Effect of pH and Salt on Adsorption of Double-Stranded DNA on Graphene Oxide

Kim, Seyeon; Park, Chanoong; Gang, Jongback

doi:10.1166/jnn.2015.11217

Cited by 12 publications

(11 citation statements)

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“…Overall, results in the presence of magnesium ions were more reproducible, consistent with the observations of Lei et al, that metallic ions, such as Mg 2+ , Ca 2+ , Na + and K + induced a good distribution of DNA macromolecules on the surface of graphene oxide and facilitated the formation of dsDNA/GO and/or ssDNA/GO complexes as metal ions neutralized the electrostatic repulsions between the macromolecule and the nanomaterials [ 30 ]. Moreover, our results confirmed that the presence of metallic ions facilitated the quenching of the dsDNA on GO and GO-COOH surfaces [ 47 ]. Double-helix formation induces a conformational length change of the joining single-stranded molecules.…”

Section: Discussionsupporting

confidence: 78%

Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength

Becheru

Vlăsceanu

Banciu

et al. 2018

IJMS

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A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial dispersion, ionic strength, and appropriate molecular interaction mechanisms. Herein we study interactions between a fluorescein-labelled DNA (FAM-DNA) probe and target single-stranded complementary DNA (cDNA) on three graphenic species, aiming to determine the most suitable platform for nucleic acid detection. Graphene oxide (GO), carboxyl graphene (GO-COOH) and reduced graphene oxide functionalized with PEGylated amino groups (rGO-PEG-NH2, PEG (polyethylene glycol)) were dispersed and characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of ionic strength on molecular interaction with DNA was examined by fluorescence resonance energy transfer (FRET) comparing fluorescence intensity and anisotropy. Results indicated an effect of graphene functionalization, dispersion and concentration-dependent quenching, with GO and GO-COOH having the highest quenching abilities for FAM-DNA. Furthermore, GO and GO-COOH quenching was accentuated by the addition of either MgCl2 or MgSO4 cations. At 10 mM MgCl2 or MgSO4, the cDNA induced a decrease in fluorescence signal that was 2.7-fold for GO, 3.4-fold for GO-COOH and 4.1-fold for rGO-PEG-NH2. Best results, allowing accurate target detection, were observed when selecting rGO-PEG-NH2, MgCl2 and fluorescence anisotropy as an advantageous combination suitable for nucleic acid detection and further rational design biosensor development.

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Section: Discussionsupporting

confidence: 78%

Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength

Becheru

Vlăsceanu

Banciu

et al. 2018

IJMS

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“…Therefore, we explored the dynamic process of the adsorption of ssDNA and dsDNA on G d rGO-PEG-NH2 under the influence of Mg 2+ and Cl − ions to better understand their impa 2,13]. Notably, we confirmed that for GO, the addition of Mg 2+ ions critically contributed DNA adsorption and provided an atomistic perspective for the adsorption process.…”

Section: Generation Of the Dna Moleculesmentioning

confidence: 68%

“…The resulting charge repulsion lowers the binding affinity of the dsDNA to the negatively charged oxygen atoms on the GO surface. Both experimental and computational studies have investigated the different aspects regarding the effect of using nucleic acids and different graphenic molecules [9][10][11][12][13]. Experimental studies showed that both Mg 2+ ions and functionalized derivatives of graphene, in particular an aminated polyethylene glycol-functionalized reduced graphene oxide (rGO-PEG-NH 2 ), markedly influenced detection of DNA hybridization [12,13].…”

