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Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are non-ergodic, including bistable Holliday junctions and part of a bistable origami. Taking an origami compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results establish an efficient framework to study free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications., 4 figures, 7 SI figures, 3 SI tables, 2 SI discussions, methods

Background: In the United States, patients with limited English proficiency face significant barriers to comprehending and acting upon health-related information, particularly during the COVID-19 pandemic. The ability of health professionals to communicate COVID-19-related information to Mandarin-speaking patients has proved critical in discussions about vaccine efficacy, side effects, and post-vaccine protection. Methods: The authors created a one-hour educational module to help Mandarin-speaking medical students better convey COVID-19 vaccine information to Mandarin-only speakers. The module is composed of an educational guide, which introduced key terminology and addressed commonly asked questions, and pre- and post-surveys. The authors recruited 59 Mandarin-speaking medical students all of whom had previously completed a medical Mandarin elective. The module and surveys were distributed and completed in August 2021. Data analysis measured the change in aggregate mean for subjective five-point Likert-scale questions and change in percent accuracy for objective knowledge-based questions. Results: The educational module significantly improved participants' subjective comfort level in discussing the COVID-19 vaccine in English and Mandarin. The largest improvement in both English and Mandarin was demonstrated in the participants ability to explain differences between the COVID-19 vaccines, with an aggregate mean improvement of 0.39 for English and 1.48 for Mandarin. Survey respondents also demonstrated increased percent accuracy in knowledge-based objective questions in Mandarin. Conclusions: This module provides Mandarin-learning medical students with skills to deliver reliable information to the general population and acts as a model for the continued development of educational modules for multilingual medical professionals.

Biology has evolved a variety of agents capable of permeabilizing and disrupting lipid membranes, from amyloid aggregates, to antimicrobial peptides, to venom compounds. While often associated with disease or toxicity, these agents are also central to many biosensing and therapeutic technologies. Here, we introduce a class of synthetic, DNA-based particles capable of disrupting lipid membranes. The particles have finely programmable size, and self-assemble from all-DNA and cholesterol-DNA nanostructures, the latter forming a membrane-adhesive core and the former a protective hydrophilic corona. We show that the corona can be selectively displaced with a molecular cue, exposing the ‘sticky’ core. Unprotected particles adhere to synthetic lipid vesicles, which in turn enhances membrane permeability and leads to vesicle collapse. Furthermore, particle-particle coalescence leads to the formation of gel-like DNA aggregates that envelop surviving vesicles. This response is reminiscent of pathogen immobilisation through immune cells secretion of DNA networks, as we demonstrate by trapping E. coli bacteria., Lipid membrane disruption is often associated with disease but is also essential to a range of biosensing and therapeutic techniques. Here, the authors report on the development of DNA-based particles that, upon exposure to an external cue, can aggregate, disrupt lipid membranes, and arrest the motion of bacteria.

The performance of DNA-PAINT in biological samples is often constrained by strong background signals and non-specific binding events, both of which are exacerbated by high imager concentrations. Here we describe the procedure for conducting Repeat Domain DNA-PAINT, a method that substantially reduces imager concentration and thus suppresses spurious signals.

It is crucial to visualize biomolecules and their molecular-interaction complexes directly within cells, to show precisely where these interactions occur and thus improve our understanding of cellular regulation. In this presentation I will present new approaches to image proteins and protein-protein interactions that are based on synthetic DNA interactions and allow localisation with ~10 nm precision. Two schemes will be presented, called PD-PAINT (proximity-dependent PAINT) and Repeat DNA-PAINT which are improvements of the localisation microscopy technique called DNA-PAINT. I will describe the basis of these approaches and demonstrate their application to biophysical questions in cardiac biophysics. We show that these schemes can be straightforwardly integrated in a multiplexed super-resolution imaging protocol and benefit from advantages of DNA-based super-resolution localization microscopy, such as high specificity, high resolution and the ability to image quantitatively.

