Light-Activated Assembly of DNA Origami into Dissipative Fibrils

Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif—protonated, self-complementary poly(adenine) sequences—can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.     

Ensuring Quality of Experience in the Connected Home: A New Battleground for Quality of Experience Differentiation

ABSTRACT

The connected home is a critical part of the network—but one that has seen little in the way of true investment in recent years. With customer loyalty and churn directly linked to quality of experience, this is a part of the network that no players in the supply chain can afford to ignore any longer. Beyond broadband experience, the addition of smart technology to the connected home also represents one of the biggest revenue growth areas in the consumer telecoms market for some time. From both a churn-reduction and a revenue-growth perspective, investment in the connected home network must accelerate. This article outlines the key trends identified by Ovum in the connected home space for 2016 and beyond.     

Structurally Defined αMHC‐II Nanobody–Drug Conjugates: A Therapeutic and Imaging System for B‐Cell Lymphoma

Antibody–drug conjugates (ADCs) of defined structure hold great promise for cancer therapies, but further advances are constrained by the complex structures of full‐sized antibodies. Camelid‐derived single‐domain antibody fragments (VHHs or nanobodies) offer a possible solution to this challenge by providing expedited target screening and validation through switching between imaging and therapeutic activities. We used a nanobody (VHH7) specific for murine MHC‐II and rendered “sortase‐ready” for the introduction of oligoglycine‐modified cytotoxic payloads or NIR fluorophores. The VHH7 conjugates outcompeted commercial monoclonal antibodies (mAbs) for internalization and exhibited high specificity and cytotoxicity against A20 murine B‐cell lymphoma. Non‐invasive NIR imaging with a VHH7–fluorophore conjugate showed rapid tumor targeting on both localized and metastatic lymphoma models. Subsequent treatment with the nanobody–drug conjugate efficiently controlled tumor growth and metastasis without obvious systemic toxicity.     

Quantification of Stereochemical Communication in Metal–Organic Assemblies

The derivation and application of a statistical mechanical model to quantify stereochemical communication in metal–organic assemblies is reported. The factors affecting the stereochemical communication within and between the metal stereocenters of the assemblies were experimentally studied by optical spectroscopy and analyzed in terms of a free energy penalty per “incorrect” amine enantiomer incorporated, and a free energy of coupling between stereocenters. These intra‐ and inter‐vertex coupling constants are used to track the degree of stereochemical communication across a range of metal–organic assemblies (employing different ligands, peripheral amines, and metals); temperature‐dependent equilibria between diastereomeric cages are also quantified. The model thus provides a unified understanding of the factors that shape the chirotopic void spaces enclosed by metal–organic container molecules.     

Complexity of Linear Circuits and Geometry

We use algebraic geometry to study matrix rigidity and, more generally, the complexity of computing a matrix–vector product, continuing a study initiated in Kumar et al. (2009), Landsberg et al. (preprint). In particular, we (1) exhibit many non-obvious equations testing for (border) rigidity, (2) compute degrees of varieties associated with rigidity, (3) describe algebraic varieties associated with families of matrices that are expected to have super-linear rigidity, and (4) prove results about the ideals and degrees of cones that are of interest in their own right.     

Decomposition of (Co)isotropic Relations

We identify 13 isomorphism classes of indecomposable coisotropic relations between Poisson vector spaces and show that every coisotropic relation between finite-dimensional Poisson vector spaces may be decomposed as a direct sum of multiples of these indecomposables. We also find a list of 13 invariants, each of which is the dimension of a space constructed from the relation, such that the 13-vector of multiplicities and the 13-vector of invariants are related by an invertible matrix over \({\mathbb{Z}}\). It turns out to be simpler to do the analysis above for isotropic relations between presymplectic vector spaces. The coisotropic/Poisson case then follows by a simple duality argument.     

