Temperature Gradient Approach for Rapidly Assessing Sensor Binding Kinetics and Thermodynamics

Wagner, Caleb E.; Macedo, Lucyano J. A.; Opdahl, Aric

doi:10.1021/acs.analchem.5b01518

Cited by 7 publications

(12 citation statements)

References 29 publications

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“…It is possible to determine the temperature and salt concentration condition that causes DNA hybrids to denature by continuously increasing temperature or decreasing ionic concentration ( Figure 1b). In the literature, measurements of the melting of DNA hybrids have been performed as function of increasing temperature using readouts based on fluorescence [5][6][7] , electrochemistry [8][9][10] , surface plasmon resonance (SPR) 11,12 , surface enhanced Raman spectroscopy (SERS) 13 , and magnetoresistive sensors 14 . Several of these readouts have significant cross-sensitivities to temperature and salt concentration and thus require extra care.…”

Section: Introductionmentioning

confidence: 99%

Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

2017

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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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Section: Introductionmentioning

confidence: 99%

Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

2017

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“…Surface plasmon resonance (SPR) is a collective charge density oscillation that occurs at a metal-dielectric interface. As SPR is extremely sensitive to the temperature-dependent refractive index (RI) just above the metal film, it has extensive applications in temperature monitoring and sensing [ 20 , 21 , 22 ]. In work performed by Chiang et al, a variation as small as 0.027 K was distinguished at 632.8 nm [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

A Novel Microfluidic Flow Rate Detection Method Based on Surface Plasmon Resonance Temperature Imaging

Deng

Wang

Liu

et al. 2016

Sensors

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A novel microfluidic flow rate detection method based on surface plasmon resonance (SPR) temperature imaging is proposed. The measurement is performed by space-resolved SPR imaging of the flow induced temperature variations. Theoretical simulations and analysis were performed to demonstrate a proof of concept using this approach. Experiments were implemented and results showed that water flow rates within a wide range of tens to hundreds of μL/min could be detected. The flow rate sensor is resistant to disturbances and can be easily integrated into microfluidic lab-on-chip systems.

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“…22 Melting curves for surface-tethered DNA probes have also been measured using fluorescence 23 and surface plasmon reso-nance. 24,25 Compared to these methods, the GMR biosensors offer high sensitivity, no dependence on temperature and are insensitive to the sample matrix as virtually all biological material is nonmagnetic. 20,26 Using our technique, we analyzed melanoma cell lines with known genetic and epigenetic alterations.…”

mentioning

confidence: 99%

“…This avoids conventional assay condition optimization since the target-probe hybrids are exposed to continuously increasing stringency during melting curve measurement . Melting curves for surface-tethered DNA probes have also been measured using fluorescence and surface plasmon resonance. , Compared to these methods, the GMR biosensors offer high sensitivity, no dependence on temperature and are insensitive to the sample matrix as virtually all biological material is nonmagnetic. , …”

mentioning

confidence: 99%

Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array

et al. 2017

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Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.

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Temperature Gradient Approach for Rapidly Assessing Sensor Binding Kinetics and Thermodynamics

Cited by 7 publications

References 29 publications

Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

A Novel Microfluidic Flow Rate Detection Method Based on Surface Plasmon Resonance Temperature Imaging

Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array

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