DNA-PAINT is a versatile optical super-resolution technique relying on the transient binding of fluorescent DNA ‘imagers’ to target epitopes. Its performance in biological samples is often constrained by strong background signals and non-specific binding events, both exacerbated by high imager concentrations. Here we describe Repeat DNA-PAINT, a method that enables a substantial reduction in imager concentration, thus suppressing spurious signals. Additionally, Repeat DNA-PAINT reduces photoinduced target-site loss and can accelerate sampling, all without affecting spatial resolution., DNA-PAINT is a super-resolution imaging technique which suffers from high background signals and non-specific binding. Here the authors report Repeat DNA-PAINT which is capable of supressing background noise and preventing photoinduced site loss, as well as decreasing the time taken for the sampling process.

Target-induced DNA strand displacement is an excellent candidate for developing analyte-responsive DNA circuitry to be used in clinical diagnostics and synthetic biology. While most available technologies rely on DNA circuitry free to diffuse in bulk, here we explore the use of liposomes as scaffolds for DNA-based sensing nanodevices. Our proof-of-concept sensing circuit responds to the presence of a model target analyte by releasing a DNA strand, which in turn activates a fluorescent reporter. Through a combination of experiments and coarse-grained Monte Carlo simulations, we demonstrate that the presence of the membrane scaffold accelerates the process of oligonucleotide release and suppresses undesired leakage reactions, making the sensor both more responsive and robust.

The bacterial soluble lytic transglycosylase (LT) breaks down the peptidoglycan (PG) layer during processes such as cell division. We present here crystal structures of the soluble LT Cj0843 from Campylobacter jejuni with and without bulgecin A inhibitor in the active site. Cj0843 has a doughnut shape similar but not identical to that of E. coli SLT70. The C-terminal catalytic domain is preceded by an L-domain, a large helical U-domain, a flexible linker, and a small N-terminal NU-domain. The flexible linker allows the NU-domain to reach over and complete the circular shape, using residues conserved in the Epsilonproteobacteria LT family. The inner surface of the Cj0843 doughnut is mostly positively charged including a pocket that has 8 Arg/Lys residues. Molecular dynamics simulations with PG strands revealed a potential functional role for this pocket in anchoring the negatively charged terminal tetrapeptide of the PG during several steps in the reaction including homing and aligning the PG strand for exolytic cleavage, and subsequent ratcheting of the PG strand to enhance processivity in degrading PG strands.

DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and bond directionality have been recognised as key design features for DNA motifs to sustain long-range order in 3D, but the practical challenges associated with prescribing building-block geometry with sufficient accuracy have limited the variety of available designs. We have recently introduced a novel platform for the one-pot preparation of crystalline DNA frameworks supported by a combination of Watson-Crick base pairing and hydrophobic forces (Brady et al 2017 Nano Lett. 17 3276-81). Here we use small angle x-ray scattering and coarse-grained molecular simulations to demonstrate that, as opposed to available all-DNA approaches, amphiphilic motifs do not rely on structural rigidity to support long-range order. Instead, the flexibility of amphiphilic DNA building-blocks is a crucial feature for successful crystallisation.

Reasons for indoor-moisture beyond the normal level can be caused by penetrating dampness, condensation-water, and apartment misuse. A fall in the air temperature below the dew point in connection with moulding inside buildings becomes evident mostly at places like badly insulated outer-walls or room-corners. In a number of houses built between 1980 and 1983 in the so called "Plattenbauweise" (prefabricated slabs), exclusively the inner-walls were covered in mould around cracks in the walls. Examinations showed connections between the apartment and the outer-corridor with a slight exchange of air through the cracks. Warm, wet air escaped from the apartment into the outer-corridor, and cold air entered the apartment from the outer-corridor. This temporary fall below the dewpoint caused by suitable variation of temperature probably resulted in the building materials and wallpapers becoming damp, as well as the growth of mould.