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Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked DNA minicircles found in certain parasites called trypanosomes. Understanding the self-assembly and replication of this structure are not only major open questions in biology but can also inform the design of synthetic topological materials. Here, we report the first high-resolution, single-molecule study of kDNA network topology using AFM and steered molecular dynamics simulations. We map out the DNA density within the network and the distribution of linking number and valence of the minicircles. We also characterize the DNA hubs that surround the network and show that they cause a buckling transition akin to that of a 2D elastic thermal sheet in the bulk. Intriguingly, we observe a broad distribution of density and valence of the minicircles, indicating heterogeneous network structure and individualism of different kDNA structures. Finally, we estimate the 2D Young modulus of the network to be orders of magnitude smaller than that of other 2D materials. Our findings explain outstanding questions in the field and offer single-molecule insights into the properties of a unique topological material.

Nuclear spins owe their long-lived magnetic states to their excellent isolation from the environment. At the same time, a finite degree of interaction with their surroundings is necessary for reading and writing the spin state. Therefore, detailed knowledge of and control over the atomic environment of a nuclear spin is key to optimizing conditions for quantum information applications. While various platforms enabled single-shot readout of nuclear spins, their direct environments were either unknown or impossible to controllably modify on the atomic scale. Scanning tunneling microscopy (STM), combined with electron spin resonance (ESR), provides atomic-scale information of individual nuclear spins via the hyperfine interaction. Here, we demonstrate single-shot readout of an individual 49 Ti nuclear spin with an STM. Employing a pulsed measurement scheme, we find its lifetime to be in the order of seconds. Furthermore, we shed light on the pumping and relaxation mechanisms of the nuclear spin by investigating its response to both ESR driving and tunneling current, which is supported by model calculations. These findings give an atomic-scale insight into the nature of nuclear spin relaxation and are relevant for the development of atomically assembled qubit platforms. Scanning tunneling microscopy combined with electron spin resonance has enabled control and measurement of individual nuclear spins, but time-domain studies remain limited. Here, the authors report single-shot readout of the nuclear spin state of a single Ti atom, revealing its lifetime and relaxation mechanisms.

Structural maintenance of chromosome (SMC) protein complexes are the key organizers of the spatiotemporal structure of chromosomes. The condensin SMC complex has recently been shown to be a molecular motor that extrudes large loops of DNA, but the mechanism of this unique motor remains elusive. Using atomic force microscopy, we show that budding yeast condensin exhibits mainly open ‘O’ shapes and collapsed ‘B’ shapes, and it cycles dynamically between these two states over time, with ATP binding inducing the O to B transition. Condensin binds DNA via its globular domain and also via the hinge domain. We observe a single condensin complex at the stem of extruded DNA loops, where the neck size of the DNA loop correlates with the width of the condensin complex. The results are indicative of a type of scrunching model in which condensin extrudes DNA by a cyclic switching of its conformation between O and B shapes.Atomic force microscopy imaging of yeast condensin indicates that condensin may extrude DNA by switching conformation between open O and collapsed B shapes, indicative of a type of scrunching model.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Over the last few years, tremendous progress has been made in visualizing biologically important macromolecules using transmission electron microscopy (TEM) and understanding their structure-function relation. Yet, despite the importance of DNA in all forms of life, TEM visualization of individual DNA molecules in its native unlabeled form has remained extremely challenging. Here, we present high-contrast images of unstained single-layer DNA nanostructures that were obtained using advanced in-focus phase contrast TEM techniques. These include sub-Ångstrom low voltage electron microscopy (SALVE), the use of a volta-potential phase plate (VPP), and dark-field (DF) microscopy. We discuss the advantages and drawbacks of these techniques for broad applications in structural biology and materials science.

Cohesin is a key protein complex that organizes the spatial structure of chromosomes during interphase. Here, we show that yeast cohesin shows pronounced clustering on DNA in an ATP-independent manner, exhibiting all the hallmarks of phase separation. In vitro visualization of cohesin on DNA shows DNA-cohesin clusters that exhibit liquid-like behavior. This includes mutual fusion and reversible dissociation upon depleting the cohesin concentration, increasing the ionic strength, or adding 1,6-hexanediol, conditions that disrupt weak interactions. We discuss how bridging-induced phase separation can explain the DNA-cohesin clustering through DNA-cohesin-DNA bridges. We confirm that, in vivo, a fraction of cohesin associates with chromatin in yeast cells in a manner consistent with phase separation. Our findings establish that SMC proteins can exhibit phase separation, which has potential to clarify previously unexplained aspects of in vivo SMC behavior and constitute an additional principle by which SMC complexes impact genome organization. Competing Interest Statement The authors have declared no competing interest.

