Determination of peptide backbone torsion angles using double-quantum dipolar recoupling solid-state NMR spectroscopy

Several approaches for utilizing dipolar recoupling solid-state NMR (ssNMR) techniques to determine local structure at high resolution in peptides and proteins have been developed. However, many of these techniques measure only one torsion angle or are accurate for only certain classes of secondary structure. Additionally, the efficiency with which these dipolar recoupling experiments suppress the deleterious effects of chemical shift anisotropy (CSA) at high magnetic field strengths varies. Dipolar recoupling with a windowless sequence (DRAWS) has proven to be an effective pulse sequence for exciting double-quantum (DQ) coherences between adjacent carbonyl carbons along the peptide backbone. By allowing this DQ coherence to evolve, it is possible to measure the relative orientations of the CSA tensors and subsequently use this information to determine the Ramachandran torsion angles phi and psi. Here, we explore the accuracies of the assumptions made in interpreting DQ-DRAWS data and demonstrate their fidelity in measuring torsion angles corresponding to a variety of secondary structures irrespective of hydrogen-bonding patterns. It is shown how a simple choice of isotopic labels and experimental conditions allows accurate measurement of backbone secondary structures without any prior knowledge. This approach is considerably more sensitive for determining structure in helices and has comparable accuracy for beta-sheet and extended conformations relative to other methods. We also illustrate the ability of DQ-DRAWS to distinguish between structures in heterogeneous samples.     

Towards zirconium phosphonate-based microarrays for probing DNA-protein interactions: critical influence of the location of the probe anchoring groups

Terminal phosphate groups on double-stranded DNA probes bind strongly to glass substrates coated with a zirconium phosphonate monolayer, and probes immobilized in this way as microarrays can be used to detect protein targets. The sensitivity of the microarray was shown to be enhanced by the use of a polyguanine segment ((G)n , n > or = 5) as a spacer between the phosphate linker and the protein interaction domain. More importantly, the presence of phosphate linkers on both ends of the dsDNA probes leads to significant enhancement of target capture. The relevant characteristics of the different probes when bound to the surface were determined, by the original use of a combination of surface characterization techniques (XPS, AFM, and Sarfus). In this context, the location of the phosphate linkers in the duplex probes was found to result in different probe surface coverage and presentation on the surface, which affect subsequent interactions with the target protein.     

Pulsed lasers versus continuous light sources in capillary electrophoresis and fluorescence detection studies: Photodegradation pathways and models

Pulsed lasers are widely used in capillary electrophoresis (CE) studies to provide laser induced fluorescence (LIF) detection. Unfortunately pulsed lasers do not give linear calibration curves over a wide range of concentrations. While this does not prevent their use in CE/LIF studies, the non-linear behavior must be understood. Using 7-hydroxycoumarin (7-HC) (10–5000 nM), Tamra (10–5000 nM) and tryptophan (1–200 μM) as dyes, we observe that continuous lasers and LEDs result in linear calibration curves, while pulsed lasers give polynomial ones. The effect is seen with both visible light (530 nm) and with UV light (355 nm, 266 nm). In this work we point out the formation of byproducts induced by pulsed laser upon irradiation of 7-HC. Their separation by CE using two Zeta LIF detectors clearly shows that this process is related to the first laser detection. All of these photodegradation products can be identified by an ESI-/MS investigation and correspond to at least two 7HC dimers. By using the photodegradation model proposed by Heywood and Farnsworth (2010) and by taking into account the 7-HC results and the fact that in our system we do not have a constant concentration of fluorophore, it is possible to propose a new photochemical model of fluorescence in LIF detection. The model, like the experiment, shows that it is difficult to obtain linear quantitation curves with pulsed lasers while UV-LEDs used in continuous mode have this advantage. They are a good alternative to UV pulsed lasers. An application involving the separation and linear quantification of oligosaccharides labeled with 2-aminobezoic acid is presented using HILIC and LED (365 nm) induced fluorescence.     

