*authors contributed equally to this work 2 DNA origami is a robust molecular assembly technique by which a single-stranded DNA template is folded by annealing it with hundreds of short 'staple' strands. 1-4 The guiding design principle of nanofabrication by DNA self-assembly is that the target structure is the single most stable configuration; 5 however, the pathway and kinetics of origami assembly are poorly understood. The folding transition is cooperative 4,6,7 , and there is a strong analogy with protein folding: both are governed by information encoded in polymer sequence. [8][9][10][11] Misfolded structures are kinetic traps. The yield of well-folded DNA origami can be low: 2 yield is improved by titration of cations 2,12 or by following empirical design rules, 12,13 but it is frequently necessary to separate wellfolded origami from misfolded objects. 2, 3, 14-16 Here, we present an origami structure that is designed to reveal the assembly process. Our system has the unusual property of having a small set of distinguishable, well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape. We obtain a high yield of well-folded origami structures, demonstrating the existence of efficient folding pathways. The distribution of shapes provides information about individual trajectories through the folding landscape. We show that the assembly pathway can be steered by rational design and identify similarities to protein folding: assembly is highly cooperative; reversible bond-formation is important in recovering from transient misfoldings; and the early formation of long-range connections can be very effective in forcing particular folds. Expanding the rational design process to include the assembly pathway is the key to reproducible synthesis, which is essential if nucleic acid selfassembly is to continue its rapid development 1-3,17-19 and become a reliable manufacturing technology. 20 3This study is based on a simplified version of the archetypal origami tile 1 and, in particular, on the distribution of observed folds of a 'dimer' variant which contains two copies of the template sequence in head-to-tail repeat. The 'monomer' tile ( Fig. . 1) (Fig. 1c); approximately 80% of tiles appear to be well folded.The 'dimer' template is also circular. It contains two identical copies of the monomer joined head-to-tail and can therefore bind two copies of each staple (Fig. 2). Each pair of body and seam staples can bind in one of two configurations (Fig. 2a) to form either an internal link within each copy of the monomer sequence or a pair of cross-links between the two copies.The total number of possible domain pairings is 2 76 ≈ 10 23 . Although many of these configurations are sterically inaccessible it is clear that the result of reducing the specificity of staple binding is that, as in the case of protein folding, the number of possible states of the system is overwhelmingly greater than the number of well-folded structures. However, in contrast to proteins (and t...

In the nacre or aragonite layer of the mollusk shell there exist proteomes which regulate both the early stages of nucleation and nano-to-mesoscale assembly of nacre tablets from mineral nanoparticle precursors. Several approaches have been developed to understand protein-associated mechanisms of nacre formation, yet we still lack insight into how protein ensembles or proteomes manage nucleation and crystal growth. To provide additional insights we have created a proportionally-defined combinatorial model consisting of two nacre-associated proteins, C-RING AP7 (shell nacre, H. rufescens) and pseudo-EF hand PFMG1 (oyster pearl nacre, P. fucata) whose individual in vitro mineralization functionalities are well-documented and distinct from one another. Using SEM, flow cell STEM, AFM, Ca(II) potentiometric titrations and QCM-D quantitative analyses, we find that both nacre proteins are functionally active within the same mineralization environments, and at 1:1 mole ratios, synergistically create calcium carbonate mesoscale structures with ordered intracrystalline nanoporosities, extensively prolong nucleation times and introduce an additional nucleation event. Further, these two proteins jointly create nanoscale protein aggregates or phases that under mineralization conditions further assemble into protein-mineral PILP-like phases with enhanced ACC stabilization capabilities, and there is evidence for intermolecular interactions between AP7 and PFMG1 under these conditions. Thus, a combinatorial model system consisting of more than one defined biomineralization protein dramatically changes the outcome of the in vitro biomineralization process.

The SARS-CoV-2 virus is primarily transmitted through virus-laden fluid particles ejected from the mouth of infected people. Face covers can mitigate the risk of virus transmission but their outward effectiveness is not fully ascertained. Objective: by using a background oriented schlieren technique, we aim to investigate the air flow ejected by a person while quietly and heavily breathing, while coughing, and with different face covers. Results: we found that all face covers without an outlet valve reduce the front flow through by at least 63% and perhaps as high as 86% if the unfiltered cough jet distance was resolved to the anticipated maximum distance of 2-3 m. However, surgical and handmade masks, and face shields, generate significant leakage jets that may present major hazards. Conclusions: the effectiveness of the masks should mostly be considered based on the generation of secondary jets rather than on the ability to mitigate the front throughflow. INDEX TERMS COVID-19 pandemic, face coverings, face masks, aerosol dispersal, aerosol generating procedures. IMPACT STATEMENT These results show the effectiveness of face coverings in mitigating aerosol dispersion and can aid policy makers to make informed decisions and PPE developers to improve their product effectiveness.

The emergence of personalized and stratified medicine requires label-free, low-cost diagnostic technology capable of monitoring multiple disease biomarkers in parallel. Silicon photonic biosensors combine high-sensitivity analysis with scalable, low-cost manufacturing, but they tend to measure only a single biomarker and provide no information about their (bio)chemical activity. Here we introduce an electrochemical silicon photonic sensor capable of highly sensitive and multiparameter profiling of biomarkers. Our electrophotonic technology consists of microring resonators optimally n-doped to support high Q resonances alongside electrochemical processes in situ. The inclusion of electrochemical control enables site-selective immobilization of different biomolecules on individual microrings within a sensor array. The combination of photonic and electrochemical characterization also provides additional quantitative information and unique insight into chemical reactivity that is unavailable with photonic detection alone. By exploiting both the photonic and the electrical properties of silicon, the sensor opens new modalities for sensing on the microscale.

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami.

We demonstrate an approach that allows attachment of single-stranded DNA (ssDNA) to a defined residue in a protein of interest (POI) so as to provide optimal and well-defined multicomponent assemblies. Using an expanded genetic code system, azido-phenylalanine (azF) was incorporated at defined residue positions in each POI; copper-free click chemistry was used to attach exactly one ssDNA at precisely defined residues. By choosing an appropriate residue, ssDNA conjugation had minimal impact on protein function, even when attached close to active sites. The protein-ssDNA conjugates were used to (i) assemble double-stranded DNA systems with optimal communication (energy transfer) between normally separate groups and (ii) generate multicomponent systems on DNA origami tiles, including those with enhanced enzyme activity when bound to the tile. Our approach allows any potential protein to be simply engineered to attach ssDNA or related biomolecules, creating conjugates for designed and highly precise multiprotein nanoscale assembly with tailored functionality.

The radiation tolerance of specific optical fibres exposed to 650 kGy(Si) of ionizing radiation To cite this article: B Arvidsson et al 2009 JINST 4 P07010 View the article online for updates and enhancements. Recent citations Gary Pickrell et al -JTAG-based remote configuration of FPGAs over optical fibers B. Deng et al