Computational investigation on DNA sequencing using functionalized graphene nanopores

Effect of surface functionalization on DNA sequencing using MXene-based nanopores

As one of the most promising types of label-free nanopores has great potential for DNA sequencing via fast detection of different DNA bases. As one of the most promising types of label-free nanopores, two-dimensional nanopore materials have been developed over the past two decades. However, how to detect different DNA bases efficiently and accurately is still a challenging problem. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A)20, poly(C)20, poly(G)20, and poly(T)20) through two-dimensional transition-metal carbide (MXene) membrane nanopores with different surface terminal groups is investigated via all-atom molecular dynamics simulations. Interestingly, it is found that the four types of bases can be distinguished by different ion currents and dwell times when they are transported through the Ti3C2(OH)2 nanopore. This is mainly attributed to the different orientation and position distributions of the bases, the hydrogen bonding inside the MXene nanopore, and the interaction of the ssDNA with the nanopore. The present study enhances the understanding of the interaction between DNA strands and MXene nanopores with different functional groups, which may provide useful guidelines for the design of MXene-based devices for DNA sequencing in the future.

Exploring the non-monotonic DNA capture behavior in a charged graphene nanopore

Nanopore-based biomolecule detection has emerged as a promising and sought-after innovation, offering high throughput, rapidity, label-free analysis, and cost-effectiveness, with potential applications in personalized medicine. However, achieving efficient and tunable biomolecule capture into the nanopore remains a significant challenge. In this study, we employ all-atom molecular dynamics simulations to investigate the capture of double-stranded DNA (dsDNA) molecules into graphene nanopores with varying positive charges. We discover a non-monotonic relationship between the DNA capture rate and the charge of the graphene nanopore. Specifically, the capture rate initially decreases and then increases with an increase in nanopore charge. This behavior is primarily attributed to differences in the electrophoretic force, rather than the influence of electroosmosis or counterions. Furthermore, we also observe this non-monotonic trend in various ionic solutions, but not in ionless solutions. Our findings shed light on the design of novel DNA sequencing devices, offering valuable insights into enhancing biomolecule capture rates in nanopore-based sensing platforms.

DNA sequencing via molecular dynamics simulation with functionalized graphene nanopore

Through this research, functionalized graphene nanopores are used to verify how effective such an apparatus for DNA sequencing is. The circular symmetric pores are functionalized with hydrogen and a hydroxyl group bonded with carbon atoms of the pore rim. Plus, two adenine bases are also put at the rim perimeter to verify whether such a combination would lead to base detection. A homopolymer of single-stranded DNA (ssDNA) is pulled through a nanopore using steered molecular dynamics (SMD) simulation. Pulling force profile, moving fashion of ssDNA in irreversible DNA pulling as well as the base orientation during translocation relative to the graphene plane, called beta angle, are assessed. Based on the studied parameters, SMD force, and base orientation, the hydrogenated and hydroxylated pores do not show a clear distinction between bases, while the adenine-functionalized pore can distinguish between adenine and cytosine. Therefore, there may be some hope for achieving single-base sequencing, while further research is needed.

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

In-plane graphene/h-BN/graphene heterostructures with nanopores for electrical detection of DNA nucleotides

The in-plane heterostructure of graphene and h-BN has unique physical and electrical characteristics, which can be exploited for single-molecule DNA sequencing. On this account, we propose a nanostructure based on a nanopore in graphene/h-BN/graphene heterostructures as a viable approach for in-plane electrical detection. The insulating h-BN layer changes the charge transport to the quantum tunneling regime, which is very sensitive to the electrostatic interactions induced by nucleotides during their translocation through the nanopore. Density functional theory (DFT) is utilized to study the membrane/nanopore interactions as well as their interactions with different nucleotides (dAMP, dGMP, dCMP, and dTMP). The results indicate that the nucleotides show stronger interactions with nanopores in h-BN rather than nanopores in pristine graphene. For the calculation of electronic transport, non-equilibrium Green's function (NEGF) formalism at the first principles level is employed. The in-plane currents at different applied voltages are calculated in the presence of different nucleotides in the nanopore. The sensitivity of the proposed nanostructure towards different nucleotides is measured based on the current modulation induced by each nucleotide. The graphene/h-BN/graphene heterostructure shows higher sensitivity toward different nucleotides compared to a similar structure consisting of pristine graphene and can be considered as a promising candidate for DNA sequencing applications.

