Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy

Unveiling the Competition among Surface Damping Pathways in Single Gold Nanorods Immobilized on Graphene Using Amine Derivatives as Adsorbates

Understanding plasmon damping in gold nanorods (AuNRs) is crucial for optimizing their use in photochemical processes and biosensing. This study used dark-field microscopy and spectroscopy to explore plasmon damping in single AuNRs on graphene monolayers (AuNR@GL) with pyridine derivatives as adsorbates. The Au-graphene heterostructure caused a Fermi-level downshift, making graphene a dominant electron acceptor. Hot electrons transferred from AuNR to graphene, leading to a redshift and broadening of the LSPR spectrum. Pyridine adsorption at the AuNR-graphene interface induced a redshift and LSPR line width narrowing due to competing surface damping pathways involving graphene and adsorbate molecules (chemical interface damping, CID). The electron-donating groups of pyridine derivatives on AuNR@1GL caused further LSPR narrowing and decreased plasmon dephasing time. Additionally, thicker graphene layers suppressed electron transfer, highlighting a dominant CID effect. This study, therefore, provides detailed insights into controlling competing plasmon decay mechanisms at the adsorbate-AuNR-graphene interface at the single-particle level.

Single-molecule dynamic structural biology with vertically arranged DNA on a fluorescence microscope

The intricate interplay between DNA and proteins is key for biological functions such as DNA replication, transcription and repair. Dynamic nanoscale observations of DNA structural features are necessary for understanding these interactions. Here we introduce graphene energy transfer with vertical nucleic acids (GETvNA), a method to investigate DNA-protein interactions that exploits the vertical orientation adopted by double-stranded DNA on graphene. This approach enables the dynamic study of DNA conformational changes via energy transfer from a probe dye to graphene, achieving spatial resolution down to the Ångström scale at subsecond temporal resolution. We measured DNA bending induced by adenine tracts, bulges, abasic sites and the binding of endonuclease IV. In addition, we observed the translocation of the O6-alkylguanine DNA alkyltransferase on DNA, reaching single base-pair resolution and detecting preferential binding to adenine tracts. This method promises widespread use for dynamical studies of nucleic acids and nucleic acid-protein interactions with resolution so far reserved for traditional structural biology techniques.

Synthesis of Multi-Functional Graphene Monolayers via Bipolar Electrochemistry

Graphene has gained substantial research interest in many fields due to its remarkable properties among many other two-dimensional materials. In this study, we propose a wireless electrochemical approach, bipolar electrochemistry, for the precise modification of single layers of graphene at predefined locations, such as distinct edges or corners, with a variety of metals or polymers, thus enabling the elaboration of multi-functional monolayer graphene sheets. We illustrate the concept e. g. by depositing multiple metals, or platinum and a catalyst-containing porous polymer on the same graphene sheet, but at separate corners. This configuration allows activating chemiluminescence on the polymer spot, and simultaneously generates the driving force for autonomous motion on the Pt side through the catalytic decomposition of hydrogen peroxide into oxygen bubbles. This integration of different chemical features on the same object, exemplified by these proof-of-principle experiments, enhances the functionality of two-dimensional materials, paving the way for the use of these hybrid materials for a variety of applications, ranging from sensing and catalysis to targeted delivery.

Expanding the range of graphene energy transfer with multilayer graphene

The interaction between single emitters and graphene in the context of energy transfer has attracted significant attention due to its potential applications in fields such as biophysics and super-resolution microscopy. In this study, we investigate the influence of the number of graphene layers on graphene energy transfer (GET) by placing single dye molecules at defined distances from monolayer, bilayer, and trilayer graphene substrates. We employ DNA origami nanostructures as chemical adapters to position the dye molecules precisely. Fluorescence lifetime measurements and analysis reveal an additive effect of graphene layers on the energy transfer rate extending the working range of GET up to distances of approximately 50-60 nm. Moreover, we show that switching a DNA pointer strand between two positions on a DNA origami nanostructure at a height of >28 nm above graphene is substantially better visualized with multilayer graphene substrates suggesting enhanced capabilities for applications such as biosensing and super-resolution microscopy for larger systems and distances. This study provides insights into the influence of graphene layers on energy transfer dynamics and offers new possibilities for exploiting graphene's unique properties in various nanotechnological applications.

