Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs.

DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules, with applications ranging from therapeutics and diagnostics to plasmonics and photonics. Imaging these structures using atomic force microscopy (AFM) or transmission electron microscope (TEM) does not capture their full conformation ensemble as they only show their shape flattened on a surface.

Single-molecule force spectroscopy of toehold-mediated strand displacement.

Toehold-mediated strand displacement (TMSD) is extensively utilized in dynamic DNA nanotechnology and for a wide range of DNA or RNA-based reaction circuits. Investigation of TMSD kinetics typically relies on bulk fluorescence measurements providing effective, bulk-averaged reaction rates. Information on individual molecules or even base pairs is scarce.

Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments.

Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles.

The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.

This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.

A simple solution to the problem of self-assembling cubic diamond crystals.

The self-assembly of colloidal diamond (CD) crystals is considered as one of the most coveted goals of nanotechnology, both from the technological and fundamental points of view. For applications, colloidal diamond is a photonic crystal which can open new possibilities of manipulating light for information processing. From a fundamental point of view, its unique symmetry exacerbates a series of problems that are commonly faced during the self-assembly of target structures, such as the presence of kinetic traps and the formation of crystalline defects and alternative structures (polymorphs).

Design and simulation of DNA, RNA and hybrid protein-nucleic acid nanostructures with oxView.

Molecular simulation has become an integral part of the DNA/RNA nanotechnology research pipeline. In particular, understanding the dynamics of structures and single-molecule events has improved the precision of nanoscaffolds and diagnostic tools. Here we present oxView, a design tool for visualization, design, editing and analysis of simulations of DNA, RNA and nucleic acid-protein nanostructures.

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly.

The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals.

A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy.

Nature-inspired molecular machines can exert mechanical forces by controlling and varying the distance between two molecular subunits in response to different inputs. Here, we present an automated molecular linear actuator composed of T7 RNA polymerase (T7RNAP) and a DNA [2]rotaxane. A T7 promoter region and terminator sequences are introduced into the rotaxane axle to achieve automated and iterative binding and detachment of T7RNAP in a self-controlled fashion.

Interaction kinetics and accessibility of sulfadiazine in model clay-humic acid suspension: Electron spin resonance investigations with nitroxide spin label.

The characterization of the interaction of sulfonamides with soil is of particular interest in environmental risk and persistence assessment. In the present work electron spin resonance spectroscopy (ESR) was used to investigate the interaction kinetics of spin labelled sulfadiazine (SL-SDZ) with model clay-humic acid suspensions. The ESR spectra showed that SL-SDZ incubated with Leonardite humic acid (LHA) and Ca-hectorite as model clay was immobilized due to covalent binding of its aniline moiety to LHA.

Fate of pendimethalin in soil and characterization of non-extractable residues (NER).

One important route of degradation of herbicide pendimethalin in soil leads to formation of non-extractable residues (NER). To investigate NER nature (irreversibly, chemically bound, including possible biogenic NER, or strongly sorbed and entrapped) residues of C-labelled pendimethalin in soil were investigated after conventional extraction with organic solvents by silylation. After 400 days of incubation, 32.

Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation.

This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results.

TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami.

Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models.

Coastal accumulation of microplastic particles emitted from the Po River, Northern Italy: Comparing remote sensing and hydrodynamic modelling with in situ sample collections.

Microplastic research has mainly concentrated on open seas, while riverine plumes remain largely unexplored despite their hypothesized importance as a microplastic source to coastal waters. This work aimed to model coastal accumulation of microplastic particles (1-5 mm) emitted by the Po River over 1.5 years.

Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles.

The field of structural DNA nanotechnology offers a wide range of design strategies with which to build structures with a desired aspect ratio, size, and shape. Compared with traditional close-packed DNA structures, triangulated wireframe structures require less material per surface or volume unit and improve the stability in biologically relevant conditions due to the reduced electrostatic repulsion. Herein, we expand the design space of the DNA single-stranded tile method to cover a range of anisotropic, finite, triangulated wireframe structures as well as a number of one-dimensional crystalline assemblies.

DNA-encircled lipid bilayers.

Lipid bilayers and lipid-associated proteins play crucial roles in biology. As in vivo studies and manipulation are inherently difficult, membrane-mimetic systems are useful for the investigation of lipidic phases, lipid-protein interactions, membrane protein function and membrane structure in vitro. In this work, we describe a route to leverage the programmability of DNA nanotechnology and create DNA-encircled bilayers (DEBs).