Synthesis of holey graphene for advanced nanotechnological applications

Holey or porous graphene, a structural derivative of graphene, has attracted immense attention due to its unique properties and potential applications in different branches of science and technology. In this review, the synthesis methods of holey or porous graphene/graphene oxide are systematically summarized and their potential applications in different areas are discussed. The process–structure–applications are explained, which helps relate the synthesis approaches to their corresponding key applications. The review paper is anticipated to benefit the readers in understanding the different synthesis methods of holey graphene, their key parameters to control the pore size distribution, advantages and limitations, and their potential applications in various fields.

The review paper presents a systematic understanding of different synthesis routes to obtain holey graphene, its properties, and key applications in different fields. The article also evaluates the current progress and future opportunities of HG.

Graphene for Biosensing Applications in Point-of-Care Testing

Graphene and graphene-related materials (GRMs) exhibit a unique combination of electronic, optical, and electrochemical properties, which make them ideally suitable for ultrasensitive and selective point-of-care testing (POCT) devices. POCT device-based applications in diagnostics require test results to be readily accessible anywhere to produce results within a short analysis timeframe. This review article provides a summary of methods and latest developments in the field of graphene and GRM-based biosensing in POCT and an overview of the main applications of the latter in nucleic acids and enzymatic biosensing, cell detection, and immunosensing. For each application, we discuss scientific and technological advances along with the remaining challenges, outlining future directions for widespread use of this technology in biomedical applications.

Molecular perspective on charge-tunable adsorption of volatile organic compounds on carbon nanotubes

Volatile organic compounds (VOCs) have been identified as highly toxic and carcinogenic pollutants threatening both human health and the living environment. Their recognition and removal are important issues. Carbon nanotubes (CNTs) have been proposed as a promising agent for the adsorption of detrimental VOC molecules. Due to the intrinsic nanoscale nature of such processes, details of molecular interactions and the adsorption mechanism remain to be clarified. This paper aims to provide a molecular perspective on the adsorption behavior of VOC molecules on both neutral and electrically charged CNTs by the means of molecular dynamics simulations. Simulation results indicate a strong correlation between the adsorption affinity and hydrophobicity of acetone, ether, methanol and toluene molecules. VOCs possessing a higher hydrophobicity demonstrate greater adsorption affinity. The adsorption of toluene and ether molecules is quite stable around the CNT surface. In contrast, hydrophilic molecules such as acetone and methanol can only be unstably adsorbed. For neutral CNTs, the van der Waals interaction is responsible for the adsorption affinity. For electrically charged CNTs, however, electrostatic attraction or repulsion with the charged groups in VOC molecules significantly affects the adsorption behavior. As a result, the introduction of charges on the CNT surface can help to optimize the adsorption process of VOC molecules. Calculations on the potentials of mean forces support the same reasonings. Simulation results about acetone, ether, methanol and toluene clearly indicate that customized strategies are needed for precisely controlling the adsorption of different VOC molecules on CNTs. The results reported in this work should be helpful for the better development of sensing and removal systems of detrimental VOC molecules.

DNA Translocation through Vertically Stacked 2D Layers of Graphene and Hexagonal Boron Nitride Heterostructure Nanopore

Cost-effective, fast, and reliable DNA sequencing can be enabled by advances in nanopore-based methods, such as the use of atomically thin graphene membranes. However, strong interaction of DNA bases with graphene leads to undesirable effects such as sticking of DNA strands to the membrane surface. While surface functionalization is one way to counter this problem, here, we present another solution based on a heterostructure nanopore system, consisting of a monolayer of graphene and hexagonal boron nitride (hBN) each. Molecular dynamics studies of DNA translocation through this heterostructure nanopore revealed a surprising and crucial influence of the heterostructure layer order in controlling the base specific signal variability. Specifically, the heterostructure with graphene on top of hBN had nearly 3-10× lower signal variability than the one with hBN on top of graphene. Simulations point to the role of differential underside sticking of DNA bases as a possible reason for the observed influence of the layer order. Our studies can guide the development of experimental systems to study and exploit DNA translocation through two-dimensional heterostructure nanopores for single molecule sequencing and sensing applications.

