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1. Magnetic domains and domain wall pinning in atomically thin CrBr3 revealed by nanoscale imaging

   https://doi.org/10.1038/s41467-021-22239-4  

   Sun, Qi-Chao; Song, Tiancheng; Anderson, Eric; Brunner, Andreas; Förster, Johannes; Shalomayeva, Tetyana; Taniguchi, Takashi; Watanabe, Kenji; Gräfe, Joachim; Stöhr, Rainer; et al (December 2021, Nature Communications)

   null (Ed.)

   Abstract The emergence of atomically thin van der Waals magnets provides a new platform for the studies of two-dimensional magnetism and its applications. However, the widely used measurement methods in recent studies cannot provide quantitative information of the magnetization nor achieve nanoscale spatial resolution. These capabilities are essential to explore the rich properties of magnetic domains and spin textures. Here, we employ cryogenic scanning magnetometry using a single-electron spin of a nitrogen-vacancy center in a diamond probe to unambiguously prove the existence of magnetic domains and study their dynamics in atomically thin CrBr 3 . By controlling the magnetic domain evolution as a function of magnetic field, we find that the pinning effect is a dominant coercivity mechanism and determine the magnetization of a CrBr 3 bilayer to be about 26 Bohr magnetons per square nanometer. The high spatial resolution of this technique enables imaging of magnetic domains and allows to locate the sites of defects that pin the domain walls and nucleate the reverse domains. Our work highlights scanning nitrogen-vacancy center magnetometry as a quantitative probe to explore nanoscale features in two-dimensional magnets. 

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2. Machine learning for composition analysis of ssDNA using chemical enhancement in SERS

   https://doi.org/10.1364/BOE.397616  

   Nguyen, Phuong_H_L; Hong, Brandon; Rubin, Shimon; Fainman, Yeshaiahu (August 2020, Biomedical Optics Express)

   Surface-enhanced Raman spectroscopy (SERS) is an attractive method for bio-chemical sensing due to its potential for single molecule sensitivity and the prospect of DNA composition analysis. In this manuscript we leverage metal specific chemical enhancement effect to detect differences in SERS spectra of 200-base length single-stranded DNA (ssDNA) molecules adsorbed on gold or silver nanorod substrates, and then develop and train a linear regression as well as neural network models to predict the composition of ssDNA. Our results indicate that employing substrates of different metals that host a given adsorbed molecule leads to distinct SERS spectra, allowing to probe metal-molecule interactions under distinct chemical enhancement regimes. Leveraging this difference and combining spectra from different metals as an input for PCA (Principal Component Analysis) and NN (Neural Network) models, allows to significantly lower the detection errors compared to manual feature-choosing analysis as well as compared to the case where data from single metal is used. Furthermore, we show that NN model provides superior performance in the presence of complex noise and data dispersion factors that affect SERS signals collected from metal substrates fabricated on different days. 

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3. Proximity and single-molecule energetics

   https://doi.org/10.1126/science.abj5860  

   Li, Linfei; Jiang, Nan (July 2021, Science)

   Probing single molecules in their nanoenvironment can reveal site-specific phenomena that would be obscured by ensemble-averaging experiments on macroscopic populations of molecules. Particularly in the past decade, major technological breakthroughs in scanning probe microscopy (SPM) have led to unprecedented spatial resolution and versatility and enabled the interrogation of molecular conformation, bond order, molecular orbitals, charge states, spins, phonons, and intermolecular interactions. On page 452 of this issue, Peng et al. ( 1 ) use SPM to directly measure the triplet lifetime of an individual pentacene molecule and demonstrate its dependence on interactions with nearby oxygen molecules with atomic precision. In addition to allowing the local tuning and probing of spin-spin interactions between molecules, this study represents a notable advance in the single-molecule regime and provides insights into many macroscopic behaviors and related applications in catalysis, energy-conversion materials, or biological systems. 

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4. Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

   https://doi.org/10.3390/ijms23147690  

   Cervantes-Salguero, Keitel; Biaggne, Austin; Youngsman, John M.; Ward, Brett M.; Kim, Young C.; Li, Lan; Hall, John A.; Knowlton, William B.; Graugnard, Elton; Kuang, Wan (July 2022, International Journal of Molecular Sciences)

   Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins. 

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5. Single molecule delivery into living cells

   https://doi.org/10.1038/s41467-024-48608-3  

   Chau, Chalmers C; Maffeo, Christopher M; Aksimentiev, Aleksei; Radford, Sheena E; Hewitt, Eric W; Actis, Paolo (May 2024, Nature Communications)

   Abstract Controlled manipulation of cultured cells by delivery of exogenous macromolecules is a cornerstone of experimental biology. Here we describe a platform that uses nanopipettes to deliver defined numbers of macromolecules into cultured cell lines and primary cells at single molecule resolution. In the nanoinjection platform, the nanopipette is used as both a scanning ion conductance microscope (SICM) probe and an injection probe. The SICM is used to position the nanopipette above the cell surface before the nanopipette is inserted into the cell into a defined location and to a predefined depth. We demonstrate that the nanoinjection platform enables the quantitative delivery of DNA, globular proteins, and protein fibrils into cells with single molecule resolution and that delivery results in a phenotypic change in the cell that depends on the identity of the molecules introduced. Using experiments and computational modeling, we also show that macromolecular crowding in the cell increases the signal-to-noise ratio for the detection of translocation events, thus the cell itself enhances the detection of the molecules delivered. 

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