Molecular Dipole-Driven Electronic Structure Modifications of DNA/RNA Nucleobases on Graphene

Yin, Yuefeng; Červenka, Jiří; Medhekar, Nikhil V.

doi:10.1021/acs.jpclett.7b01283

Cited by 17 publications

(8 citation statements)

References 62 publications

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“…The work function (Δ W ) shows substantial increase after DNA absorption. These behaviors are consistent with those of current and previous calculations of graphene-based systems 35 . Distinctly and importantly, we found that by comparison with graphene, antimonene exhibits the much stronger interaction with ssDNA, as indicated by the higher adsorption energies (for the ssDNA absorption case, Fig.…”

Section: Resultssupporting

confidence: 93%

Ultrasensitive detection of miRNA with an antimonene-based surface plasmon resonance sensor

et al. 2019

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MicroRNA exhibits differential expression levels in cancer and can affect cellular transformation, carcinogenesis and metastasis. Although fluorescence techniques using dye molecule labels have been studied, label-free molecular-level quantification of miRNA is extremely challenging. We developed a surface plasmon resonance sensor based on two-dimensional nanomaterial of antimonene for the specific label-free detection of clinically relevant biomarkers such as miRNA-21 and miRNA-155. First-principles energetic calculations reveal that antimonene has substantially stronger interaction with ssDNA than the graphene that has been previously used in DNA molecule sensing, due to thanking for more delocalized 5s/5p orbitals in antimonene. The detection limit can reach 10 aM, which is 2.3–10,000 times higher than those of existing miRNA sensors. The combination of not-attempted-before exotic sensing material and SPR architecture represents an approach to unlocking the ultrasensitive detection of miRNA and DNA and provides a promising avenue for the early diagnosis, staging, and monitoring of cancer.

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Section: Resultssupporting

confidence: 93%

Ultrasensitive detection of miRNA with an antimonene-based surface plasmon resonance sensor

et al. 2019

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“…The trends obtained from our MD simulation agree with the first-principles DFT results [38] suggesting that the tilt of the bases is due to the dominance of intermolecular interactions, especially at high surface coverage. Using vdW dispersion-corrected DFT at the wB97XD/6-31 G (d, p) level of theory (see section SI of supporting information), we compared the energy landscape of a cytosine molecule adsorbed on graphene in the perpendicular, tilted and parallel orientations.…”

Section: Self-assembly Of C N On Graphene Surfacesupporting

confidence: 82%

Dynamics of self-assembled cytosine nucleobases on graphene

Saikia¹,

Johnson²,

Waters³

et al. 2018

Nanotechnology

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Molecular self-assembly of cytosine (C ) bases on graphene was investigated using molecular dynamics methods. For free-standing C bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.

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“…This is consistent with earlier experimental and theoretical reports. 21,47 It is shown that the charge transfer for planar nucleobases (ssDNA) is considerably higher compared to tilted (dsDNA) adsorption, which is perfectly matching with our optical ultrafast graphene-optofluidic device ( Figure 2C), CD spectroscopy ( Figure 2D), and Raman spectroscopy ( Figure 1D) results, respectively. The amount of charge transfer from graphene to nucleobases in tilted adsorption (dsDNA) cases is onlỹ 10% of that in planar adsorption (ssDNA).…”

Section: Density Functional Theory Calculations Of Adsorption Of Dnsupporting

confidence: 83%

Probing the dynamic structural changes of DNA using ultrafast laser pulse in graphene‐based optofluidic device

Shivananju

Zhou

Yin

et al. 2020

InfoMat

Self Cite

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The ultrafast monitoring of deoxyribonucleic acid (DNA) dynamic structural changes is an emerging and rapidly growing research topic in biotechnology. The existing optical spectroscopy used to identify different dynamical DNA structures lacks quick response while requiring large consumption of samples and bulky instrumental facilities. It is highly demanded to develop an ultrafast technique that monitors DNA structural changes with the external stimulus or cancer-related disease scenarios. Here, we demonstrate a novel photonic integrated graphene-optofluidic device to monitor DNA structural changes with the ultrafast response time. Our approach is featured with an effective and straightforward design of decoding the electronic structure change of graphene induced by its interactions with DNAs in different conformations using ultrafast nanosecond pulse laser and achieving refractive index sensitivity of~3 × 10 −5 RIU. This innovative technique for the first time allows us to perform ultrafast monitoring of the conformational changes of special DNA molecules structures, including G-quadruplex formation by K + ions and i-motif formation by the low pH stimulus. The graphene-optofluidic device as presented here provides a new

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Molecular Dipole-Driven Electronic Structure Modifications of DNA/RNA Nucleobases on Graphene

Cited by 17 publications

References 62 publications

Ultrasensitive detection of miRNA with an antimonene-based surface plasmon resonance sensor

Ultrasensitive detection of miRNA with an antimonene-based surface plasmon resonance sensor

Dynamics of self-assembled cytosine nucleobases on graphene

Probing the dynamic structural changes of DNA using ultrafast laser pulse in graphene‐based optofluidic device

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