Dynamics of K+ counterions around DNA double helix in the external electric field: A molecular dynamics study

The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study was performed for the system of DNA double helix with neutralizing K⁺ counterions and for the system of KCl salt solution in an external electric field of different strength (up to 32mV/Å). The analysis of ionic conductivities of these systems has shown that the counterions around the DNA double helix are slowed down compared with the KCl salt solution. The calculated values of ion mobility are within (0.05-0.4)mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K⁺ counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30mV/Å the double helix undergoes a phase transition from a double-stranded to a single-strand state.

Controlling ion transport in a C2N-based nanochannel with tunable interlayer spacing

Selective ion transport through a nanochannel formed by stacked two-dimensional materials plays a key role in water desalination, nanofiltration, and ion separation. Although there have been many functional nanomaterials used in these applications, how to well control ion transport in a laminar structure so as to obtain the desired selectivity still remains a challenging problem. In the present work, the transport of ions through a C₂N-based nanochannel is investigated by using all-atom molecular dynamics simulation. It is found that C₂N-based nanochannels with different interlayer spacing posses diverse ion selectivity, which is mainly attributed to the distinct loading capability among ions and the different velocity of ions inside the nanochannel. Moreover, we also find that the ion selectivity is dependent on the electric field, but nearly independent of the salt concentration. The present study may provide some physical insights into the experimental design of C₂N-based nanodevices in nanofiltration.

Computational investigation of geometrical effects in 2D boron nitride nanopores for DNA detection

Nanopore-based DNA detection and analysis have been intensively pursued theoretically and experimentally over the past decade. Owing to their nanometer thickness, 2D nanopores, such as boron nitride nanopores, show great potential for achieving DNA detection at base resolution. Although 2D nanopore devices hold great promise for next-generation DNA detection, efficiently and reliably detecting different DNA sequences is still a challenging problem. To date, most of the investigated nanopores adopt circular shapes. Because of the successful fabrication of triangular nanopores, investigating the shape effect of nanopores for DNA detection has become more and more important. In this study, boron nitride nanopores with circular, hexagonal, quadrangular and triangular shapes were modeled at various sizes. The translocation of homogeneous dsDNA through these nanopores was investigated by all-atom molecular dynamic simulations. The ionic conductivity of these nanopores was characterized and formulas for the total resistance based on the pore and access resistance were derived. The ionic current, dwell time and conductance blockade of homogeneous dsDNA were compared for nanopores with different shapes. We demonstrate that the charge distribution at the pore mouth plays an important role in the transportation of ions and DNA molecules. Our findings may shed light on the design of 2D nanopores and can facilitate the development of fast, low-cost and reliable nanopore-based DNA detection.

DNA Translocation through Hybrid Bilayer Nanopores

Pore functionalization has been explored by several groups as a strategy to control DNA translocation through solid-state nanopores. Here we present a hybrid nanopore system consisting of single-layer graphene and a DNA origami layer to achieve base-selective control of DNA translocation rate through aligned nanopores of the two layers. This is achieved by incorporating unpaired dangling bases called overhangs to the origami near the pore region. Molecular dynamics simulations were used to optimize the design of the origami nanopore and the overhangs. Specifically, we considered the influence of the number and spatial distribution of overhangs on translocation times. The simulations revealed that specific interactions between the overhangs and the translocating single-stranded DNA resulted in base-specific residence times.

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.

Ion transport through a nanoporous C2N membrane: the effect of electric field and layer number

Using all-atom molecular dynamic simulations, we show that a monolayer C₂N membrane possesses higher permeability and excellent ion selectivity, and that multilayer C₂N membranes have promising potential for water desalination.