Dataset for Automated Purification of DNA Origami with SPRI Beads

The data set contains relevant information for the associated manuscript "Automated Purification of DNA Origami with SPRI Beads". It contains the Supporting Information 2, the origami design file and AFM images used in the publication

Tuning the translational freedom of DNA for high speed AFM

Direct observation is arguably the preferred way to investigate the interactions between two molecular complexes. With the development of high speed atomic force microscopy it is becoming possible to observe directly DNA protein interactions with relevant spatial and temporal resolutions. These interactions are of central importance to biology, bio-nanotechnology but also functional biologically inspired materials. Critically, sample preparation plays a central role in all microscopy studies and minimal perturbation of the sample is desired. Here, we demonstrate the ability to tune the interactions of DNA molecules with the surface such that an association strong enough to enable high resolution AFM imaging while providing sufficient translational freedom to allow the relevant protein DNA interactions to take place, can be maintained. Furthermore, we describe a quantitative method for measuring the DNA mobility, which also allows the dissection of the different contributions to the overall movement of the DNA molecules. We find that for weak surface association, a significant contribution to the movement arises from the interaction of the AFM tip with the DNA. In combination, these methods enable the tuning of the surface translational freedom of DNA molecules to allow the direct study of a wide range of nucleo-protein interactions by high speed atomic force microscopy

Improving the dielectric properties of ethylene-glycol alkanethiol self-assembled monolayers.

Self-assembled monolayers (SAMs) can be formed at the interface between solids and fluids, and are often used to modify the surface properties of the solid. One of the most widely employed SAM systems is exploiting thiol-gold chemistry, which, together with alkane-chain-based molecules, provides a reliable way of SAM formation to modify the surface properties of electrodes. Oligo ethylene-glycol (OEG) terminated alkanethiol monolayers have shown excellent antifouling properties and have been used extensively for the coating of biosensor electrodes to minimize nonspecific binding. Here, we report the investigation of the dielectric properties of COOH-capped OEG monolayers and demonstrate a strategy to improve the dielectric properties significantly by mixing the OEG SAM with small concentrations of 11-mercaptoundecanol (MUD). The monolayer properties and composition were characterized by means of impedance spectroscopy, water contact angle, ellipsometry and X-ray photoelectron spectroscopy. An equivalent circuit model is proposed to interpret the EIS data and to determine the conductivity of the monolayer. We find that for increasing MUD concentrations up to about 5% the resistivity of the SAM steadily increases, which together with a considerable decrease of the phase of the impedance, demonstrates significantly improved dielectric properties of the monolayer. Such monolayers will find widespread use in applications which depend critically on good dielectric properties such as capacitive biosensor

A mobile EEG study on the psychophysiological effects of walking and crowding in indoor and outdoor urban environments

Environmental psychologists have established multiple psychological benefits of interaction with natural, compared to urban, environments on emotion, cognition, and attention. Yet, given the increasing urbanisation worldwide, it is equally important to understand how differences within different urban environments influence human psychological experience. We developed a laboratory experiment to examine the psychophysiological effects of the physical (outdoor or indoor) and social (crowded versus uncrowded) environment in healthy young adults, and to validate the use of mobile electroencephalography (EEG) and electrodermal activity (EDA) measurements during active walking. Participants (N = 42) were randomly assigned into a walking or a standing group, and watched six 1-min walk-through videos of green, urban indoor and urban outdoor environments, depicting high or low levels of social density. Self-reported emotional states show that green spaces is perceived as more calm and positive, and reduce attentional demands. Further, the outdoor urban space is perceived more positively than the indoor environment. These findings are consistent with earlier studies on the psychological benefits of nature and confirm the effectiveness of our paradigm and stimuli. In addition, we hypothesised that even short-term exposure to crowded scenes would have negative psychological effects. We found that crowded scenes evoked higher self-reported arousal, more negative self-reported valence, and recruited more cognitive and attentional resources. However, in walking participants, they evoked higher frontal alpha asymmetry, suggesting more positive affective responses. Furthermore, we found that using recent signal-processing methods, the EEG data produced a comparable signal-to-noise ratio between walking and standing, and that despite differences between walking and standing, skin-conductance also captured effectively psychophysiological responses to stimuli. These results suggest that emotional responses to visually presented stimuli can be measured effectively using mobile EEG and EDA in ambulatory settings, and that there is complex interaction between active walking, the social density of urban spaces, and direct and indirect affective responses to such environments.ISSN:2045-232