Structures, reductive dechlorination, and electron affinities of selected polychlorinated dibenzo-p-dioxins: density functional theory study

Density functional theory calculations were performed to obtain the structures, vertical electron affinities, and adiabatic affinities of 15 polychlorinated dibenzo-p-dioxins (PCDDs), including several extremely toxic congeners. A three-parameter hybrid density functional, B3LYP, was utilized with two different basis sets, 6-311G(d,p) and 6-311+G(2d,2p). The optimized structures of all PCDDs under consideration were planar, while all corresponding anions attained nonplanar geometries. One of the C-Cl bonds on each PCDD anion was considerably elongated, and the dechlorination of PCDDs occurred as the departing chlorine bent off the aromatic ring plane for effective pi-sigma orbital mixing. The characteristic electron energy-dependent regioselective chloride ion loss channels for 1,2,3,7,8-pentaCDD were elucidated by transition-state theory calculations. The relative low-energy barrier for the dechlorination of 1,2,3,7,8-pentaCDD indicated the high likelihood of obtaining reductive dechlorination (RD) products that are more toxic than the parent species. The calculated vertical electron affinities of PCDDs are consistent with the available experimental attachment energies, and the positive adiabatic electron affinities suggest that PCDDs may act as electron acceptors in living cells.     

Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA

M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base pair, as in G-Zn-C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensive ab initio study of eight G-Zn-C models in the gas phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only one which preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the nonplanar models, there is one that requires less than 8 kcal/mol to flatten (both in gas and solvent conditions), and we propose that it is a plausible model for building an antiparallel duplex. In this duplex, the imino proton would be replaced by Zn, in accordance with experimental models. Neither planar nor nonplanar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether density functional theory (DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronic properties of G-Co-C base pairs. We have found that when self-interaction corrections (SIC) are not included the HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC are considered. This result indicates that caution should be exercised when studying the electronic properties of M-DNAs with functionals that do not account for strong electronic correlations.     

On the Generalized Enveloping Algebra of a Color Lie Algebra

Let G be an abelian group, ε an anti-bicharacter of G and L a G-graded ε Lie algebra (color Lie algebra) over a field of characteristic zero. We prove that for all G-graded, positively filtered A such that the associated graded algebra is isomorphic to the G-graded ε-symmetric algebra S(L), there is a G- graded ε-Lie algebra L and a G-graded scalar two cocycle , such that A is isomorphic to U _ω (L) the generalized enveloping algebra of L associated with ω. We also prove there is an isomorphism of graded spaces between the Hochschild cohomology of the generalized universal enveloping algebra U(L) and the generalized cohomology of the color Lie algebra L. Supported by the EC project Liegrits MCRTN 505078.     

The Hyperfine Transition for the Definition of the Second

The unit of time of the International System of Units (SI), the “atomic second” was defined through a constant of physics in 1967. It is derived from the frequency of the hyperfine transition of the atom of cesium 133. From the astronomical definition of the second until today, the accuracy of the realization of the second has improved by eight orders of magnitude, with a rate that has increased since the development of the cesium frequency standards, to reach parts in 10¹⁶ for the best clocks today. In 2018, when the new SI was adopted, the time metrology community proved that a new generation of frequency standards operating in optical wavelengths has uncertainties at the level of 10^–18, and challenge the implementation of high accurate frequency and time comparison techniques to decide on a revision of the definition of the second. Herein, the progress in the definition and realization of the second from astronomy until today is reviewed, an inventory of the present resources is assembled and a brief view for the future given.     

Charge Reconfiguration in Isolated Quantum Dot Arrays

A high level of tunability and control over arrays of quantum dots are key ingredients toward the goal of scalable‐based qubit architectures. Increasing array size simultaneously increases the parameter space and therefore the tuning complexity. The electron reconfiguration behavior of quantum dot arrays isolated from the electron reservoirs is studied experimentally. Isolating a quantum dot array from the reservoirs does not only enable a high degree of control over the tunnel couplings but at the same time drastically simplifies the stability diagrams for small numbers of electrons trapped in the array. Experimental results on double, triple, and quadruple quantum dot arrays are presented and complementary model calculations allow the identification of all transitions observed in the experiment. Highly tunable long‐range transitions are observed in isolated triple quantum dots and evidence of higher‐order cotunneling is found for the quadruple quantum dot array.