A graphene-based platform for single nucleotide polymorphism (SNP) genotyping

Liu, Meng; Zhao, Huimin; Chen, Shuo; Yu, Hongtao; Zhang, Yaobin; Quan, Xie

doi:10.1016/j.bios.2011.03.023

Cited by 21 publications

(13 citation statements)

References 54 publications

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“…In contrast, for the mutant-type target, the fluorescence signal increased rapidly, suggesting that the hairpin probe was effectively degraded by T7 Exo. The signal-tobackground ratio of the mutant type was 11 times that of the wild-type target, indicating that T7 Exo had high specificity in discriminating single-base matches, which was comparable to those using high-specificity ligases [29,30]. We also evaluated the selectivity by comparison of 3-base mismatch DNA and 5-base mismatch DNA (see Electronic Supplementary Material (ESM) Fig.…”

Section: Feasibility Testingmentioning

confidence: 99%

Improving the sensitivity and selectivity of a DNA probe using graphene oxide-protected and T7 exonuclease-assisted signal amplification

Zhang

Chen

et al. 2020

Anal Bioanal Chem

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The accurate analysis of single-nucleotide polymorphisms is of great significance for clinical detection and diagnosis. Based on the hybridization hindrance caused by graphene oxide (GO) and hairpin probe, we report a T7 Exo-assisted cyclic amplification technique to distinguish single-base mismatch for highly sensitive and selective detection of mutant-type DNA. When the mutant-type target is completely complementary to the probe, the T7 Exo hydrolyzes the probe and releases the fluorescent molecule from the GO surface, resulting in a fluorescence signal. Conversely, when the wild-type mismatch target is present, the weak hybridization prevents the release of FAM-labeled probe from the GO surface. Therefore, the FAM-labeled probe cannot be degraded efficiently by T7 Exo, and the fluorescence is still quenched by GO. The detection limit of the proposed method can be as low as 34 fM due to the cyclic signal amplification. The experimental results showed that the established method could be used to detect single-nucleotide polymorphisms accurately and sensitively at low cost.

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Section: Feasibility Testingmentioning

confidence: 99%

Improving the sensitivity and selectivity of a DNA probe using graphene oxide-protected and T7 exonuclease-assisted signal amplification

Zhang

Chen

et al. 2020

Anal Bioanal Chem

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“…With the aid of DNA ligase, fluorescent DNA single-nucleotide polymorphism (SNP) detection was achieved based on the quenching capacity of graphene [34]. By using in situ-generated hydroxyl radical ( · OH), which caused DNA damage by abstracting an H atom from phosphate backbone, the interaction between ssDNA and graphene was regulated.…”

Section: Fluorescent Assaymentioning

confidence: 99%

Graphene for DNA Biosensing

Han

et al. 2014

SpringerBriefs in Molecular Science

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Graphene (or GO) is an excellent candidate for biomolecules anchoring and detection due to its large surface area (up to 2,630 m 2 /g) and unique sp 2 (sp 2 /sp 3 )-bonded network. According to the binding affinity difference between single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) to graphene sheet, GO has been successfully adopted as a platform to discriminate DNA sequences. Fluorescent, electrochemical, electrical, surface-enhanced Raman scattering (SERS) and other methods have been utilized to achieve the sensitive, selective, and accurate DNA recognition. Both theoretical and experimental results illustrate that ssDNA sequences are adsorbed on the surface of graphene sheet with all nucleobases lying nearly flat. DNA or RNA sequencing through graphene nanopore, nanogap, and nanoribbon has also attracted much interest because it is a label-free, amplification-free, and single-molecule approach that can be scaled up for high-throughput DNA or RNA analysis. Meanwhile, miRNA detection is achieved by forming DNA-miRNA duplex helixes, and strong emission is observed due to the poor interaction between the helix and GO.Keywords DNA sequencing Á miRNA detection Á Fluorescent spectroscopy Á Electrochemical method Á Electrical method Á Graphene nanopore Á Graphene nanogap Á Graphene nanoribbon Investigation of DNA and Graphene Binding InteractionThe large surface area (up to 2,630 m 2 /g) and unique sp 2 (sp 2 /sp 3 )-bonded network make graphene (GO) an excellent candidate for biomolecules anchoring and detection. Taking DNA for the first example, various strategies have been adopted to nucleic acid sequence recognition [1][2][3][4][5][6][7][8][9][10]. To better illustrate the interaction, how nucleobases interact with graphene should be addressed, which may be inspired by the interaction of nucleobases with CNTs [11-13] and highly oriented pyrolytic graphite (HOPG) [14].

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“…Moreover, the graphitic carbon of GO allows the quenching of nearby fluorescent species, such as dyes6, conjugated polymers7, and quantum dots8, by both long-range energy-transfer and electron-transfer processes91011. Based on these unique optical properties, many solution-based sensors employing fluorescence quenching based on fluorescence resonance energy transfer (FRET)123 or non-radiative dipole-dipole coupling1678 have been exploited for the homogeneous detection of DNA11121314151617, proteins8181920212223, enzymes242526272829, metal ions30313233, and cancer cells34.…”

mentioning

confidence: 99%

“…Ionic groups and aromatic domains in GO allow it to bind dye-labeled single-stranded DNAs (ssDNAs) and charged proteins via electrostatic and π-π stacking interactions, resulting in the quenching of adjacent dyes1231112131415161718192021222324252627282930313233. However, in the presence of the target analyte, the competitive binding of the target molecule for dye-labeled probes allows desorption of probes from the GO surface, leading to recovery of the initially quenched fluorescence.…”

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confidence: 99%

Highly Tunable Aptasensing Microarrays with Graphene Oxide Multilayers

Jung

Lee

Shin

et al. 2013

Sci Rep

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A highly tunable layer-by-layer (LbL)-assembled graphene oxide (GO) array has been devised for high-throughput multiplex protein sensing. In this array, the fluorescence of different target-bound aptamers labeled with dye is efficiently quenched by GO through fluorescence resonance energy transfer (FRET), and simultaneous multiplex target detection is performed by recovering the quenched fluorescence caused by specific binding between an aptamer and a protein. Thin GO films consisting of 10 bilayers displayed a high quenching ability, yielding over 85% fluorescence quenching with the addition of a 2 μM dye-labeled aptamer. The limit for human thrombin detection in the 6- and 10-bilayered GO array is estimated to be 0.1 and 0.001 nM, respectively, indicating highly tunable nature of LbL assembled GO multilayers in controlling the sensitivity of graphene-based FRET aptasensor. Furthermore, the GO chip could be reused up to four times simply by cleaning it with distilled water.

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A graphene-based platform for single nucleotide polymorphism (SNP) genotyping

Cited by 21 publications

References 54 publications

Improving the sensitivity and selectivity of a DNA probe using graphene oxide-protected and T7 exonuclease-assisted signal amplification

Improving the sensitivity and selectivity of a DNA probe using graphene oxide-protected and T7 exonuclease-assisted signal amplification

Graphene for DNA Biosensing

Highly Tunable Aptasensing Microarrays with Graphene Oxide Multilayers

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