Precise distance measurements in DNA G-quadruplex dimers and sandwich complexes by pulsed dipolar EPR spectroscopy

DNA G-quadruplexes show a pronounced tendency to form higher-order structures, such as π-stacked dimers and aggregates with aromatic binding partners. Reliable methods for determining the structure of these non-covalent adducts are scarce. Here, we use artificial square-planar Cu(pyridine)4 complexes, covalently incorporated into tetramolecular G-quadruplexes, as rigid spin labels for detecting dimeric structures and measuring intermolecular Cu2+–Cu2+ distances via pulsed dipolar EPR spectroscopy. A series of G-quadruplex dimers of different spatial dimensions, formed in tail-to-tail or head-to-head stacking mode, were unambiguously distinguished. Measured distances are in full agreement with results of molecular dynamics simulations. Furthermore, intercalation of two well-known G-quadruplex binders, PIPER and telomestatin, into G-quadruplex dimers resulting in sandwich complexes was investigated, and previously unknown binding modes were discovered. Additionally, we present evidence that free G-tetrads also intercalate into dimers. Our transition metal labeling approach, combined with pulsed EPR spectroscopy, opens new possibilities for examining structures of non-covalent DNA aggregates

Kinetics of bis-allylic hydroperoxide synthesis in the iron-containing lipoxygenase 2 from cyanothece and the effects of manganese substitution.

Lipoxygenases (LOX) catalyze the regio- and stereospecific insertion of dioxygen into polyunsaturated fatty acids. While the catalytic metal of LOX is typically a non-heme iron, some fungal LOX contain manganese as catalytic metal (MnLOX). In general, LOX insert dioxygen at C9 or C13 of linoleic acid leading to the formation of conjugated hydroperoxides. MnLOX (EC 1.13.11.45), however, catalyze the oxygen insertion also at C11, resulting in bis-allylic hydroperoxides. Interestingly, the iron-containing CspLOX2 (EC 1.13.11.B6) from Cyanothece PCC8801 also produces bis-allylic hydroperoxides. What role the catalytic metal plays and how this unusual reaction is catalyzed by either MnLOX or CspLOX2 is not understood. Our findings suggest that only iron is the catalytically active metal in CspLOX2. The enzyme loses its catalytic activity almost completely when iron is substituted with manganese, suggesting that the catalytic metal is not interchangeable. Using kinetic and spectroscopic approaches, we further found that first a mixture of bis-allylic and conjugated hydroperoxy products is formed. This is followed by the isomerization of the bis-allylic product to conjugated products at a slower rate. These results suggest that MnLOX and CspLOX2 share a very similar reaction mechanism and that LOX with a Fe or Mn cofactor have the potential to form bis-allylic products. Therefore, steric factors are probably responsible for this unusual specificity. As CspLOX2 is the LOX with the highest proportion of the bis-allylic product known so far, it will be an ideal candidate for further structural analysis to understand the molecular basis of the formation of bis-allylic hydroperoxides

Coupling of terminal iridium nitrido complexes.

The oxidative coupling of nitride ligands (N3−) to dinitrogen and its microscopic reverse, N2-splitting to nitrides, are important elementary steps in chemical transformations, such as selective ammonia oxidation or nitrogen fixation. Here an experimental and computational evaluation is provided for the homo- and heterocoupling of our previously reported iridium(IV) and iridium(V) nitrides [IrN(PNP)]n (n = 0, +1; PNP = N(CHCHPtBu2)2). All three formal coupling products [(PNP)IrN2Ir(PNP)]n (n = 0–+2) were structurally characterized. While the three coupling reactions are all thermodynamically feasible, homocoupling of [IrN(PNP)]+ is kinetically hindered. The contributing parameters to relative coupling rates are discussed providing qualitative guidelines for the stability of electron rich transition metal nitrides

An Examination of Indigenous Heritage representation in Grenada’s Primary Schools from Teachers’ Perspective.

