Free-solution electrophoresis of DNA modified with drag-tags at both ends

In end-labeled free-solution electrophoresis (ELFSE), DNA molecules are labeled with a frictional modifier or "drag-tag", allowing their size-based electrophoretic separation in free solution. Among the interesting observations from early work with dsDNA using streptavidin as a drag-tag was that the drag induced by including a streptavidin label at both ends was significantly more than double that from a single streptavidin (Heller, C. et al.., J. Chromatogr. A 1998, 806, 113-121). This finding was assumed to be in error, and subsequent work focused on experiments in which only a single drag-tag is appended to one end of the DNA molecule. Recent theoretical work (McCormick, L. C., Slater, G. W., Electrophoresis 2005, 26, 1659-1667) has examined the contribution of end-effects to the free-solution electrophoretic mobility of charged-uncharged polymer conjugates, reopening the question of enhanced drag from placing a drag-tag at both ends. In this study, this effect is investigated experimentally, using custom-synthesized ssDNA oligonucleotides allowing the attachment of drag-tags to one or both ends, as well as dsDNA PCR products generated with primers appropriate for the attachment of drag-tags at one or both ends. A range of sizes of drag-tags are used, including synthetic polypeptoid drag-tags as well as genetically engineered protein polymer drag-tags. The enhanced drag arising from labeling both ends has been confirmed, with 6-9% additional drag for the ssDNA and 10-23% additional drag for the dsDNA arising from labeling both ends than would be expected from simply doubling the size of the drag-tag at one end. The experimental results for ssDNA labeled at both ends are compared to the predictions of the recent theory of end-effects, with reasonably good quantitative agreement. These experimental findings demonstrate the feasibility of enhancing ELFSE separations by labeling both ends of the DNA molecule, leading to greater resolving power and a wider range of applications for this technique.     

Inferring social structure from continuous‐time interaction data

Relational event data, which consist of events involving pairs of actors over time, are now commonly available at the finest of temporal resolutions. Existing continuous‐time methods for modeling such data are based on point processes and directly model interaction “contagion,” whereby one interaction increases the propensity of future interactions among actors, often as dictated by some latent variable structure. In this article, we present an alternative approach to using temporal‐relational point process models for continuous‐time event data. We characterize interactions between a pair of actors as either spurious or as resulting from an underlying, persistent connection in a latent social network. We argue that consistent deviations from expected behavior, rather than solely high frequency counts, are crucial for identifying well‐established underlying social relationships. This study aims to explore these latent network structures in two contexts: one comprising of college students and another involving barn swallows.     

Reductive side of water splitting in artificial photosynthesis: new homogeneous photosystems of great activity and mechanistic insight

Rhodamine photosensitizers (PSs) substituting S or Se for O in the xanthene ring give turnover numbers (TONs) as high as 9000 for the generation of hydrogen via the reduction of water using [Co(III)(dmgH)(2)(py)Cl] (where dmgH = dimethylglyoximate and py = pyridine) as the catalyst and triethanolamine as the sacrificial electron donor. The turnover frequencies were 0, 1700, and 5500 mol H(2)/mol PS/h for O, S, and Se derivatives, respectively (Φ(H(2)) = 0%, 12.2%, and 32.8%, respectively), which correlates well with relative triplet yields estimated from quantum yields for singlet oxygen generation. Phosphorescence from the excited PS was quenched by the sacrificial electron donor. Fluorescence lifetimes were similar for the O- and S-containing rhodamines (～2.6 ns) and shorter for the Se analog (～0.1 ns). These data suggest a reaction pathway involving reductive quenching of the triplet excited state of the PS giving the reduced PS(-) that then transfers an electron to the Co catalyst. The longer-lived triplet state is necessary for effective bimolecular electron transfer. While the cobalt/rhodamine/triethanolamine system gives unprecedented yields of hydrogen for the photoreduction of water, mechanistic insights regarding the overall reaction pathway as well as system degradation offer significant guidance to developing even more stable and efficient photocatalytic systems.     

