Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study

Kabeláč, Martin; Kroutil, Ondřej; Předota, Milan; Lankaš, Filip; Šíp, Miroslav

doi:10.1039/c2cp23540d

Cited by 27 publications

(37 citation statements)

References 59 publications

(73 reference statements)

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“…Parameters of zero charged graphene were produced using antechamber assigning the atom type ca from the GAFF force field. 27,28 Cellulose was modelled using the GLYCAM06h force field. 29 Scaling factors for 1-4 electrostatic and van der Waals interactions were both taken as unity for cellulose; and the AMBER defaults of 1.2 and 2.0 respectively for graphene.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

“…Whilst COSMO has its limitations as an implicit solvent model 42 , recent work has shown PM6-DH2 calculations in COSMO solvent to give generally good agreement with potential of mean force calculations of adsorption energies in explicit aqueous solvent for compounds on graphene. 28 The adhesion energy in gas-phase and solution was computed as an average of interaction energies computed for structures taken at 20 ns intervals over the last 100 ns of the trajectory. All quantum chemical calculations were performed with MOPAC version 14.128L.…”

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confidence: 99%

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Molecular Dynamics of Cellulose Amphiphilicity at the Graphene–Water Interface

2015

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Molecular dynamics (MD) simulations have been applied to study the interactions between hydrophobic and hydrophilic faces of ordered cellulose chains and a single layer of graphene in explicit aqueous solvent. The hydrophobic cellulose face is predicted to form a stable complex with graphene. This interface remains solvent-excluded over the course of simulations; the cellulose chains contacting graphene in general preserve intra-and inter-chain hydrogen bonds and a tg orientation of hydroxymethyl groups. Greater flexibility is observed in the more solvent-exposed cellulose chains of the complex. By contrast, the hydrophilic face of cellulose exhibits progressive rearrangement over the course of MD simulations, as it seeks to present its hydrophobic face, with disrupted intra-and interchain hydrogen bonding; residue twisting to form CH- interactions with graphene; and partial permeation of water. This transition is also accompanied by a more favorable cellulose-graphene adhesion energy as predicted at the PM6-DH2 level of theory. The stability of the cellulose-graphene hydrophobic interface in water exemplifies the amphiphilicity of cellulose and provides insight into favored interactions within graphene-cellulose materials. Furthermore, partial permeation of water between exterior cellulose chains may indicate potential in addressing cellulose recalcitrance.3

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Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

mentioning

confidence: 99%

Molecular Dynamics of Cellulose Amphiphilicity at the Graphene–Water Interface

2015

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“…Two single-stranded sequences, DNA 1 and DNA 2 , were separately added to GO solutions to form DNA 1 -GO and DNA 2 -GO complexes, respectively. DNA 1 had a target-specific sequence complementary to target DNA (T-DNA) and a d(GT) 15 tail at the 5′ terminus to facilitate the assembly of DNA 1 on GO nanosheets. DNA 2 also had a complementary sequence to T-DNA with a d(GT) 15 tail at the 3′ terminus.…”

Section: Other Detection Mannersmentioning

confidence: 99%

“…DNA 1 had a target-specific sequence complementary to target DNA (T-DNA) and a d(GT) 15 tail at the 5′ terminus to facilitate the assembly of DNA 1 on GO nanosheets. DNA 2 also had a complementary sequence to T-DNA with a d(GT) 15 tail at the 3′ terminus. In the mixture of the two DNA 1 -GO and DNA 2 -GO complexes, T-DNA hybridized with both DNA 1 and DNA 2 , which resulted in an assembly of GO nanosheets.…”

Section: Other Detection Mannersmentioning

confidence: 99%

“…Employing various strategies and techniques, researchers tried to illustrate the interactions between DNA and graphene. Molecular dynamics (MD) simulations of ssDNA and dsDNA anchored via an aliphatic linker to a graphene surface were performed in order to investigate the role of the surface charge density in the structure and orientation of attached DNA [15]. A considerable difference in the behavior of the ssDNA and dsDNA anchored to graphene layer was observed.…”

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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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Hygroscopy of Single‐Stranded DNA Nano‐Brushes: Atomic Workings of its Hydration‐Induced Deformation

Ortega

Vilhena

Pérez

2022

Adv Materials Inter

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Hydration control of structure and mechanical properties is a process widely exploited in living organisms for key biological functions and, most recently, also in man‐made smart materials. Here, the challenge of unveiling the underlying atomistic mechanisms of this phenomenon using all‐atom Molecular Dynamics (MD) simulations to model the hygroscopic properties of polymer‐brushes composed by single‐stranded DNA (ssDNA) molecules is faced. The simulations identify three swelling regimes with a markedly different mechanical response. This evolution is produced by the competition between the formation of additional water–ssDNA and water–water hydrogen bonds, in a subtle interplay with the co‐evolving structure of the ssDNA SAM. This cooperative interaction between conformational and hydration degrees of freedom should be applicable to other polymer brushes and related hydrogen‐bonded systems. The results have direct implications for the use of ssDNA SAMs as sequencing devices, explaining the crucial role of the polymer‐brush density in the SAM collective response to hydration, and for the alternative design of hygroscopic materials, that exploit the extreme hygroscopic power of biological polymers like ssDNA brushes.

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Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study

Cited by 27 publications

References 59 publications

Molecular Dynamics of Cellulose Amphiphilicity at the Graphene–Water Interface

Molecular Dynamics of Cellulose Amphiphilicity at the Graphene–Water Interface

Graphene for DNA Biosensing

Hygroscopy of Single‐Stranded DNA Nano‐Brushes: Atomic Workings of its Hydration‐Induced Deformation

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