Effect of the cyclobutane cytidine dimer on the properties of Escherichia coli DNA photolyase

Cyclobutane pyrimidine dimer (CPD) photolyases are structure specific DNA-repair enzymes that specialize in the repair of CPDs, the major photoproducts that are formed upon irradiation of DNA with ultraviolet light. The purified enzyme binds a flavin adenine dinucleotide (FAD), which is in the neutral radical semiquinone (FADH(*)) form. The CPDs are repaired by a light-driven, electron transfer from the anionic hydroquinone (FADH(-)) singlet excited state to the CPD, which is followed by reductive cleavage of the cyclobutane ring and subsequent monomerization of the pyrimidine bases. CPDs formed between two adjacent thymidine bases (T< >T) are repaired with greater efficiency than those formed between two adjacent cytidine bases (C< >C). In this paper, we investigate the changes in Escherichia coli photolyase that are induced upon binding to DNA containing C< >C lesions using resonance Raman, UV-vis absorption, and transient absorption spectroscopies, spectroelectrochemistry, and computational chemistry. The binding of photolyase to a C< >C lesion modifies the energy levels of FADH(*), the rate of charge recombination between FADH(-) and Trp(306)(*), and protein-FADH(*) interactions differently than binding to a T< >T lesion. However, the reduction potential of the FADH(-)/FADH(*) couple is modified in the same way with both substrates. Our calculations show that the permanent electric dipole moment of C< >C is stronger (12.1 D) and oriented differently than that of T< >T (8.7 D). The possible role of the electric dipole moment of the CPD in modifying the physicochemical properties of photolyase as well as in affecting CPD repair will be discussed.     

Solvent dependence of the g-anisotropy in the ESR of cyanide-bridged mixed-valence complexes

The low temperature (approximately 5 K) X-band ESR spectra are reported of the cyanide-bridged mixed-valence complexes [(OC)5Cr(mu-CN)M(NH3)5]X2 (M = Ru, Os; X = PF6(-)) in frozen matrices formed from nitromethane, acetonitrile and dimethylformamide with toluene. The anisotropy (g paralell-g perpendicular) is greater for the ruthenium than for the osmium complex. It is positive in all cases and is strongly dependent on the hydrogen-bonding interaction between the solvent matrix and the metal-ammine fragment, decreasing in the order nitromethane > acetonitrile > dimethylformamide. The axial ligand field parameter, Delta, is quite insensitive to the ammine metal (M) and is mainly determined by the solvent matrix. Density functional calculations, together with a simplified MO model, show that: (a) The value of Delta is dominated by the interaction between the filled cyanide pi-orbitals and the ammine-metal d(xz,yz) orbitals, (b) Delta decreases with increasing solvent donicity because the resulting positive shift of the d-orbital energies reduces this interaction, (c) the insensitivity of Delta to the ammine-metal arises because an increase in the energy mismatch between the cyanide pi-orbitals and the d-orbitals in osmium compound is offset by an increase in the 5d resonance integrals relative to those in the 4d shell. Semi-quantitative values are obtained for the pi and pi* resonance integrals. We point out that g paralell determines that portion of the ammine-metal spin population that interacts with the cyanide bridge, and should therefore be correlated with the degree of metal-metal charge transfer in low-spin d6-d5 intervalence compounds. X-band ESR spectra of the polycrystalline powders (M = Ru, Os; X = CF3SO3(-)) are rhombic with similar axial and rhombic ligand field parameters. The rhombicity is interpreted as resulting from asymmetric cation-anion hydrogen-bonding that is apparent in the crystal structures of these isomorphous compounds.     

Development of saw palmetto (Serenoa repens) fruit and extract standard reference materials

As part of a collaboration with the National Institutes of Health’s Office of Dietary Supplements and the Food and Drug Administration’s Center for Drug Evaluation and Research, the National Institute of Standards and Technology has developed two standard reference materials (SRMs) representing different forms of saw palmetto (Serenoa repens), SRM 3250 Serenoa repens fruit and SRM 3251 Serenoa repens extract. Both of these SRMs have been characterized for their fatty acid and phytosterol content. The fatty acid concentration values are based on results from gas chromatography with flame ionization detection (GC-FID) and mass spectrometry (GC/MS) analysis while the sterol concentration values are based on results from GC-FID and liquid chromatography with mass spectrometry analysis. In addition, SRM 3250 has been characterized for lead content, and SRM 3251 has been characterized for the content of β-carotene and tocopherols. SRM 3250 (fruit) has certified concentration values for three phytosterols, 14 fatty acids as triglycerides, and lead along with reference concentration values for four fatty acids as triglycerides and 16 free fatty acids. SRM 3251 (extract) has certified concentration values for three phytosterols, 17 fatty acids as triglycerides, β-carotene, and γ-tocopherol along with reference concentration values for three fatty acids as triglycerides, 17 fatty acids as free fatty acids, β-carotene isomers, and δ-tocopherol and information values for two phytosterols. These SRMs will complement other reference materials currently available with concentrations for similar analytes and are part of a series of SRMs being developed for dietary supplements. Contribution of the US Government; not subject to copyright     