Structural Maintenance of Chromosome (SMC) protein complexes are the key organizers of the spatiotemporal structure of chromosomes. The condensin SMC complex, which compacts DNA during mitosis, was recently shown to be a molecular motor that extrudes large loops of DNA. The mechanism of this unique motor, which takes large steps along DNA at low ATP consumption, remains elusive however. Here, we use Atomic Force Microscopy (AFM) to visualize the structure of yeast condensin and condensin-DNA complexes. Condensin is found to exhibit mainly open O-shapes and collapsed B-shapes, and it cycles dynamically between these two states over time. Condensin binds double-stranded DNA via a HEAT subunit and, surprisingly, also via the hinge domain. On extruded DNA loops, we observe a single condensin complex at the loop stem, where the neck size of the DNA loop correlates with the width of the condensin complex. Our results suggest that condensin extrudes DNA by a fast cyclic switching of its conformation between O and B shapes, consistent with a scrunching model.

We have realized a microstrip based THz near field cantilever which enables quantitative measurements of the impedance of the probe tip at THz frequencies (0.3 THz). A key feature is the on-chip balanced hybrid coupler which serves as an interferometer for passive signal cancellation to increase the readout circuit sensitivity despite extreme impedance mismatch at the tip. We observe distinct changes in the reflection coefficient of the tip when brought into contact with different dielectric (Si, SrTiO3) and metallic samples (Au). By comparing to finite element simulations we determine the sensitivity of our THz probe to be well below 0.25 fF. The cantilever further allows for topography imaging in a conventional atomic force microscope mode. Our THz cantilever removes several critical technology challenges and thus enables a shielded cantilever based THz near field microscope.

High frequency acoustic devices based on two-dimensional (2D) materials are unique platforms to design and manipulate the spatiotemporal response of acoustic waves for next-generation sensing and contactless actuation applications. Conventional methods for actuating suspended membranes, however, cannot be applied to all 2D materials, or are limited in frequency. There is, therefore, a need for a universal high-frequency, on-chip actuation technique that can be applied to all types of membranes. Here, we demonstrate that surface acoustic waves (SAWs) can be used to efficiently actuate suspended 2D materials by exciting suspended graphene membranes with high-frequency (375 MHz) Rayleigh surface waves and mapping the resulting vibration field with atomic force acoustic microscopy (AFAM). Acoustic waves travelling from supported to suspended graphene experience a reduction in acoustic wavelength from 10 \\mu m to ~2 \\mu um due to the decrease in effective bending rigidity, leading to a decrease in wave velocity on suspended graphene. By varying the excitation frequency, we observed a change in phase velocity from ~160 m/s to ~700 m/s. This behavior is consistent with the nonlinear dispersion of acoustic waves, as predicted by plate theory, in suspended graphene membranes. The geometry and bending rigidity of the membrane thus play key roles in modulating the acoustic wave pattern and wavelength. This combined SAW actuation and AFAM visualization scheme can give new insights into the fundamentals of acoustic transport at the nanoscale limit and provides a route towards the manipulation of localized wavefields for on-chip patterning and transport over 2D materials surfaces.

Nuclear spins owe their long-lived magnetic states to their excellent isolation from the environment. At the same time, a finite degree of interaction with their surroundings is necessary for reading and writing the spin state. Therefore, detailed knowledge of and control over the atomic environment of a nuclear spin is key to optimizing conditions for quantum information applications. While various platforms enabled single-shot readout of nuclear spins, their direct environments were either unknown or impossible to controllably modify on the atomic scale. Scanning tunnelling microscopy (STM), combined with electron spin resonance (ESR), provides atomic-scale information of individual nuclear spins via the hyperfine interaction. Here, we demonstrate single-shot readout of an individual \\(^{\\text{49}}\\)Ti nuclear spin with an STM. Employing a pulsed measurement scheme, we find its lifetime to be in the order of seconds. Furthermore, we shed light on the pumping and relaxation mechanisms of the nuclear spin by investigating its response to both ESR driving and tunnelling current, which is supported by model calculations. These findings give an atomic-scale insight into the nature of nuclear spin relaxation and are relevant for the development of atomically assembled qubit platforms.