DNA-Functionalized Gold Nanoparticles in Macromolecularly Crowded Polymer Solutions

This document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Physical Chemistry B, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp310662mDNA-functionalized gold nanoparticles (AuNPs) are one of the most commonly used reagents in nanobiotechnology. They are important not only for practical applications in analytical chemistry and drug delivery, but also for fundamental understanding of nanoscience. For biological samples such as blood serum or for intracellular applications, the effects of crowded cellular proteins and nucleic acids need to be considered. The thermodynamic effect of crowding is to induce nanoparticle aggregation. But before such aggregation can take place, there might also be a depletion repulsive barrier. Polyethylene glycol (PEG) is one of the most frequently used polymers to mimic the crowded cellular environment. We show herein that while DNA-functionalized AuNPs are very stable in buffer (e.g., no PEG) and citrate-capped AuNPs are very stable in PEG, DNA-functionalized AuNPs are unstable in PEG and are easily aggregated. Although such aggregation in PEG is mediated by DNA, no sharp melting transition typical for DNA-linked AuNPs is observed. We attribute this broad melting to depletion force instead of DNA base pairing. The effects of PEG molecular weight, concentration and temperature have been studied in detail and we also find an interesting PEG phase separation and AuNP partition into the water-rich phase at high temperature.University of Waterloo || Canadian Foundation for Innovation || Natural Sciences and Engineering Research Council || Ontario Ministry of Research and Innovation |

Fire and biodiversity in the Anthropocene

The workshop leading to this paper was funded by the Centre Tecnològic Forestal de Catalunya and the ARC Centre of Excellence for Environmental Decisions. L.T.K. was supported by a Victorian Postdoctoral Research Fellowship (Victorian Government), a Centenary Fellowship (University of Melbourne), and an Australian Research Council Linkage Project Grant (LP150100765). A.R. was supported by the Xunta de Galicia (Postdoctoral Fellowship ED481B2016/084-0) and the Foundation for Science and Technology under the FirESmart project (PCIF/MOG/0083/2017). A.L.S. was supported by a Marie Skłodowska-Curie Individual Fellowship (746191) under the European Union Horizon 2020 Programme for Research and Innovation. L.R. was supported by the Australian Government’s National Environmental Science Program through the Threatened Species Recovery Hub. L.B. was partially supported by the Spanish Government through the INMODES (CGL2014-59742-C2-2-R) and the ERANET-SUMFORESTS project FutureBioEcon (PCIN-2017-052). This research was supported in part by the U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station.BACKGROUND Fire has shaped the diversity of life on Earth for millions of years. Variation in fire regimes continues to be a source of biodiversity across the globe, and many plants, animals, and ecosystems depend on particular temporal and spatial patterns of fire. Although people have been using fire to modify environments for millennia, the combined effects of human activities are now changing patterns of fire at a global scale—to the detriment of human society, biodiversity, and ecosystems. These changes pose a global challenge for understanding how to sustain biodiversity in a new era of fire. We synthesize how changes in fire activity are threatening species with extinction across the globe, highlight forward-looking methods for predicting the combined effects of human drivers and fire on biodiversity, and foreshadow emerging actions and strategies that could revolutionize how society manages fire for biodiversity in the Anthropocene. ADVANCES Our synthesis shows that interactions with anthropogenic drivers such as global climate change, land use, and biotic invasions are transforming fire activity and its impacts on biodiversity. More than 4400 terrestrial and freshwater species from a wide range of taxa and habitats face threats associated with modified fire regimes. Many species are threatened by an increase in fire frequency or intensity, but exclusion of fire in ecosystems that need it can also be harmful. The prominent role of human activity in shaping global ecosystems is the hallmark of the Anthropocene and sets the context in which models and actions must be developed. Advances in predictive modeling deliver new opportunities to couple fire and biodiversity data and to link them with forecasts of multiple drivers including drought, invasive plants, and urban growth. Making these connections also provides an opportunity for new actions that could revolutionize how society manages fire. Emerging actions include reintroduction of mammals that reduce fuels, green fire breaks comprising low-flammability plants, strategically letting wildfires burn under the right conditions, managed evolution of populations aided by new genomics tools, and deployment of rapid response teams to protect biodiversity assets. Indigenous fire stewardship and reinstatement of cultural burning in a modern context will enhance biodiversity and human well-being in many regions of the world. At the same time, international efforts to reduce greenhouse gas emissions are crucial to reduce the risk of extreme fire events that contribute to declines in biodiversity. OUTLOOK Conservation of Earth’s biological diversity will be achieved only by recognition of and response to the critical role of fire in shaping ecosystems. Global changes in fire regimes will continue to amplify interactions between anthropogenic drivers and create difficult trade-offs between environmental and social objectives. Scientific input will be crucial for navigating major decisions about novel and changing ecosystems. Strategic collection of data on fire, biodiversity, and socioeconomic variables will be essential for developing models to capture the feedbacks, tipping points, and regime shifts characteristic of the Anthropocene. New partnerships are also needed to meet the challenges ahead. At the local and regional scale, getting more of the “right” type of fire in landscapes that need it requires new alliances and networks to build and apply knowledge. At the national and global scale, biodiversity conservation will benefit from greater integration of fire into national biodiversity strategies and action plans and in the implementation of international agreements and initiatives such as the UN Convention on Biological Diversity. Placing the increasingly important role of people at the forefront of efforts to understand and adapt to changes in fire regimes is central to these endeavors.PostprintPeer reviewe