Ferrous Iron Binding Key to Mms6 Magnetite Biomineralisation: A Mechanistic Study to Understand Magnetite Formation Using pH Titration and NMR Spectroscopy

Formation of magnetite nanocrystals by magnetotactic bacteria is controlled by specific proteins which regulate the particles’ nucleation and growth. One such protein is Mms6. This small, amphiphilic protein can self‐assemble and bind ferric ions to aid in magnetite formation. To understand the role of Mms6 during in vitro iron oxide precipitation we have performed in situ pH titrations. We find Mms6 has little effect during ferric salt precipitation, but exerts greatest influence during the incorporation of ferrous ions and conversion of this salt to mixed‐valence iron minerals, suggesting Mms6 has a hitherto unrecorded ferrous iron interacting property which promotes the formation of magnetite in ferrous‐rich solutions. We show ferrous binding to the DEEVE motif within the C‐terminal region of Mms6 by NMR spectroscopy, and model these binding events using molecular simulations. We conclude that Mms6 functions as a magnetite nucleating protein under conditions where ferrous ions predominate.     

Analysis and deconvolution of dimethylnaphthalene isomers using gas chromatography vacuum ultraviolet spectroscopy and theoretical computations

An issue with most gas chromatographic detectors is their inability to deconvolve coeluting isomers. Dimethylnaphthalenes are a class of compounds that can be particularly difficult to speciate by gas chromatography – mass spectrometry analysis, because of their significant coelution and similar mass spectra. As an alternative, a vacuum ultraviolet spectroscopic detector paired with gas chromatography was used to study the systematic deconvolution of mixtures of coeluting isomers of dimethylnaphthalenes. Various ratio combinations of 75:25; 50:50; 25:75; 20:80; 10:90; 5:95; and 1:99 were prepared to test the accuracy, precision, and sensitivity of the detector for distinguishing overlapping isomers that had distinct, but very similar absorption spectra. It was found that, under reasonable injection conditions, all of the pairwise overlapping isomers tested could be deconvoluted up to nearly two orders of magnitude (up to 99:1) in relative abundance. These experimental deconvolution values were in agreement with theoretical covariance calculations performed for two of the dimethylnaphthalene isomers. Covariance calculations estimated high picogram detection limits for a minor isomer coeluting with low to mid-nanogram quantity of a more abundant isomer. Further characterization of the analytes was performed using density functional theory computations to compare theory with experimental measurements. Additionally, gas chromatography – vacuum ultraviolet spectroscopy was shown to be able to speciate dimethylnaphthalenes in jet and diesel fuel samples.     

Antagonistic Effects of Endogenous Nitric Oxide in a Glioblastoma Photodynamic Therapy Model

Gliomas are aggressive brain tumors that are resistant to conventional chemotherapy and radiotherapy. Much of this resistance is attributed to endogenous nitric oxide (NO). Recent studies revealed that 5‐aminolevulinic acid (ALA)‐based photodynamic therapy (PDT) has advantages over conventional treatments for glioblastoma. In this study, we used an in vitro model to assess whether NO from glioblastoma cells can interfere with ALA‐PDT. Human U87 and U251 cells expressed significant basal levels of neuronal NO synthase (nNOS) and its inducible counterpart (iNOS). After an ALA/light challenge, iNOS level increased three‐ to fourfold over 24 h, whereas nNOS remained unchanged. Elevated iNOS resulted in a large increase in intracellular NO. Extent of ALA/light‐induced apoptosis increased substantially when an iNOS inhibitor or NO scavenger was present, implying that iNOS/NO was acting cytoprotectively. Moreover, cells surviving a photochallenge exhibited a striking increase in proliferation, migration and invasion rates, iNOS/NO again playing a dominant role. Also observed was a large iNOS/NO‐dependent increase in matrix metalloproteinase‐9 activity, decrease in tissue inhibitor of metalloproteinase‐1 expression and increase in survivin and S100A4 expression, each effect being consistent with accelerated migration/invasion as a prelude to metastasis. Our findings suggest introduction of iNOS inhibitors as pharmacologic adjuvants for glioblastoma PDT.