Adsorption of nucleobase pairs on hexagonal boron nitride sheet: hydrogen bonding versus stacking

Exploring the fascinating interplay of epigenetically modified DNA bases with two dimensional bare and P-doped Si2BN and BN sheets for biosensing applications: A compelling DFT perspective

Detecting epigenetically modified (EM) bases is crucial for disease detection, biosensing, and DNA sequencing. Two-dimensional P-doped Si2BN and BN sheets are used as sensing substrates in density functional theory (DFT) studies. Both the sheets are doped with a phosphorous atom at various atomic sites to examine the sheet's potential in detecting 5-hydroxymethylcytosine (5hmc), 5-methylcytosine (5mc), 7-methylguanine (7 mg) and 8-oxoguanine (8oxg) bases. Doping of the P atom in the Si2BN sheet improves the adsorption energy (Ead) of Ab+5hmc (-107.16 kcal/mol) and Ab+5mc (-78.36 kcal/mol), As+7 mg (-84.31 kcal/mol) in the gas and aqueous phase Ab+5hmc (-93.28 kcal/mol), An+7 mg (-78.92 kcal/mol) and As+5mc (-77.52 kcal/mol) respectively. Standard deviation (θ) indicates that As complexes have high θ values ranging from 4.55 to 37.77, suggesting a high likelihood of distinguishing the bases. The P-doped BN complexes exhibit noticeable work functional shifting (Δϕ%) recommended that they can be used as ϕ-based sensors. Time-dependent DFT results suggest that when EM bases interact with P-doped Si2BN complexes, significant blue shifts (hypsochromic) and red shifts (bathochromic) are observed in the visible and near-infrared spectrum. Hence, the above finding suggests that P-doped Si2BN sheets are highly effective for sensing EM bases and are recommended for DNA/RNA sequencing applications.

Label-Free Imaging of DNA Interactions with 2D Materials

Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.

Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study

Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.

Possible effects of fluxionality of a cavitand on its catalytic activity through confinement

The discovery of fullerenes was a huge milestone in the scientific community, and with it came the urge to discover and analyze various small and large atomic and molecular clusters having a cavity. These cavitands of varied shapes and sizes have wide applications in the encapsulation of rare gas atoms to induce bond formation between them, storage of hydrogen and hydrocarbons to be used as alternative sources of fuel, catalyzation of otherwise slow reactions without using a catalyst, activation of small gas molecules, etc. Various cavitands like fullerenes, [ExBox]4+, cucurbit[n]urils, borospherenes, octa acid, etc. have been used for this purpose. Some clusters including cavitands exhibit fluxional behaviour. Systems in a confined environment often manifest interesting variations in their properties and behaviour, compared to their unconfined counterparts, facilitating the aforementioned applications. In this perspective article, we explore the possibility of making use of this extra degree of freedom, viz., the fluxionality, in changing the catalytic activity of the cavitand.

Revealing the mechanism of DNA passing through graphene and boron nitride nanopores

Nanopores on 2D materials have great potential for DNA sequencing, which is attributed to their high sequencing speed and reduced cost. However, identifying DNA bases at such a high speed with nanometer precision has remained a big challenge. Here, we implemented theoretical calculations to show the translocation of single-stranded DNA (ssDNA) through solid-state nanopores on a 2D hexagonal boron nitride (h-BN) and graphene sheet. A base-specific ssDNA sequencing technique was devised, based on the individual differences in the ion current responses for the (polyA)₁₆, (polyG)₁₆, (polyC)₁₆, and (polyT)₁₆ bases of ssDNA. Our sequential procedure for sequencing is built on a comparative approach between the current signals obtained from the nanopores to achieve base-specific detection. Our results indicate that at higher voltages (1.0, 1.2, 1.4, 1.6, 1.8 and 2.0 V nm^-1), DNA translocation is tracked though the 1.5 and 2.0 nm nanopores, and at the 1.5 nm pore size, folded ssDNA close to the nanopore accounts for 93% and 81% of events for graphene and h-BN. Our calculations indicate charge transfer from the graphene to ssDNA, while the reverse happens in the case of the h-BN membrane. These results provide critical insights into our understanding of single molecule sequencing through solid-state nanopore research.

Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics

This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an "on/off"-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system's π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO  is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.