From Bulk to Single Molecules: Surface-Enhanced Raman Scattering of Cytochrome C Using Plasmonic DNA Origami Nanoantennas

Cytochrome C, an evolutionarily conserved protein, plays pivotal roles in cellular respiration and apoptosis. Understanding its molecular intricacies is essential for both academic inquiry and potential biomedical applications. This study introduces an advanced single-molecule surface-enhanced Raman scattering (SM-SERS) system based on DNA origami nanoantennas (DONAs), optimized to provide unparalleled insights into protein structure and interactions. Our system effectively detects shifts in the Amide III band, thereby elucidating protein dynamics and conformational changes. Additionally, the system permits concurrent observations of oxidation processes and Amide bands, offering an integrated view of protein structural and chemical modifications. Notably, our approach diverges from traditional SM-SERS techniques by de-emphasizing resonance conditions for SERS excitation, aiming to mitigate challenges like peak oversaturation. Our findings underscore the capability of our DONAs to illuminate single-molecule behaviors, even within aggregate systems, providing clarity on molecular interactions and behaviors.

Highly sensitive fluorescent explosives detection via SERS: based on fluorescence quenching of graphene oxide@Ag composite aerogels

High fluorescence background poses a substantial challenge to surface-enhanced Raman scattering (SERS), thereby limiting its broader applicability across diverse domains. In this work, silver nanoparticle (Ag NP)-loaded graphene oxide aerogel nanomaterials (GO-Ag ANM) were prepared for sensitive SERS detection of fluorescent explosive 2,4,8,10-tetranitrobenzo-1,3a,6,6a-tetraazapentaenopyridine (BPTAP) by a fluorescence quenching strategy. By harnessing the fluorescence quenching properties of graphene and the localized surface plasmon resonance of silver nanoparticles, the synthesized aerogels exhibited effective fluorescence quenching and Raman enhancement capabilities when employed for BPTAP analysis with 532 nm laser excitation. Significantly, precise control over the loading quantity of silver nanoparticles (Ag NPs) resulted in the remarkable sensitivity of the surface-enhanced Raman scattering (SERS) effect. This method allowed for the detection of fluorescent explosive BPTAP at an extraordinarily low concentration of 1 × 10-7 M. Furthermore, the approach also demonstrated excellent detection capabilities for the dyes R6G, CV, and RhB. This study offers valuable insights for the sensitive detection of fluorescent molecules.

Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials

Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.

Deep-LASI: deep-learning assisted, single-molecule imaging analysis of multi-color DNA origami structures

Single-molecule experiments have changed the way we explore the physical world, yet data analysis remains time-consuming and prone to human bias. Here, we introduce Deep-LASI (Deep-Learning Assisted Single-molecule Imaging analysis), a software suite powered by deep neural networks to rapidly analyze single-, two- and three-color single-molecule data, especially from single-molecule Förster Resonance Energy Transfer (smFRET) experiments. Deep-LASI automatically sorts recorded traces, determines FRET correction factors and classifies the state transitions of dynamic traces all in ~20-100 ms per trajectory. We benchmarked Deep-LASI using ground truth simulations as well as experimental data analyzed manually by an expert user and compared the results with a conventional Hidden Markov Model analysis. We illustrate the capabilities of the technique using a highly tunable L-shaped DNA origami structure and use Deep-LASI to perform titrations, analyze protein conformational dynamics and demonstrate its versatility for analyzing both total internal reflection fluorescence microscopy and confocal smFRET data.

Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA

The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.

