Stick-Slip Motion of ssDNA over Graphene

Critical peeling of tethered nanoribbons

The peeling of an immobile adsorbed membrane is a well-known problem in engineering and macroscopic tribology. In the classic setup, picking up at one extreme and pulling off result in a peeling force that is a decreasing function of the pickup angle. As one end is lifted, the detachment front retracts to meet the immobile tail. At the nanoscale, interesting situations arise with the peeling of graphene nanoribbons (GNRs) on gold, as realized, e.g., by atomic force microscopy. The nanosized system shows a constant-force steady peeling regime, where the tip lifting h produces no retraction of the ribbon detachment point, and just an advancement h of the free tail end. This is opposite to the classic case, where the detachment point retracts and the tail end stands still. Here we characterise, by analytical modeling and numerical simulations, a third, experimentally relevant setup where the nanoribbon, albeit structurally lubric, does not have a freely moving tail end, which is instead elastically tethered. Surprisingly, novel nontrivial scaling exponents appear that regulate the peeling evolution. As the detachment front retracts and the tethered tail is stretched, power laws of h characterize the shrinking of the adhered length, the growth of peeling force and the peeling angle. These exponents precede the final total detachment as a critical point, where the entire ribbon eventually hangs suspended between the tip and the tethering spring. These analytical predictions are confirmed by realistic MD simulations, retaining the full atomistic description, also confirming their survival at finite experimental temperatures.

Probing the adsorption behavior and free energy landscape of single-stranded DNA oligonucleotides on single-layer MoS2with molecular dynamics

Interfacing single-stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self-assembled hybrids is still not well understood. Here, atomistic molecular dynamics simulation is employed to study the distinct adsorption behavior of ssDNA on a single-layer MoS₂in aqueous environment. The ssDNA sequences [T₁₀, G₁₀, A₁₀, C₁₀, U₁₀, (GT)₅, and (AC)₅] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waalsπ-stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly-purines demonstrate two concurrently competingπ-stacking interactions: nucleobase-nucleobase (intramolecular) and nucleobase-MoS₂(intermolecular). The poly-pyrimidines, on the other hand, reveal enhancedπ-stacking interactions, thereby maximizing the number of contacts. The results provide new molecular-level understanding of ssDNA adsorption on the MoS₂surface and facilitate future studies in design of functional DNA/MoS₂structure-based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.

Defect-Induced Double-Stranded DNA Unwinding on Graphene

Several works have shown that graphene materials can effectively regulate the double-stranded DNA (dsDNA) structures and are used to remove antibiotic resistance genes in the environment, during which the morphology of the graphene surface plays a key role. However, the mechanism of how different graphene surfaces interact with dsDNA is poorly documented. Here, the interactions of dsDNA with defective graphene (D-Gra) and pristine graphene (P-Gra) have been explored by molecular dynamics simulations. Our data clearly showed that both D-Gra and P-Gra were able to attract dsDNA to form stable bindings. However, the structure evolutions of dsDNA are distinctly different. In detail, D-Gra can initiate quick unwinding of dsDNA and cause significant structural disruption. While for P-Gra, it demonstrated a much weaker capability to disrupt the dsDNA structure. This difference is due to the strong electrostatic interaction between defects and DNA nucleotides. Nucleotides can be highly restricted by the defect while the other parts of dsDNA could move along the transverse directions of D-Gra. This effectively introduces a "pulling force" from the defect that causes the breaking of the hydrogen bonds between dsDNA base pairs. Such force finally leads to the serious unwinding of dsDNA. Our present findings could help us to better understand the molecular mechanism of how the dsDNA canonical B-form was lost upon adsorption to graphene. The findings of the key roles of defects on graphene are beneficial for the design of functional graphenic materials for biological and medical applications through nanostructure engineering.

Assessment of AMBER Force Fields for Simulations of ssDNA

Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.

Sequential Bending and Twisting around C-C Single Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer

Bending and twisting around carbon-carbon single bonds are ubiquitous in natural and synthetic polymers. Force-induced changes were so far not measured at the single-monomer level, owing to limited ways to apply local forces. We quantified down to the submolecular level the mechanical response within individual poly-pyrenylene chains upon their detachment from a gold surface with an atomic force microscope at 5 K. Computer simulations based on a dedicated force field reproduce the experimental traces and reveal symmetry-broken bent and rotated conformations of the sliding physisorbed segment besides steric hindrance of the just lifted monomer. Our study also shows that the tip-molecule bond remains intact but remarkably soft and links force variations to complex but well-defined conformational changes.

Conformations and cryo-force spectroscopy of spray-deposited single-strand DNA on gold

Cryo-electron microscopy can determine the structure of biological matter in vitrified liquids. However, structure alone is insufficient to understand the function of native and engineered biomolecules. So far, their mechanical properties have mainly been probed at room temperature using tens of pico-newton forces with a resolution limited by thermal fluctuations. Here we combine force spectroscopy and computer simulations in cryogenic conditions to quantify adhesion and intra-molecular properties of spray-deposited single-strand DNA oligomers on Au(111). Sub-nanometer resolution images reveal folding conformations confirmed by simulations. Lifting shows a decay of the measured stiffness with sharp dips every 0.2-0.3 nm associated with the sequential peeling and detachment of single nucleotides. A stiffness of 30-35 N m^-1 per stretched repeat unit is deduced in the nano-newton range. This combined study suggests how to better control cryo-force spectroscopy of adsorbed heterogeneous (bio)polymer and to potentially enable single-base recognition in DNA strands only few nanometers long.

Detachment Dynamics of Graphene Nanoribbons on Gold

Metal-surface physisorbed graphene nanoribbons (GNRs) constitute mobile nanocontacts whose interest is simultaneously mechanical, electronic, and tribological. Previous work showed that GNRs adsorbed on Au(111) generally slide smoothly and superlubrically owing to the incommensurability of their structures. We address here the nanomechanics of detachment, as realized when one end is picked up and lifted by an AFM cantilever. AFM nanomanipulations and molecular-dynamics (MD) simulations identify two successive regimes, characterized by (i) a progressively increasing local bending, accompanied by the smooth sliding of the adhered part, followed by (ii) a stick-slip dynamics involving sudden bending relaxation associated with intermittent jumps of the remaining adhered GNR segment and tail end. AFM measurements of the vertical force exhibit oscillations which, compared with MD simulations, can be associated with the successive detachment of individual GNR unit cells of length 0.42 nm. Extra modulations within one single period are caused by steplike advancements of the still-physisorbed part of the GNR. The sliding of the incommensurate moiré pattern that accompanies the GNR lifting generally yields an additional long-period oscillation: while almost undetectable when the GNR is aligned in the standard "R30" orientation on Au(111), we predict that such feature should become prominent in the alternative rotated "R0" orientation on the same surface, or on a different surface, such as perhaps Ag(111).