Surface Science of DNA Adsorption onto Citrate-Capped Gold Nanoparticles

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Langmuir copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Zhang, X., Servos, M. R., & Liu, J. (2012). Surface Science of DNA Adsorption onto Citrate-Capped Gold Nanoparticles. Langmuir, 28(8), 3896–3902. https://doi.org/10.1021/la205036pSingle-stranded DNA can be adsorbed by citrate capped gold nanoparticles (AuNPs), resulting in increased AuNP stability, which forms the basis of a number of biochemical and analytical applications, but the fundamental interaction of this adsorption reaction remains unclear. In this study, we measured DNA adsorption kinetics, capacity, and isotherms, demonstrating that the adsorption process is governed by electrostatic forces. The charge repulsion among DNA strands and between DNA and AuNPs can be reduced by adding salt, reducing pH or by using noncharged peptide nucleic acid (PNA). Langmuir adsorption isotherms are obtained, indicating the presence of both adsorption and desorption of DNA from AuNPs. While increasing salt concentration facilitates DNA adsorption, the desorption rate is also enhanced in higher salt due to DNA compaction. DNA adsorption capacity is determined by DNA oligomer length, DNA concentration, and salt. Previous studies indicated faster adsorption of short DNA oligomers by AuNPs, we find that once adsorbed, longer DNAs are much more effective in protecting AuNPs from aggregation. DNA adsorption is also facilitated by using low pH buffers and high alcohol concentrations. A model based on electrostatic repulsion on AuNPs is proposed to rationalize the DNA adsorption/desorption behavior.University of Waterloo || Canadian Foundation for Innovation || Ontario Ministry of Research & Innovation || Canadian Institutes of Health Research || Natural Sciences and Engineering Research Council |

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution

Magnetic Particle-Scanning for Ultrasensitive Immunodetection On-Chip

We describe the concept of magnetic particle-scanning for on-chip detection of biomolecules: a magnetic particle, carrying a low number of antigens (Ag's) (down to a single molecule), is transported by hydrodynamic forces and is subjected to successive stochastic reorientations in an engineered magnetic energy landscape. The latter consists of a pattern of substrate-bound small magnetic particles that are functionalized with antibodies (Ab's). Subsequationuent counting of the captured Ag-carrying particles provides the detection signal. The magnetic particle-scanning principle is investigated in a custom-built magneto-microfluidic chip and theoretically described by a random walk-based model, in which the trajectory of the contact point between an Ag-carrying particle and the small magnetic particle pattern is described by stochastic moves over the surface of the mobile particle, until this point coincides with the position of an Ag, resulting in the binding of the particle. This model explains the particular behavior of previously reported experimental dose-response curves obtained for two different ligand-receptor systems (biotin/streptavidin and TNF-alpha) over a wide range of concentrations. Our model shows that magnetic particle-scanning results in a very high probability of irrununocomplex formation for very low Ag concentrations, leading to an extremely low limit of detection, down to the single molecule-per-particle level. When compared to other types of magnetic particle-based surface coverage assays, our strategy was found to offer a wider dynamic range (>8 orders of magnitude), as the system does not saturate for concentrations as high as 10(11) Ag molecules in a 5 mu L drop. Furthermore, by emphasizing the importance of maximizing the encounter probability between the Ag and the Ab to improve sensitivity, our model also contributes to explaining the behavior of other particle-based heterogeneous immunoassays