Boron-Carbon-Nitride Sheet as a Novel Surface for Biological Applications: Insights from Density Functional Theory

Understanding the interaction between nanoscale materials and nucleobases is essential for their use in nanobiotechnology and nanomedicine. Our ab initio calculations indicate that the interaction of nucleobases [adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)] with boron-carbon-nitride (BCN) is mainly governed by van der Waals interactions. The adsorption energies, ranging from -0.560 to -0.879 eV, decrease in the order of G > A > T > C > U, which can be attributed to π-π interactions and different side groups of the nucleobases. We found that anions (N and O atoms) of nucleobases prefer to stay on top of cation (B) of the substrate. The results also showed that BCN exhibits superior binding strength than graphene and boron-nitride-based materials. We also found that upon adsorption, the fundamental properties of BCN and nucleobases remains unaltered, which suggests that BCN is a promising template for self-assembly of nucleobases.

Inverted vortex fluidic exfoliation and scrolling of hexagonal-boron nitride

Exfoliation or scrolling of hexagonal boron nitride (h-BN) occurs in a vortex fluidic device (VFD) operating under continuous flow, with a tilt angle of −45° relative to the horizontal position. This new VFD processing strategy is effective in avoiding the build-up of material that occurs when the device is operated using the conventional tilt angle of +45°, where the h-BN precursor and scrolls are centrifugally held against the wall of the tube. At a tilt angle of −45° the downward flow aided by gravity facilitates material exiting the tube with the exfoliation of h-BN and formation of h-BN scrolls then optimized by systematically varying the other VFD operating parameters, including flow rate and rotational speed, along with concentration of h-BN and the choice of solvent. Water was the most effective solvent, which enhances the green chemistry metrics of the processing.

Exfoliation or scrolling of h-BN occurs in a vortex fluidic device under downward continuous flow.

Association of Nucleobases in Hydrated Ionic Liquid from Biased Molecular Dynamics Simulations

We employed metadynamics-based classical molecular dynamics simulations to methylated adenine-thymine (mA-mT) and guanine-cytosine (mG-mC) base pairs to see favorable conformations in various concentrations of hydrated 1-ethyl, 3-methyl imidazolium acetate. We investigated various stacked and hydrogen-bonded conformations of association of base pairs through appropriately chosen collective variables. Stacked conformations more favored in water for both base pairs, whereas Watson-Crick (WC) hydrogen-bonding conformations are favored in pure and hydrated ionic liquids (ILs) except for 0.75 mol fraction IL. We observe that EMIm cations surround the base pairs in WC conformations creating a kind of hydrophobic cavity and protect the hydrogen bonds between base pairs. However, the five-membered heteroaromatic rings of cations stack with the nucleobases in the cation-base-cation (π-π-π) model, which resembles the base-base-base stacking in a DNA duplex. Interestingly, from additional simulations of 0.5 mol fraction hydrated choline dihydrogen phosphate IL, we observe that the stacked conformations become more favored than the WC conformation due to the absence of π-bonds in cations. The calculated values of relative solubility of base pairs in pure and hydrated ionic liquids compared to those in pure water correlate well with the free energy values of WC and stacked conformations.

"Haeckelite", a new low dimensional cousin of boron nitride for biosensing with ultra-fast recovery time: a first principles investigation

We performed state-of-the-art first principles calculations under the framework of dispersion corrected density functional theory to investigate the electronic and vibrational properties of a recently found allotrope of BN, with octagonal and square ring forming planar haeckelite structures (haeck-BN). We further investigated the adsorption mechanism of five nucleobases adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) over haeck-BN to explore its applicability in biosensing. The dispersion correction (DFT-D2) is included to appropriately consider van der Waals interactions. The order of adsorption energy of nucleobases over haeck-BN has the following order: G > T > A ≈ C > U. Significant variation in electronic properties, density of states and work function confirm the adsorption of nucleobases. To check the reusability of haeck-BN as a biosensor toward nucleobases, we calculated the recovery time. Ultrafast recovery times (in millisecond) of 292 ms, 130 ms, 120 ms, 160 ms and 0.6 ms were predicted for G, A, C, T and U, respectively. Our finding suggests that haeck-BN can be utilized as a biosensor for the detection of nucleobases due to its superiority to graphene, h-BN and boron nitride nanotubes, and can be further explored for photocatalysis.

Dynamics of self-assembled cytosine nucleobases on graphene

Molecular self-assembly of cytosine (C _n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C _n 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 _n 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 _n 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.