Bioconjugation of D‐glucuronic acid sodium salt to well‐defined primary amine‐containing homopolymers and block copolymers

The synthesis of well‐defined carboxylic acid‐functionalized glycopolymers prepared via one‐step postpolymerization modification of poly(N‐[3‐aminopropyl] methacrylamide) (PAPMA), a water‐soluble primary amine methacrylamide, in aqueous medium is demonstrated. PAPMA was first polymerized via aqueous reversible addition‐fragmentation chain transfer polymerization in aqueous buffer using 4‐cyanopentanoic acid dithiobenzoate as the chain transfer agent and 4,4′‐azobis(4‐cyanovaleric acid) (V‐501) as the initiator at 70 °C. The resulting well‐defined PAPMA was then conjugated with D ‐glucuronic acid sodium salt through reductive amination in alkaline medium (pH 8.5) at 45 °C. The successful bioconjugation was proven through proton (¹H) and carbon (¹³C) nuclear magnetic resonance spectroscopy and matrix‐assisted laser desorption/ionization time of flight mass spectrometry analysis, which indicated near quantitative conversion. A similar bioconjugation reaction was conducted with poly(2‐aminoethyl methacrylate) (PAEMA) and poly(2‐aminoethyl methacrylate‐b‐poly(N‐[2‐hydroxypropyl]methacrylamide) (PAEMA‐b‐PHPMA). For the PAEMA homopolymers and block copolymers, however, lower conversion was obtained, most likely because of degradation reactions of PAEMA in alkaline medium. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3052–3061, 2010     

Instability of the Kolmogorov flow in a soap film

We examine the instability of a soap film flow driven by a time-independent force that is spatially periodic in the direction perpendicular to the forcing (Kolmogorov flow). Linear stability analysis of an idealized model of this flow predicts a critical Reynolds number R(c) is approximately equal to the square root of 2. In our soap film experiment, we find a critical value R(c) is approximately equal to 70. This discrepancy can be ascribed to frictional effects from viscous coupling of gas to the film, which is neglected in the idealized model. The kinematic viscosity of the surrounding gas and the thickness of gas layers on each side of the soap film are varied in the experiments to better understand these frictional effects. Our observations indicate that flow in the soap film cannot be decoupled from flow in the surrounding gas.     

1H fast MAS NMR studies of hydrogen-bonding interactions in self-assembled monolayers

The structures formed by the adsorption of carboxyalkylphosphonic acids on metal oxides were investigated by (1)H fast magic angle spinning (MAS), heteronuclear correlation (HETCOR), and (1)H double-quantum (DQ) MAS solid-state NMR experiments. The diacids HO(2)C(CH(2))(n)PO(3)H(2) (n = 2, 3, 11, and 15) were adsorbed on TiO(2) and two types of ZrO(2) powders having average particle sizes of 20, 30, and 5 nm, respectively. Carboxyalkylphosphonic acids bind selectively via the phosphonate group, forming monolayers with pendant carboxylic acid groups. Whereas dipolar coupled P-OH protons are detected on TiO(2), there are only isolated residual P-OH groups on ZrO(2), reflecting the relative binding strengths of phosphonic acids on these two substrates. From a comparative (1)H MAS NMR study with an analogous monolayer system, HO(2)C(CH(2))(7)SH coated gold nanoparticles, the hydrogen-bonding network at the monolayer/air interface is found to be quite disordered, at least for SAMs deposited on nonplanar substrates. Whereas only hydrogen-bonded homodimers occur in the bulk diacids, hydrogen bonding between the carboxylic and phosphonic acid groups is present in multilayers of the diacids on the ZrO(2) nanopowder.     

Diffusion coefficient of DNA molecules during free solution electrophoresis

The free-draining properties of DNA normally make it impossible to separate nucleic acids by free-flow electrophoresis. However, little is known, either theoretically or experimentally, about the diffusion coefficient of DNA molecules during free-flow electrophoresis. In fact, many authors simply assume that the Nernst-Einstein relation between the mobility and the diffusion coefficient still holds under such conditions. In this paper, we present an experimental study of the diffusion coefficient of both ssDNA and dsDNA molecules during free-flow electrophoresis. Our results unequivocally show that a simplistic use of Nernst-Einstein's relation fails, and that the electric field actually has no effect on the thermal diffusion process. Finally, we compare the dependence of the diffusion coefficient upon DNA molecular size to results obtained previously by other groups and to Zimm's theory.