Role of Low Molecular Weight Polymers on the Dynamics of Silicon Anodes During Casting

This work probes the slurry architecture of a high silicon content electrode slurry with and without low molecular weight polymeric dispersants as a function of shear rate to mimic electrode casting conditions for poly(acrylic acid) (PAA) and lithium neutralized poly(acrylic acid) (LiPAA) based electrodes. Rheology coupled ultra-small angle neutron scattering (rheo-USANS) was used to examine the aggregation and agglomeration behavior of each slurry as well as the overall shape of the aggregates. The addition of dispersant has opposing effects on slurries made with PAA or LiPAA binder. With a dispersant, there are fewer aggregates and agglomerates in the PAA based silicon slurries, while LiPAA based silicon slurries become orders of magnitude more aggregated and agglomerated at all shear rates. The reorganization of the PAA and LiPAA binder in the presence of dispersant leads to a more homogeneous slurry and a more heterogeneous slurry, respectively. This reorganization ripples through to the cast electrode architecture and is reflected in the electrochemical cycling of these electrodes.     

Threading synthetic polyelectrolytes through protein pores

We have measured the ionic current signatures of sodium poly(styrene sulfonate) as its single molecules translocate through an alpha-hemolysin pore embedded into a bilayer in a salty aqueous medium under an externally applied electric field. As in the previous experiments involving DNA and RNA, the pore current, which is a measure of the ionic conductivity of the low molar mass electrolyte ions, is significantly reduced when the polymer molecule translocates through the pore. The magnitude and the duration of the reduction in the pore current are measured for each of the translocation events. By studying thousands of events of reduction in the ionic current, we have constructed distribution functions for the extent of the reduced current and for the translocation time. The details of these distribution functions are significantly different from those for DNA and RNA. By investigating over two orders of magnitude in the molecular weight of the polymer, the average translocation time is found to be proportional to the molecular weight and inversely proportional to the applied voltage. This demonstration of threading a synthetic polyelectrolyte through a protein pore opens up many opportunities to systematically explore the fundamental physical principles behind translocation of single macromolecules, by resorting to the wide variety of synthetically available polymers without the complexities arising from the sequences of biological polymers. In addition, the present experiments suggest yet another experimental protocol for separation of polymer molecules directly in aqueous media.     

Arenes to anilines and aryl ethers by sequential iridium-catalyzed borylation and copper-catalyzed coupling

[reaction: see text] N-Alkyl- and N-arylanilines were synthesized from arenes by a two-step sequence of iridium-catalyzed borylation and copper-catalyzed coupling with amines. Diaryl ethers were obtained by a related sequence of arene borylation, followed by coupling with phenols. In particular, 3,5-disubstituted arylamines and aryl ethers were prepared by initiating this sequence with meta-substituted arenes.     

Characterization of a suite of ginkgo-containing standard reference materials

A suite of three ginkgo-containing dietary supplement Standard Reference Materials (SRMs) has been issued by the National Institute of Standards and Technology (NIST) with certified values for flavonoid aglycones, ginkgolides, bilobalide, and selected toxic trace elements. The materials represent a range of matrices (i.e., plant, extract, and finished product) that provide different analytical challenges. The constituents have been determined by at least two independent analytical methods with measurements performed by NIST and at least one collaborating laboratory. The methods utilized different extractions, chromatographic separations, modes of detection, and approaches to quantitation. The SRMs are primarily intended for method validation and for use as control materials to support the analysis of dietary supplements and related botanical materials. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Electrospray ionization mass spectra of acyl carrier protein are insensitive to its solution phase conformation

Electrospray ionization mass spectrometry (ESI-MS) can be used to monitor conformational changes of proteins in solution based on the charge state distribution (CSD) of the corresponding gas-phase ions, although relatively few studies of acidic proteins have been reported. Here, we have compared the CSD and solution structure of recombinant Vibrio harveyi acyl carrier protein (rACP), a small acidic protein whose secondary and tertiary structure can be manipulated by pH, fatty acylation, and site-directed mutagenesis. Circular dichroism and intrinsic fluorescence demonstrated that apo-rACP adopts a folded helical conformation in aqueous solution below pH 6 or in 50% acetonitrile/0.1% formic acid, but is unfolded at neutral and basic pH values. A rACP mutant, in which seven conserved acidic residues were replaced with their corresponding neutral amides, was folded over the entire pH range of 5 to 9. However, under the same solvent conditions, both wild type and mutant ACPs exhibited similar CSDs (6(+)-9(+) species) at all pH values. Covalent attachment of myristic acid to the phosphopantetheine prosthetic group of rACP, which is known to stabilize a folded conformation in solution, also had little influence on its CSD in either positive or negative ion modes. Overall, our results are consistent with ACP as a "natively unfolded" protein in a dynamic conformational equilibrium, which allows access to (de)protonation events during the electrospray process.     

Development of glycyl radical parameters for the OPLS-AA/L force field

On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.