Nonconductive layered hexagonal boron nitride exfoliation by bipolar electrochemistry

Boron nitride (h-BN), which is an isoelectronic analogue of graphite, has received immense attention due to its unique physical and chemical properties. Numerous methods have been developed to isolate few-layered h-BN nanosheets. These include chemical vapour deposition, solution-based exfoliation and ball-milling amongst others. The bipolar electrochemical method is one of the popular, scalable and water based exfoliation methods which has been applied to graphite, layered transition metal dichalcogenides and black phosphorus. This method was not applied to insulators as this has been assumed to be an impossible task. In this study, we report a solution-based, scalable and time efficient bipolar electrochemical method for the direct exfoliation of bulk insulator, layered h-BN into few-layered h-BN nanosheets based on bipolar electrochemistry. The electrochemical exfoliation of nonconductive materials, h-BN, opens the way to the application of this scalable method to the whole spectrum of non-conductive layered materials. This facile method offers an alternative platform for h-BN electrochemical exfoliation in wide-ranging fields encompassing electronics and biomedical science.

Theoretical study of gas and solvent phase stability and molecular adsorption of noncanonical guanine bases on graphene

The gas and solvent phase stability of noncanonical (Gua)_n nucleobases is investigated in the framework of dispersion-corrected density functional theory (DFT). The calculated results strongly support the high tendency for the dimerization of (Gua)_n bases in both gas and solvent phases. An interplay between intermolecular and bifurcated H-bonds is suggested to govern the stability of (Gua)_n bases which bears a correlation with the description of dispersion correction terms employed in the DFT calculations. For example, a higher polarity is predicted for (Gua)_n bases by the dispersion-corrected DFT in contrast to the non-polar nature of (Gua)₃ and (Gua)₄ predicted by the hybrid meta-GGA calculations. This distinct variation becomes significant under physiological conditions as polar (Gua)_n is likely to exhibit greater stabilization in the gas phase compared to solvated (Gua)_n. Graphene acting as a substrate induces modification in base configurations via maximization of π-orbital overlap between the base and substrate. In solvent, the substrate-induced effects are further heightened with lowering of the dipole moments of (Gua)_n as also displayed by the corresponding isosurface of the electrostatic potential. The graphene-induced stability in both gas and solvent phases appears to fulfill one of the prerequisite criteria for molecular self-assembly. The DFT results therefore provide atomistic insights into the stability and molecular assembly of free-standing noncanonical (Gua)_n nucleobases which can be extended to understanding the self-assembly process of functional biomolecules on 2D materials for potential biosensing applications.

Controlling the orientation of nucleobases by dipole moment interaction with graphene/h-BN interfaces

The interfaces in 2D hybrids of graphene and h-BN provide interesting possibilities of adsorbing and manipulating atomic and molecular entities. In this paper, with the aid of density functional theory, we demonstrate the adsorption characteristics of DNA nucleobases at different interfaces of 2D hybrid nanoflakes of graphene and h-BN. The interfaces provide stronger binding to the nucleobases in comparison to pure graphene and h-BN nanoflakes. It is also revealed that the individual dipole moments of the nucleobases and nanoflakes dictate the orientation of the nucleobases at the interfaces of the hybrid structures. The results of our study point towards a possible route to selectively control the orientation of individual molecules in biosensors.

The interfaces in 2D hybrids of graphene and h-BN provide interesting possibilities of adsorbing and manipulating atomic and molecular entities.

Continuous flow synthesis of phosphate binding h-BN@magnetite hybrid material

Hexagonal boron nitride (h-BN) is rendered magnetically responsive in aqueous media by binding superparamagnetic magnetite nanoparticles 8.5–18.5 nm in diameter on the surface. The composite material was generated under continuous flow in water in a dynamic thin film in a vortex fluidic device (VFD) with the source of iron generated by laser ablation of a pure iron metal target in the air above the liquid using a Nd:YAG pulsed laser operating at 1064 nm and 360 mJ. Optimum operating parameters of the VFD were a rotational speed of 7.5k rpm for the 20 mm OD (17.5 mm ID) borosilicate glass tube inclined at 45 degrees, with a h-BN concentration at 0.1 mg mL⁻¹, delivered at 1.0 mL min⁻¹ using a magnetically stirred syringe to keep the h-BN uniformly dispersed in water prior to injection into the base of the rapidly rotating tube. The resulting composite material, containing 5.75% weight of iron, exhibited high phosphate ion adsorption capacity, up to 171.2 mg PO₄³⁻ per gram Fe, which was preserved on recycling the material five times.