Archaeological studies are not part of the school curriculum in Grenada. Thus, students and the larger population have limited knowledge of previous civilisations, and this limited knowledge limits society’s understanding of its history. In many schools, students learn about Grenada’s post-colonial history, while ignoring its pre-Colombian past that includes the island’s indigenous inhabitants. This thesis highlights some significant deficiencies within the present structure of education which continue to effectuate a colonial type education that ignores the pre-Colombian history of Indigenous Peoples. The thesis examines the history and formation of modern Grenadian society and suggests that the role of colonialism in the formation of modern Grenadian society is a contributing factor that creates a situation in which pre-Columbian history is not considered as part of Grenada's heritage. From a theoretical perspective, the thesis attempts to make a link between national heritage and national identity. The lack of appreciation or knowledge of Grenada's heritage is a direct link to the strength of its national identity. Grenada's national identity appears to have been derailed by the colonial powers for other identities such as race and class. Thus, the thesis argues that there is a need for teacher education on pre-history and the need for curriculum development in the primary school system in the areas of History, Geography and Social Studies. The thesis further states that the dissemination of indigenous archaeological knowledge to teachers through the school curriculum in the three subject areas can help equip students with the indigenous knowledge, particularly, pre-Columbian history. The thesis makes the claim that raising awareness for the preservation and protection of indigenous heritage in the tri-island state of Grenada, is one way to overcome the myth of the non-presence of Indigenous peoples. Learning and (re)interpreting the prehistory about Grenada through archaeological data can strengthen its national heritage and build a strong sense of national identity for the current and future generations

Characterization of a Triplet Vinylidene

Singlet vinylidenes (R2C═C:) are proposed as intermediates in a series of organic reactions, and very few have been studied by matrix isolation or gas-phase spectroscopy. Triplet vinylidenes, however, featuring two unpaired electrons at a monosubstituted carbon atom are thus far only predicted as electronically excited-state species and represent an unexplored class of carbon-centered diradicals. We report the photochemical generation and low-temperature EPR/ENDOR characterization of the first ground-state high-spin (triplet) vinylidene. The zero-field splitting parameters (D = 0.377 cm–1 and |E|/D = 0.028) were determined, and the 13C hyperfine coupling tensor was obtained by 13C-ENDOR measurements. Most strikingly, the isotropic 13C hyperfine coupling constant (50 MHz) is far smaller than the characteristic values of triplet carbenes, demonstrating a unique electronic structure which is supported by quantum chemical calculations

Properties of site-specifically incorporated 3-Aminotyrosine in proteins to study redox-active tyrosines: E. coli ribonucleotide reductase as a paradigm.

3-Aminotyrosine (NH2Y) has been a useful probe to study the role of redox active tyrosines in enzymes. This report describes properties of NH2Y of key importance for its application in mechanistic studies. By combining the tRNA/NH2Y-RS suppression technology with a model protein tailored for amino acid redox studies (α3X, X = NH2Y), the formal reduction potential of NH2Y32(O•/OH) (E°’ = 395 ± 7 mV at pH 7.08 ± 0.05) could be determined using protein film voltammetry. We find that the ΔE°’ between NH2Y32(O•/OH) and Y32(O•/OH) when measured under reversible conditions is ~300 – 400 mV larger than earlier estimates based on irreversible voltammograms obtained on aqueous NH2Y and Y. We have also generated D6-NH2Y731-α2 of RNR, which when incubated with β2/CDP/ATP generates the D6-NH2Y731•-α2/β2 complex. By multi-frequency EPR (35, 94 and 263 GHz) and 34 GHz 1H ENDOR spectroscopies, we determined the hyperfine coupling (hfc) constants of the amino protons that establishes RNH2• planarity and thus minimal perturbation of the reduction potential by the protein environment. The amount of Y in the isolated NH2Y-RNR incorporated by infidelity of the tRNA/NH2Y-RS pair was determined by a generally useful LC-MS method. This information is essential to the utility of this NH2Y probe to study any protein of interest and is employed to address our previously reported activity associated with NH2Y-substituted RNR

¹H high field electron-nuclear double resonance spectroscopy at 263 GHz/9.4 T.

We present and discuss the performance of 1H electron-nuclear double resonance (ENDOR) at 263 GHz/9.4 T by employing a prototype, commercial quasi optical spectrometer. Basic instrumental features of the setup are described alongside a comprehensive characterization of the new ENDOR probe head design. The performance of three different ENDOR pulse sequences (Davies, Mims and CP-ENDOR) is evaluated using the 1H BDPA radical. A key feature of 263 GHz spectroscopy - the increase in orientation selectivity in comparison with 94 GHz experiments - is discussed in detail. For this purpose, the resolution of 1H ENDOR spectra at 263 GHz is verified using a representative protein sample containing approximately 15 picomoles of a tyrosyl radical. Davies ENDOR spectra recorded at 5 K reveal previously obscured spectral features, which are interpreted by spectral simulations aided by DFT calculations. Our analysis shows that seven internal proton couplings are detectable for this specific radical if sufficient orientation selectivity is achieved. The results prove the fidelity of 263 GHz experiments in reporting orientation-selected 1H ENDOR spectra and demonstrate that new significant information can be uncovered in complex molecular systems, owing to the enhanced resolution combined with high absolute sensitivity and no compromise in acquisition time