Colorimetric aptasensor based on assembly of salt-induced gold nanoparticles (AuNPs) is a promising biosensor. However, the molecular mechanism of the aptasensor is far from being fully understood. Herein, molecular dynamics (MD) simulation was used to investigate molecular interactions in the detection of ochratoxin A (OTA) including the following: (i) the molecular recognition of the anti-OTA aptamer, (ii) OTA-aptamer interactions in monovalent (Na) and divalent (Mg) electrolytes, (iii) the binding mode of citrate on the AuNP surface, (iv) interactions of the aptamer with citrate-capped AuNPs, and (v) a detailed mechanism of the aptasensor. Our MD simulations revealed a specific binding of the OTA-aptamer complex, compared with OTB and warfarin. Compared with Na, Mg ions exerted a more effective attractive force between OTA and anti-OTA aptamer. Three different binding modes of citrate on AuNP surfaces were found. The kinetics of the adsorption of unfolded aptamers onto the citrate-capped AuNP was also elucidated. Most importantly, our MD simulation revealed an insightful analysis of the molecular mechanisms in the AuNP-based aptasensor and paved the way for the design of a novel colorimetric aptasensor for other target molecules, which is not limited to OTA detection.
The concentration
of 8-oxo-7,8-dihydro-2′-deoxyguanosine
(8-oxo-dG) in urine or serum is associated with the degree of oxidative
damage of DNA and broadly used as a sensitive biomarker for various
diseases. However, determination of a low concentration of 8-oxo-dG
in biosamples is not an easy task owing to the complexity of coexisting
substances. Herein, we design an aptasensor based on aptamer-mediated
aggregation of cysteamine-capped gold nanoparticles (Cyst/AuNPs) for
the detection of 8-oxo-dG by molecular dynamics simulation. Our simulations
reveal that a positively charged Cyst modified onto the surfaces of
AuNP exists in two conformers including gauche and trans. The trans conformer was prevalent
on the AuNP surfaces and can stabilize AuNPs in the aqueous solution,
even in the presence of 8-oxo-dG. Molecular recognition between 8-oxo-dG
and the aptamer was demonstrated and bonding between these biomolecules
was thoroughly elucidated. During the complex formation, van der Waals
stacking interactions between 8-oxo-dG molecules were observed and
found to play a significant role in the binding stability. The sensing
mechanism of the colorimetric aptasensor was studied and the feasibility
study of the proposed aptasensor was assessed by experimental validation.
The experimental results are in good agreement with the computational
study. Our in silico design can pave the way for,
but is not limited to, a highly sensitive aptasensor for the naked-eye
detection of 8-oxo-dG.
In cancer genomes, DNA methylation
results in the formation of
a distinct methylation landscape (methylscape) characterized by clustered
methylation at regulatory regions separated by extensive intergenic
tracks of hypomethylated regions. This methylscape is expressed in
the majority of cancer types, thus serving as a universal biomarker
for cancer. The aim of the present study was to distinguish between
normal and cancer DNA on the basis of their distinct methylscapes
using cysteamine-capped gold nanoparticles (Cyst/AuNPs). The signature
interactions between cancer DNA and the positively charged AuNPs were
revealed by molecular dynamics (MD) simulations and density functional
theory (DFT) calculations. Our simulations demonstrate that DNA aggregates
in aqueous solution in a methylation-dependent manner, due primarily
to the increased hydrophobic force caused by the addition of the methyl
group. This suggests that the distinct methylscapes of cancer and
normal DNA may result in different agglomerations in aqueous solutions.
Cyst/AuNP adsorption patterns on normal and cancer DNA aggregates
were also observed to be distinct in MgCl2 solution. Using
MD simulations, we discovered that the backbone of oligonucleotides
plays a significant role in DNA adsorption onto the gold surface.
In addition to that, our DFT calculations indicate that 5-methylcytosine
(5-mC) adsorbed on the gold surface has a lower adsorption energy
in comparison to cytosine, suggesting that 5-mC is a more favorable
site for AuNP adsorption. Due to the methylation-dependent adsorption
of Cyst/AuNPs on DNA aggregates, this enables the use of Cyst/AuNPs
in cancer screening on the basis of the dispersion of AuNPs adsorbed
on DNA aggregates, which is consistent with our experimental validation.
This work paves the way for the development of a rapid colorimetric
AuNP-based biosensor for methylscape detection that could be used
for universal cancer screening.
DNA methylation is an epigenetic
modification involving the transfer
of a methyl group to cytosine residues of a DNA molecule. Altered
DNA methylation of certain genes is associated with several diseases
including cancer. Nanomaterials, such as graphene oxide (GO), offer
great potential as sensing elements for methylated DNA (mDNA) detection
due to their distinct properties. Understanding molecular interactions
between mDNA and GO can make provision for developing a universal
cancer screening test. Molecular dynamics (MD) simulation and density
functional theory (DFT) calculation have been employed for investigating
their detailed macro- and microscale interactions. Based upon the
MD simulation, different adsorption levels of methylated and unmethylated
DNAs on GO were represented by a contacting surface area (CSA), which
depends on surrounding conditions (in water or a MgCl2 solution).
In water, the CSAs of the methylated and unmethylated single-stranded
DNA (ssDNA) were ≈13 and ≈5 nm2, respectively,
representing more preferable adsorption on GO for the methylated ssDNA.
In the presence of divalent ions (Mg2+), the CSAs of both
methylated and unmethylated DNA molecules were ≈8 nm2, suggesting that there was no significant difference in adsorption
in a saline solution. To reveal the electrical property of GO covered
by either methylated or unmethylated DNA, its electronic structure
was investigated by the DFT calculation. The energy gaps of pristine
graphene (pG) and GO adsorbed by 5-methylcytosine (5mC) were 1.6 and
12.9 meV, respectively, while cytosine adsorption resulted in lower
energy gaps (1.2 meV for pG and 9.5 meV for GO). When comparing methylated
DNA-covered GO with that covered with unmethylated DNA, remarkable
differences in electrical conductivity, which were caused by the electronic
structure of GO, were observed. These findings will provide a new
route for an efficient detection method of DNA methylation, which
can further be used to develop a universal cancer test.
Paraquat is a widely used herbicide for controlling weeds and grasses in agriculture, and its contaminated residues in agricultural areas are of increasing concern. This work reports the development of the sensitive and easy‐to‐use colorimetric aptasensor for screening paraquat residues in agricultural soil. The short DNA fragments derived from the original aptamer were analyzed for their capability to interact with paraquat by molecular dynamic simulation. The paraquat‐aptasensor was developed using the selected DNA fragment and gold nanoparticles. Its limit of detection (LOD) for paraquat is 2.76 nM, which is more sensitive than the aptasensor with long‐length aptamer (LOD = 12.98 nM). The developed aptasensor shows the selectivity to paraquat, but not to other tested herbicides; ametryn, atrazine, difenzoquat, 2,4‐D‐dimethyl ammonium, and glufosinate. The recovery rates of paraquat detection in the spiked soil samples were in a range of 99.5%–105.1%, with relative standard deviation values of <4%. The developed aptasensor was used to screen for paraquat residues in agricultural soils, and three out of 23 soil samples were tested positive for paraquat, which was confirmed by a high‐performance liquid chromatography analysis. These results suggested the potential application of the developed aptasensor to detect paraquat residues in agricultural sites.
The methylation landscape (Methylscape) of normal and malignant DNAs is different, resulting in unique self-assembly patterns in solution. The dispersion of cysteamine-capped AuNPs adsorbed onto DNA clusters could be employed to identify cancer DNA.
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