The effect of base-pair sequence on electrochemically driven denaturation

Johnson, Robert P.; Gao, Rachel; Brown, Tom; Bartlett, Philip N.

doi:10.1016/j.bioelechem.2011.11.003

Cited by 17 publications

(25 citation statements)

References 65 publications

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“…E-melting also allows for straightforward identification of single-nucleotide polymorphisms (SNPs) in target detection through a characteristic effective melting potential, E m (ref. 24). …”

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confidence: 99%

Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

et al. 2017

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The study of biomolecular interactions at the single-molecule level holds great potential for both basic science and biotechnology applications. Single-molecule studies often rely on fluorescence-based reporting, with signal levels limited by photon emission from single optical reporters. The point-functionalized carbon nanotube transistor, known as the single-molecule field-effect transistor, is a bioelectronics alternative based on intrinsic molecular charge that offers significantly higher signal levels for detection. Such devices are effective for characterizing DNA hybridization kinetics and thermodynamics and enabling emerging applications in genomic identification. In this work, we show that hybridization kinetics can be directly controlled by electrostatic bias applied between the device and the surrounding electrolyte. We perform the first single-molecule experiments demonstrating the use of electrostatics to control molecular binding. Using bias as a proxy for temperature, we demonstrate the feasibility of detecting various concentrations of 20-nt target sequences from the Ebolavirus nucleoprotein gene in a constant-temperature environment.

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Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

et al. 2017

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“…The dehybridization kinetics of the fully matched dsDNA shows initially an unexpected behavior. The signal intensity initially increases upon application of the denaturing potential for 20 s which might be explained by orientation changes of the dsDNA at the electrode surface leading to a modulation of the orientation of the Cy3 label at the SERS active electrode surface and consequently to an increased signal . Since SERS amplification crucially depends on the distance between the analyte molecule and the nanostructure, minor orientation changes originating from the decrease in the dsDNA coverage on the surface, may affect the signal intensity substantially.…”

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confidence: 99%

“…Bartlett et al. showed that the so‐called DNA melting potential ( E m ) strongly depends on DNA base sequences and the ionic strength ,. Accordingly, SNP analysis was achieved by defining DNA melting potentials for a number of different oligonucleotides .…”

Section: Introductionmentioning

confidence: 99%

Monitoring Potential‐Induced DNA Dehybridization Kinetics for Single Nucleotide Polymorphism Detection by using In Situ Surface Enhanced Raman Scattering

et al. 2018

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Changes in temperature, ionic strength or electrical field are generally employed to dehybridize double‐stranded DNA (dsDNA). In contrast, we propose potential‐induced dsDNA dehybridization to distinguish fully matched target DNA (tDNA) from tDNA with a single nucleotide polymorphism (SNP) by following their dehybridization kinetics through in situ surface enhanced Raman scattering (SERS). The determination of the potential that evokes notable dehybridization of dsDNA without causing any desorption of the immobilized probe DNA (pDNA) from the electrode surface was performed by investigating the desorption kinetics of labelled single‐stranded DNA (ssDNA) and dehybridization kinetics of dsDNA with labelled tDNA. This comparatively simple approach allows for SNP detection within minutes.

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“…More precisely, we showed discrimination of genetic markers and pathogenic bacteria by targeting short tandem repeats [44] and single nucleotide polymorphism [37,38,45] with detection limits of 0.3 μM without the need for prior-purification of the DNA samples. In addition, electrochemical potentials were found to be insensitive to changes in the local pH over the range 6-8 [46].…”

Section: Introductionmentioning

confidence: 99%

“…In our work a DNA target labelled with a fluorophore is hybridised to a surface bound probe, followed by the application of a suitably negative potential so that the dsDNA melts [37]. E-melting curves, constructed by plotting the SERS intensity of the fluorophore Raman signal against the electrode potential, are then used to discriminate DNA sequences based on differences in the stability of the dsDNA [38]. This technique relies on the fact that the less stable DNA duplexes e.g.…”

Section: Introductionmentioning

confidence: 99%

The effect of temperature on electrochemically driven denaturation monitored by SERS

Papadopoulou

Meneghello

Marafini

et al. 2015

Bioelectrochemistry

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The effect of base-pair sequence on electrochemically driven denaturation

Cited by 17 publications

References 65 publications

Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

Monitoring Potential‐Induced DNA Dehybridization Kinetics for Single Nucleotide Polymorphism Detection by using In Situ Surface Enhanced Raman Scattering

The effect of temperature on electrochemically driven denaturation monitored by SERS

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