Section: Introductionmentioning

confidence: 99%

“…Both experimental and computational studies have investigated the different aspects regarding the effect of using nucleic acids and different graphenic molecules [9][10][11][12][13]. Experimental studies showed that both Mg 2+ ions and functionalized derivatives of graphene, in particular an aminated polyethylene glycol-functionalized reduced graphene oxide (rGO-PEG-NH 2 ), markedly influenced detection of DNA hybridization [12,13]. Previous computational studies investigated the mechanism of adsorption between DNA molecules and graphene only in the presence of Na + ions and indicated it is governed by π-π stacking between the aromatic rings of the graphene layer and the exposed bases of the oligonucleotides, hydrogen bonds and electrostatic interactions [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions

et al. 2020

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Graphene and its functionalised derivatives are transforming the development of biosensors that are capable of detecting nucleic acid hybridization. Using a Molecular Dynamics (MD) approach, we explored single-stranded or double-stranded deoxyribose nucleic acid (ssDNA or dsDNA) adsorption on two graphenic species: graphene oxide (GO) and reduced graphene oxide functionalized with aminated polyethylene glycol (rGO-PEG-NH2). Innovatively, we included chloride (Cl−) and magnesium (Mg2+) ions that influenced both the ssDNA and dsDNA adsorption on GO and rGO-PEG-NH2 surfaces. Unlike Cl−, divalent Mg2+ ions formed bridges between the GO surface and DNA molecules, promoting adsorption through electrostatic interactions. For rGO-PEG-NH2, the Mg2+ ions were repulsed from the graphenic surface. The subsequent ssDNA adsorption, mainly influenced by electrostatic forces and hydrogen bonds, could be supported by π–π stacking interactions that were absent in the case of dsDNA. We provide a novel insight for guiding biosensor development.

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“…33 By contrast, some surfactants, such as Tween 20 and Triton X-100, strongly interfere with the formation of dsDNA/GO complexes. 30,34 We deduced that the short primer-dimers (usually less than 40 bp) might be selectively adsorbed by GO from PCR products under a carefully optimized condition. As a result, this new test strip coupled with the on-strip GO purification should be able to overcome the troubles associated with the conventional antibody-based method without causing any inconvenience to the overall detection process.…”

mentioning

confidence: 99%

Integrated Graphene Oxide Purification-Lateral Flow Test Strips (iGOP-LFTS) for Direct Detection of PCR Products with Enhanced Sensitivity and Specificity

Lyu³

et al. 2017

Anal. Chem.

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An integrated graphene oxide purification-lateral flow test strip (iGOP-LFTS) was developed for on-strip purifying and visually detecting polymerase chain reaction (PCR) products with an improved sensitivity as well as a more stringent specificity. PCR products amplified with a pair of biotin- and digoxin-labeled primers were directly pipetted onto GO pads, on which graphene oxide selectively adsorbed residual primers and primer-dimers with the aid of a running buffer containing MgCl and Tween 20. By stacking up three GO pads to increase the surface area for adsorption, 83.4% of double-stranded DNA with a length of 30 bp and 98.6% of 20-nt primers could be removed from a 10-μL DNA mixture. Since no primers interfered with detection, the increase of the sample loading volume from 5 to 20 μL could improve the signal-to-noise ratio of the test line 1.6 fold using the iGOP-LFTS while no changes were observed using the conventional LFTS. The limit of detection of the iGOP-LFTS was determined to be 30 copies of bacteriophage λ-DNA with naked eyes and this limit could be further decreased to 3 copies by loading 20 μL of the sample, which corresponded to a 1000-fold improvement compared to that of the LFTS detected by naked eyes. When the ImageJ analysis was employed, a 100-fold decrease of the detection limit can be obtained. In addition, due to the removal of the primer-dimers, the dim test line observed in the negative control of the LFTS was eliminated using the iGOP-LFTS. A mock clinical specimen spiked with defective HIV-1 (human immunodeficiency virus) viruses was successfully analyzed using a two-step reverse transcription-PCR with 30 amplification cycles followed by the iGOP-LFTS detection. These significant improvements were achieved without introducing any additional hands-on operations and instrumentations.

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Effect of pH and Salt on Adsorption of Double-Stranded DNA on Graphene Oxide

Cited by 12 publications

References 0 publications

Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength

Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength

Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions

Integrated Graphene Oxide Purification-Lateral Flow Test Strips (iGOP-LFTS) for Direct Detection of PCR Products with Enhanced Sensitivity and Specificity

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