Comparison and evaluation of ocular biometry using a new noncontact optical low-coherence reflectometer

PURPOSE: To evaluate a new high-resolution noncontact biometer (Lenstar; Haag-Streit AG, Koeniz, Switzerland) using optical low-coherence reflectometry and to compare the clinical measurements with those obtained from the IOLMaster (Carl Zeiss, Jena, Germany) and the Pachmumeter (Haag-Streit AG). DESIGN: Exploratory evaluation of diagnostic technology and nonrandomized, prospective clinical trial. PARTICIPANTS: Eighty subjects (144 eyes) aged 20 to 90 years with cataractous, pseudophakic, aphakic, silicon oil-filled, or normal eyes. METHODS: Measurements of axial length (AL), anterior chamber depth (ACD), central corneal thickness (CCT), corneal radius (R1 [flattest radius of corneal curvature] and R2 [steep radius, 90 degrees apart from R1]), and axis of the flattest radius (Ax1) obtained with the Lenstar were compared with those obtained with the IOLMaster or Pachmumeter. The results were evaluated using Bland-Altman analyses. The differences between both methods were assessed using the paired t test, and its correlation was evaluated by Pearson coefficient. MAIN OUTCOME MEASURES: Axial length, CCT, ACD, R1, R2, and Ax1. RESULTS: The overall mean AL measured with the Lenstar and the IOLMaster was 24.1 mm (r = 0.999). Anterior chamber depth was 3.19 mm (Lenstar) and 3.17 mm (IOLMaster; r = 0.875). Excellent correlations also were found for the corneal radius and the axis of flattest radius (R1, r = 0.927; R2, r = 0.929; and Ax1, r = 0.938). Mean CCT was 0.557 mm (r = 0.978) for both Lenstar and Pachmumeter. CONCLUSIONS: Measurements with the new Lenstar correlated well with those with the IOLMaster and Pachmumeter in cataractous, pseudophakic, aphakic, silicon oil-filled, and normal eyes. It is an accurate, fast instrument that provides additional information of interest to any cataract or refractive surgeon

Multiplexed detection of proteins in cell lysate using high-density microarrays

<p><b>Copyright information:</b></p><p>Taken from "Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays"</p><p>http://jbiol.com/content/7/1/3</p><p>Journal of Biology 2008;7(1):3-3.</p><p>Published online 31 Jan 2008</p><p>PMCID:PMC2246035.</p><p></p> Cyclic voltammogram of an individual microelectrode protected with an mPEG protein-inhibiting layer (black line), and following electrochemical desorption of the mPEG monolayer (blue line), and after functionalization with peptide aptamer STM(orange line). Δ() of the complex impedance for microelectrodes functionalized with mPEG (black circles), STM(orange circles) and STM(blue circles) following exposure to a lysate containing CDK2. As (b) but following exposure to cell lysate containing CDK4

Electrochemical impedance spectroscopy of the interaction of STMwith recombinant CDK2

<p><b>Copyright information:</b></p><p>Taken from "Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays"</p><p>http://jbiol.com/content/7/1/3</p><p>Journal of Biology 2008;7(1):3-3.</p><p>Published online 31 Jan 2008</p><p>PMCID:PMC2246035.</p><p></p> EIS () data for a gold surface functionalized with STM(orange circles) and subsequently exposed to recombinant CDK2 (blue circles). As (a) but following exposure of STM to rCDK2. Phase shift (Δ()) of STMand an STM layer on two independent gold electrodes following exposure to rCDK2. Concentration dependence of the phase shift at 70 Hz. The solid line is a linear fit to the data (see text) provided as a guide to the eye