DNA Sequencing Sensors: An Overview

Garrido-Cárdenas, José Antonio; Garcı́a-Maroto, Federico; Bermejo, José Antonio Álvarez; Manzano‐Agugliaro, Francisco

doi:10.3390/s17030588

Cited by 73 publications

(64 citation statements)

References 60 publications

(59 reference statements)

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“…Glucose biosensors accounts for about 85% of biosensors industry. In fact, reliable and fast monitoring of glucose represents an important analytical tool in many scientific and technology fields such as health [1], food industry [2], environmental assessment [3], and molecular biology [4]. In particular, diabetes pathologies pushed the research to develop self-monitoring glucose and non-invasive glucose monitoring systems [5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Dewetted Gold Nanostructures onto Exfoliated Graphene Paper as High Efficient Glucose Sensor

et al. 2019

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Non-enzymatic electrochemical glucose sensing was obtained by gold nanostructures on graphene paper, produced by laser or thermal dewetting of 1.6 and 8 nm-thick Au layers, respectively. Nanosecond laser annealing produces spherical nanoparticles (AuNPs) through the molten-phase dewetting of the gold layer and simultaneous exfoliation of the graphene paper. The resulting composite electrodes were characterized by X-ray photoelectron spectroscopy, cyclic voltammetry, scanning electron microscopy, micro Raman spectroscopy and Rutherford back-scattering spectrometry. Laser dewetted electrode presents graphene nanoplatelets covered by spherical AuNPs. The sizes of AuNPs are in the range of 10–150 nm. A chemical shift in the XPS Au4f core-level of 0.25–0.3 eV suggests the occurrence of AuNPs oxidation, which are characterized by high stability under the electrochemical test. Thermal dewetting leads to electrodes characterized by faceted not oxidized gold structures. Glucose was detected in alkali media at potential of 0.15–0.17 V vs. saturated calomel electrode (SCE), in the concentration range of 2.5μM−30 mM, exploiting the peak corresponding to the oxidation of two electrons. Sensitivity of 1240 µA mM−1 cm−2, detection limit of 2.5 μM and quantifications limit of 20 μM were obtained with 8 nm gold equivalent thickness. The analytical performances are very promising and comparable to the actual state of art concerning gold based electrodes.

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Section: Introductionmentioning

confidence: 99%

Dewetted Gold Nanostructures onto Exfoliated Graphene Paper as High Efficient Glucose Sensor

et al. 2019

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“…In the 1990’s, electrochemists turned their attention to DNA hybridization studies with labeled synthetic ODN's at gold electrodes in the hope that electrochemical methods will be widely applied for genomic sequencing. With the arrival of the “next generation DNA sequencing” methods such hopes are gradually disappearing. Nevertheless, there are still numerous possibilities where electrochemical methods can be very useful in the analysis of nucleic acids, including DNA and RNA aptamers, microRNA and pathogen detection, cell‐free DNA, DNA methylation, DNA‐protein interaction analysis, etc.…”

Section: Discussionmentioning

confidence: 99%

J. Heyrovský's Oscillographic Polarography. Roots of Present Chronopotentiometric Analysis of Biomacromolecules

2018

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In 1941 J. Heyrovský invented Oscillographic Polarography (OP) with controlled alternating current (a.c.). The method was developed during the World War and the first commercially available instruments for OP were produced in Czechoslovakia at the beginning of the 1950’s. Such instruments offered derivative and cyclic OP curves allowing simple analysis of various compounds and stimulated the publication of hundreds of papers. Thanks to OP, electrochemical analysis of DNA started already in 1958. According to the present nomenclature, OP can be denominated as a.c. chronopotentiometry. Surprisingly, authors who later described derivative and cyclic chronopotentiometry did not consider J. Heyrovský’s OP methodology in their work. Present electrochemical studies of biomacromolecules take advantage of modern instruments for constant current chronopotentiometric stripping, allowing DNA and protein structure‐sensitive analysis. Recent progress in these studies is reviewed.

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“…Meanwhile, significant advances have been made since the invention of second generation sequencing (SGS) [ 31 , 32 ]. Third generation sequencing (TGS) platforms, for example single molecule real-time sequencing technology (SMRT) [ 33 ] and nanopore sequencing [ 34 ], offer read lengths up to 20,000 base pairs but currently is associated with 60–100 higher costs per (Giga-) base than SGS on the Illumina platform [ 32 ]. As splice-site observation probability is not improved by longer reads and considerable amounts of samples are required for the detection of occasionally observed splice-sites, TGS unlikely will replace SGS here.…”

Section: Discussionmentioning

confidence: 99%

Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data

Kaisers

Schwender

Schaal

2017

IJMS

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Merging data from multiple samples is required to detect low expressed transcripts or splicing events that might be present only in a subset of samples. However, the exact number of required replicates enabling the detection of such rare events often remains a mystery but can be approached through probability theory. Here, we describe a probabilistic model, relating the number of observed events in a batch of samples with observation probabilities. Therein, samples appear as a heterogeneous collection of events, which are observed with some probability. The model is evaluated in a batch of 54 transcriptomes of human dermal fibroblast samples. The majority of putative splice-sites (alignment gap-sites) are detected in (almost) all samples or only sporadically, resulting in an U-shaped pattern for observation probabilities. The probabilistic model systematically underestimates event numbers due to a bias resulting from finite sampling. However, using an additional assumption, the probabilistic model can predict observed event numbers within a <10% deviation from the median. Single samples contain a considerable amount of uniquely observed putative splicing events (mean 7122 in alignments from TopHat alignments and 86,215 in alignments from STAR). We conclude that the probabilistic model provides an adequate description for observation of gap-sites in transcriptome data. Thus, the calculation of required sample sizes can be done by application of a simple binomial model to sporadically observed random events. Due to the large number of uniquely observed putative splice-sites and the known stochastic noise in the splicing machinery, it appears advisable to include observation of rare splicing events into analysis objectives. Therefore, it is beneficial to take scores for the validation of gap-sites into account.

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DNA Sequencing Sensors: An Overview

Cited by 73 publications

References 60 publications

Dewetted Gold Nanostructures onto Exfoliated Graphene Paper as High Efficient Glucose Sensor

Dewetted Gold Nanostructures onto Exfoliated Graphene Paper as High Efficient Glucose Sensor

J. Heyrovský's Oscillographic Polarography. Roots of Present Chronopotentiometric Analysis of Biomacromolecules

Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data

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