Spatial Precision Tailoring the Catalytic Activity of Graphene Monolayers for Designing Janus Swimmers

Graphene monolayers have interesting applications in many fields due to their intrinsic physicochemical properties, especially when they can be postmodified with high precision. Herein, we describe the highly site-selective functionalization of freestanding graphene monolayers with platinum (Pt) clusters by bipolar electrochemistry. The deposition of such metal spots leads to catalytically active hybrid two-dimensional (2D) nanomaterials. Their catalytic functionality is illustrated by the spatially controlled decomposition of hydrogen peroxide, inducing motion at the water/air interface due to oxygen bubble evolution. A series of such 2D Janus structures with Pt deposition at predefined positions (corners and edges) is studied with respect to the generation of autonomous motion. The type and speed of motion can be fine-tuned by controlling the deposition time and location of the Pt clusters. These proof-of-principle experiments indicate that this type of hybrid 2D object opens up interesting perspectives in terms of applications, such as environmental detection or remediation.

Combining pMINFLUX, graphene energy transfer and DNA-PAINT for nanometer precise 3D super-resolution microscopy

3D super-resolution microscopy with nanometric resolution is a key to fully complement ultrastructural techniques with fluorescence imaging. Here, we achieve 3D super-resolution by combining the 2D localization of pMINFLUX with the axial information of graphene energy transfer (GET) and the single-molecule switching by DNA-PAINT. We demonstrate <2 nm localization precision in all 3 dimension with axial precision reaching below 0.3 nm. In 3D DNA-PAINT measurements, structural features, i.e., individual docking strands at distances of 3 nm, are directly resolved on DNA origami structures. pMINFLUX and GET represent a particular synergetic combination for super-resolution imaging near the surface such as for cell adhesion and membrane complexes as the information of each photon is used for both 2D and axial localization information. Furthermore, we introduce local PAINT (L-PAINT), in which DNA-PAINT imager strands are equipped with an additional binding sequence for local upconcentration improving signal-to-background ratio and imaging speed of local clusters. L-PAINT is demonstrated by imaging a triangular structure with 6 nm side lengths within seconds.

Understanding Förster Resonance Energy Transfer in the Sheet Regime with DNA Brick-Based Dye Networks

Controlling excitonic energy transfer at the molecular level is a key requirement for transitioning nanophotonics research to viable devices with the main inspiration coming from biological light-harvesting antennas that collect and direct light energy with near-unity efficiency using Förster resonance energy transfer (FRET). Among putative FRET processes, point-to-plane FRET between donors and acceptors arrayed in two-dimensional sheets is predicted to be particularly efficient with a theoretical 1/r⁴ energy transfer distance (r) dependency versus the 1/r⁶ dependency seen for a single donor-acceptor interaction. However, quantitative validation has been confounded by a lack of robust experimental approaches that can rigidly place dyes in the required nanoscale arrangements. To create such assemblies, we utilize a DNA brick scaffold, referred to as a DNA block, which incorporates up to five two-dimensional planes with each displaying from 1 to 12 copies of five different donor, acceptor, or intermediary relay dyes. Nanostructure characterization along with steady-state and time-resolved spectroscopic data were combined with molecular dynamics modeling and detailed numerical simulations to compare the energy transfer efficiencies observed in the experimental DNA block assemblies to theoretical expectations. Overall, we demonstrate clear signatures of sheet regime FRET, and from this we provide a better understanding of what is needed to realize the benefits of such energy transfer in artificial dye networks along with FRET-based sensing and imaging.

Graphene Energy Transfer for Single-Molecule Biophysics, Biosensing, and Super-Resolution Microscopy

Graphene is considered a game-changing material, especially for its mechanical and electrical properties. This work exploits that graphene is almost transparent but quenches fluorescence in a range up to ≈40 nm. Graphene as a broadband and unbleachable energy-transfer acceptor without labeling, is used to precisely determine the height of molecules with respect to graphene, to visualize the dynamics of DNA nanostructures, and to determine the orientation of Förster-type resonance energy transfer (FRET) pairs. Using DNA origami nanopositioners, biosensing, single-molecule tracking, and DNA PAINT super-resolution with <3 nm z-resolution are demonstrated. The range of examples shows the potential of graphene-on-glass coverslips as a versatile platform for single-molecule biophysics, biosensing, and super-resolution microscopy.