for Strategic Research , FFL15-0174Swedish Research Council, VR 2014-5588Wallenberg FoundationsAvailable from: 2019-11-25 Created: 2019-11-25 Last updated: 2020-03-20Bibliographically approved
In thesis
1. Interface Studies for Gold-based Electrochemical DNA Sensors
Open this publication in new window or tab >>Interface Studies for Gold-based Electrochemical DNA Sensors
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Gold based label-free electrochemical DNA sensors have been widely studied for biomarker diagnostics. The sensitivity and reproducibility of these sensors are determined by the sensing interface: the DNA modified gold surfaces. This thesis systematically studies the preparation processes of the DNA sensor interfaces as well as their effects on the sensor performance. First, three pretreatment methods to clean the gold electrode surface and their influence on the subsequent binding of thiolated molecules were carefully investigated. As we found that the surface pretreatment method involving cyclic voltammetry (CV) in H2SO4 may induce structural changes to the gold surface, thus greatly impacting the thiolated molecule binding, the factors influencing this pretreatment method were studied. Practical guidelines were summarized for preparing a clean and reproducible gold surface prior to functionalization. Afterwards, the effects of the surface coverage density of probe DNA and the salt concentration on the probe-target DNA hybridization on a gold sensing surface were systematically investigated using surface plasmon resonance (SPR) analysis. Based on the SPR results, the maximum potentiometric signal that could be generated by the DNA hybridization on the surface, and the detection limits, were estimated for different experimental conditions. These estimations were further compared with experimental results obtained using silicon nanowire field effect transistors (SiNW FET) with DNA modified gold on the gate oxide. Practical limitations for the potentiometric DNA sensor were analysed and discussed. Finally, the stability and reproducibility issues on the electrochemical impedance spectroscopy (EIS) analyses of DNA hybridization were also studied on the aptamer/mercaptohexanol (MCH)-modified gold surface. The root cause for the drift problems in this type of sensor and the temperature effects on the aptamer/MCH modified surface were identified. This thesis could serve as a practical reference for the preparation and understanding of the sensing interface of gold-based electrochemical DNA sensors.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 83
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1882
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
urn:nbn:se:uu:diva-397807 (URN)978-91-513-0824-1 (ISBN)
Public defence
2020-01-20, Polhemsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 09:15 (English)
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Supervisors
Available from: 2019-12-18 Created: 2019-11-25 Last updated: 2020-01-14

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Xu, XingxingMakaraviciute, AstaAbdurakhmanov, EldarLi, ShiyuDanielson, U. HelenaNyholm, LeifZhang, Zhen

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