On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

Rizzi, Giovanni; Østerberg, Frederik Westergaard; Henriksen, Anders Dahl; Dufva, Martin; Hansen, Mikkel Fougt

doi:10.1016/j.jmmm.2014.09.004

Cited by 22 publications

(20 citation statements)

References 25 publications

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“…After low stringency hybridization it was not possible to genotype SNPs since both perfectly matched and single point mismatched hybrids were stable in those conditions. We have previously demonstrated that single base mismatches can be detected using a magnetoresistive sensor platform by challenging the hybrids with a stringent washing (Rizzi et al, 2014) and/or increasing temperature (Rizzi et al, 2015) to characterize the melting profiles for the WT and MT probes.…”

Section: Strategies For Detection Of Ds-pcr Productsmentioning

confidence: 99%

Denaturation strategies for detection of double stranded PCR products on GMR magnetic biosensor array

Rizzi

Lee

Guldberg

et al. 2017

Biosensors and Bioelectronics

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Microarrays and other surface-based nucleic acid detection schemes rely on the hybridization of the target to surface-bound detection probes. We present the first comparison of two strategies to detect DNA using a giant magnetoresistive (GMR) biosensor platform starting from an initially double-stranded DNA target. The target strand of interest is biotinylated and detected by the GMR sensor by linking streptavidin magnetic nanoparticles (MNPs) to the sensor surface. The sensor platform has a dynamic detection range from 40pM to 40nM with highly reproducible results and is used to monitor real-time binding signals. The first strategy, using off-chip heat denaturation followed by sequential on-chip incubation of the nucleic acids and MNPs, produces a signal that stabilizes quickly but the signal magnitude is reduced due to competitive rehybridization of the target in solution. The second strategy, using magnetic capture of the double-stranded product followed by denaturing, produces a higher signal but the signal increase is limited by diffusion of the MNPs. Our results show that both strategies give highly reproducible results but that the signal obtained using magnetic capture is higher and insensitive to rehybridization.

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Section: Strategies For Detection Of Ds-pcr Productsmentioning

confidence: 99%

Denaturation strategies for detection of double stranded PCR products on GMR magnetic biosensor array

Rizzi

Lee

Guldberg

et al. 2017

Biosensors and Bioelectronics

Self Cite

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“…The melting data was corrected for the temperature dependence of the sensor sensitivity using a reference sweep from T=70°C to 20°C measured after complete denaturation of the hybrids as described previously. 14…”

Section: Temperature Meltingmentioning

confidence: 99%

“…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%

“…16,17 Detecting magnetic nanoparticle labels present an attractive approach as magnetic sensors are only very weakly sensitive to variations in temperature and salt concentration. 14,18,19 Further, they can be made in a compact format and with a scalable number of sensors. 20 Recently, we demonstrated the use of so-called planar Hall effect bridge (PHEB) sensors for real-time measurements of the temperature melting of DNA hybrids.…”

Section: Introductionmentioning

confidence: 99%

“…20 Recently, we demonstrated the use of so-called planar Hall effect bridge (PHEB) sensors for real-time measurements of the temperature melting of DNA hybrids. 14 In the present work, we further investigate the combined effect of temperature and salt concentration. We demonstrate two-dimensional salt and temperature denaturing mapping of a target to WT and MT probes to investigate salt concentration melting and to identify optimum conditions for discrimination between matching and mismatching target-probe hybrids.…”

Section: Introductionmentioning

confidence: 99%

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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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The future point-of-care detection of disease and its data capture and handling

2016

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Point-of-care detection is a widely studied area that attracts effort and interest from a large number of fields and companies. However, there is also increased interest from the general public in this type of device, which has driven enormous changes in the design and conception of these developments and the way data is handled. Therefore, future point-of-care detection has to include communication with front-end technology, such as smartphones and networks, automation of manufacture, and the incorporation of concepts like the Internet of Things (IoT) and cloud computing. Three key examples, based on different sensing technology, are analyzed in detail on the basis of these items to highlight a route for the future design and development of point-of-care detection devices and their data capture and handling.

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On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

Cited by 22 publications

References 25 publications

Denaturation strategies for detection of double stranded PCR products on GMR magnetic biosensor array

Denaturation strategies for detection of double stranded PCR products on GMR magnetic biosensor array

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

The future point-of-care detection of disease and its data capture and handling

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