Structural Transformation of Wireframe DNA Origami via DNA Polymerase Assisted Gap-Filling.

The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer.

Considerations of temperature in the context of the persistence classification in the EU.

Simulation degradation studies for industrial chemicals, biocidal products and plant protection products are required in the EU to estimate half-lives in soil, water and sediment for the comparison to persistence criteria for hazard (P/vP) assessment, and for use in exposure assessments. There is a discrepancy between European regulatory approaches regarding the temperature at which degradation half-lives should be (1) measured in simulation degradation testing of environmental compartments, and (2) compared to the P/vP criteria. In this paper, an opinion is provided on the options for the experimental temperature and extrapolation to other conditions.

Block Copolymer Micellization as a Protection Strategy for DNA Origami.

DNA nanotechnology enables the synthesis of nanometer-sized objects that can be site-specifically functionalized with a large variety of materials. For these reasons, DNA-based devices such as DNA origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases.

Critical assessment of pendimethalin in terms of persistence, bioaccumulation, toxicity, and potential for long-range transport.

Pendimethalin (PND, CAS registry number 40487-42-1) is a dinitroaniline herbicide that selectively controls broad-leaf and grassy weeds in a variety of crops and in noncrop areas. It has been on the market for about 30 yr and is currently under review for properties related to persistence (P), bioaccumulation (B), and toxicity (T) in the European Union (EU). A critical review of these properties as well as potential for long-range transport (LRT) was conducted.

The origin and evolution of assessment criteria for persistent, bioaccumulative and toxic (PBT) chemicals and persistent organic pollutants (POPs).

General public concern over the effects of persistent chemicals began in the early 1960s. Since then, significant scientific advances have increased our understanding of persistent, bioaccumulative, and toxic (PBT) chemicals and the properties and processes that influence their fates in, and adverse effects on, human health and the environment. In addition to the scientific advances, a number of legislations and agreements for national, international, and global identification and control of PBT chemicals have been adopted.

Design and Synthesis of Triangulated DNA Origami Trusses.

DNA nanotechnology offers unique control over matter on the nanoscale. Here, we extend the DNA origami method to cover a range of wireframe truss structures composed of equilateral triangles, which use less material per volume than standard multiple-helix bundles. From a flat truss design, we folded tetrahedral, octahedral, or irregular dodecahedral trusses by exchanging few connector strands.

Switchable Reconfiguration of a Seven-Ring Interlocked DNA Catenane Nanostructure.

The synthesis, purification, and structure characterization of a seven-ring interlocked DNA catenane is described. The design of the seven-ring catenane allows the dynamic reconfiguration of any of the four rings (R1, R3, R4, and R6) on the catenane scaffold, or the simultaneous switching of any combination of two, three, or all four rings to yield 16 different isomeric states of the catenane. The dynamic reconfiguration across the states is achieved by implementing the strand-displacement process in the presence of appropriate fuel/antifuel strands and is probed by fluorescence spectroscopy.

Comparative analysis of time series of marine litter surveyed on beaches and the seafloor in the southeastern North Sea.

The comparative analysis of marine litter in different marine compartments has rarely been attempted. In this study, long-term time series of marine litter abundance on the seafloor and on the coast, both from the southeastern North Sea, were analyzed for temporal trends and correlations. On four beach sections of 100 m length, mean abundances of total beach litter collected four times a year from 2002 to 2008 varied between 105 and 435 items.

Marine litter ensemble transport simulations in the southern North Sea.

The drift of marine litter in the southern North Sea was simulated with the offline Lagrangian transport model PELETS-2D. Assuming different source regions, passive tracer particles were released every 28 h within a nine-year period. Based on pre-calculated hourly wind and ocean current data, drift simulations were carried out forward and backward in time with and without the assumption of extra wind forces influencing particle movement.

Artificial neural networks for modeling time series of beach litter in the southern North Sea.

In European marine waters, existing monitoring programs of beach litter need to be improved concerning litter items used as indicators of pollution levels, efficiency, and effectiveness. In order to ease and focus future monitoring of beach litter on few important litter items, feed-forward neural networks consisting of three layers were developed to relate single litter items to general categories of marine litter. The neural networks developed were applied to seven beaches in the southern North Sea and modeled time series of five general categories of marine litter, such as litter from fishing, shipping, and tourism.