Vortex fluidic fabricated h-BN@magnetite under continuous flow in water exhibits recyclable high phosphate ion adsorption capacity.

Nucleobases-decorated boron nitride nanoribbons for electrochemical biosensing: a dispersion-corrected DFT study

The study suggests that BNNRs may act as superior material for future sensing and DNA sequencing applications.

Hierarchical Self-Assembly of Noncanonical Guanine Nucleobases on Graphene

Self-assembly characterizes the fundamental basis toward realizing the formation of highly ordered hierarchical heterostructures. A systematic approach toward the supramolecular self-assembly of free-standing guanine nucleobases and the role of graphene as a substrate in directing the monolayer assembly are investigated using the molecular dynamics simulation. We find that the free-standing bases in gas phase aggregate into clusters dominated by intermolecular H-bonds, whereas in solvent, substantial screening of intermolecular interactions results in π-stacked configurations. Interestingly, graphene facilitates the monolayer assembly of the bases mediated through the base-substrate π-π stacking. The bases assemble in a highly compact network in gas phase, whereas in solvent, a high degree of immobilization is attributed to the disruption of intermolecular interactions. Graphene-induced stabilization/aggregation of free-standing guanine bases appears as one of the prerequisites governing molecular ordering and assembly at the solid/liquid interface. The results demonstrate an interplay between intermolecular and π-stacking interactions, central to the molecular recognition, aggregation dynamics, and patterned growth of functional molecules on two-dimensional nanomaterials.

DNA Sequencing by Hexagonal Boron Nitride Nanopore: A Computational Study

The single molecule detection associated with DNA sequencing has motivated intensive efforts to identify single DNA bases. However, little research has been reported utilizing single-layer hexagonal boron nitride (hBN) for DNA sequencing. Here we employ molecular dynamics simulations to explore pathways for single-strand DNA (ssDNA) sequencing by nanopore on the hBN sheet. We first investigate the adhesive strength between nucleobases and the hBN sheet, which provides the foundation for the hBN-base interaction and nanopore sequencing mechanism. Simulation results show that the purine base has a more remarkable energy profile and affinity than the pyrimidine base on the hBN sheet. The threading of ssDNA through the hBN nanopore can be clearly identified due to their different energy profiles and conformations with circular nanopores on the hBN sheet. The sequencing process is orientation dependent when the shape of the hBN nanopore deviates from the circle. Our results open up a promising avenue to explore the capability of DNA sequencing by hBN nanopore.

Liquid phase exfoliation and crumpling of inorganic nanosheets

Experiment and simulation demonstrate the polymer-assisted dispersion of inorganic 2D layered nanomaterials such as boron nitride nanosheets (BNNSs), MoS₂ nanosheets, and WS₂ nanosheets; spray drying can be used to alter such nanosheets into a crumpled morphology.

Adsorption of nucleobases on 2D transition-metal dichalcogenides and graphene sheet: a first principles density functional theory study

Adsorption of nucleobases A, T, G, C and U on transition-metal dichalcogenides such as MoS₂ and WS₂ is studied using PBE, DFT-D2 and vdW-DF methods.

Adsorption of choline benzoate ionic liquid on graphene, silicene, germanene and boron-nitride nanosheets: a DFT perspective

This work assesses the adsorption of choline benzoate ionic liquid on the surface of different nanosheets through DFT simulations.

Fluorescent sensors using DNA-functionalized graphene oxide

In the past few years, graphene oxide (GO) has emerged as a unique platform for developing DNA-based biosensors, given the DNA adsorption and fluorescence-quenching properties of GO. Adsorbed DNA probes can be desorbed from the GO surface in the presence of target analytes, producing a fluorescence signal. In addition to this initial design, many other strategies have been reported, including the use of aptamers, molecular beacons, and DNAzymes as probes, label-free detection, utilization of the intrinsic fluorescence of GO, and the application of covalently linked DNA probes. The potential applications of DNA-functionalized GO range from environmental monitoring and cell imaging to biomedical diagnosis. In this review, we first summarize the fundamental surface interactions between DNA and GO and the related fluorescence-quenching mechanism. Following that, the various sensor design strategies are critically compared. Problems that must be overcome before this technology can reach its full potential are described, and a few future directions are also discussed.

The effect of grain boundaries on the mechanical properties and failure behavior of hexagonal boron nitride sheets

Grain boundaries have great effects on the mechanical properties and failure behaviors of h-BN sheets.