Formation of modified cytosine residues in the presence of depurinated DNA

[Chemical reaction: See text] Depurination is an important degradation pathway for antisense phosphorothioate oligonucleotides under conditions of thermal stress. We present evidence showing that depurinated oligonucleotides react with cytosine-containing sequences giving products containing a 6-(2-deoxy-beta-D-erythro-pentofuranosyl)-3-(2-oxopropyl)imidazo[1,2-c]pyrimidin-5(6H)-one residue. Further, we demonstrate that the same product is formed upon treatment of 2'-deoxycytidine with 4-oxo-2-pentenal, the latter being an expected byproduct of serial elimination reactions at apurinic sites. In addition to being important for synthetic oligonucleotides, apurinic site formation in cellular DNA is a common occurrence. Because repair of these sites can result in the production of 4-oxo-2-pentenal, it is interesting to speculate whether 6-(2-deoxy-beta-D-erythro-pentofuranosyl)-3-(2-oxopropyl)imidazo[1,2-c]pyrimidin-5(6H)-one residues can form in vivo.     

Tandem conjugate cyanide addition-Dieckmann condensation in the synthesis of the ABCD-ring system of lactonamycin

An efficient synthesis of the ABCD-ring system of lactonamycin (1) is reported in this Letter. The key step is the tandem cyanide conjugate addition-Dieckmann condensation of alkyne 17 to afford a fully functionalized anthracene. Selective reduction of the cyano group with subsequent lactam formation affords the tetracyclic core of lactonamycin 19. [reaction: see text]     

Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor,colleague, collaborator,and innovator

Journal of Computer-Aided Molecular Design - In May 2022, JCAMD published a Special Issue in honor of Gerald (Gerry) Maggiora, whose scientific leadership over many decades advanced the fields of...     

Automated cell culture in high density tubeless microfluidic device arrays

Microfluidics is poised to have an impact on life sciences research. However, current microfluidic methods are not compatible with existing laboratory liquid dispensing and detection infrastructure. This incompatibility is a barrier to adoption of microfluidic systems and calls for improved approaches that will enhance performance and promote acceptance of microfluidic systems in the life sciences. Ease of use, standardized interfaces and automation remain critical challenges. We present a platform based on surface tension effects, where the difference in pressure inside drops of unequal volume drives flow in passive structures. We show integration with existing laboratory infrastructure, microfluidic operations such as pumping, routing and compartmentalization without discrete micro-components as well as cell patterning in both monolayer and three-dimensional cell culture.     

Synthesis and spin-trapping properties of a new spirolactonyl nitrone

Spin trapping using electron paramagnetic resonance (EPR) spectroscopy is commonly employed for the identification of transient radicals in chemical and biological systems. A spirolactonyl-nitrone with rigid H-bond acceptor, 7-oxa-1-azaspiro[4.4]non-1-en-6-one 1-oxide, CPCOMPO, has been synthesized and characterized, and its spin-trapping properties were investigated. The rate of formation of CPCOMPO-O2H was determined using competition kinetics between the superoxide/hydroperoxyl radical (O2*-/HO2*) trapping by CPCOMPO and the spontaneous dismutation of this radical in aqueous media. The rate constant of 60 M-1.s-1 is the highest rate constant thus far observed at neutral pH for any nitrones using the kinetic method employed. Decay kinetics were also experimentally investigated for CPCOMPO-O2H. The effect of rigid H-bond acceptor on the stability of the CPCOMPO-O2H were computationally rationalized and compared to that of EMPO-O2H, which has flexible H-bond acceptor, and results show the need of a "loose" H-bond acceptor for improved adduct stability.     

Local structure and local conduction paths in amorphous (In,Ga,Hf)–ZnO semiconductor thin films

The local structure and local conduction paths of Ga–In–Zn–O (GIZO) and Hf–In–Zn–O (HIZO) amorphous thin films were investigated by the extended X-ray absorption fine structure (EXAFS). We found that the local hindrance paths of In–Ga and In–Hf exist in the conduction paths of amorphous GIZO and HIZO semiconductor thin films, respectively.     

Track effects in the radiolysis of aromatic liquids

The chemical effects induced by the track structure of heavy ions have been exploited to show that H₂ production in the radiolysis of simple aromatic liquids (benzene, pyridine, toluene and aniline) is primarily due to second order processes. Similar dependences of H₂ yields on the linear energy transfer, LET, for each of these compounds suggest a common mechanism for H₂ formation. Furthermore, the yields of H₂ are significant at very high LET and they approach that found with aliphatic compounds. Yields of “dimers” (biphenyl, bibenzyl, dipyridyl, and diphenylamine for benzene, toluene, pyridine, and aniline, respectively) have different dependences on LET reflecting the variety of pathways leading to their production. Bibenzyl formation in toluene exhibits a complex dependence on LET suggesting several competing pathways for its production whereas biphenyl formation in benzene is nearly independent of LET suggesting a unimolecular process. Dipyridyl, and diphenylamine yields in pyridine and aniline, respectively, decrease with increasing LET, which indicates that their precursor is being depleted.     

Quantitative SNIFTIRS studies of (bi)sulfate adsorption at the Pt(111) electrode surface

Subtractively normalized interfacial Fourier transform infrared reflection spectroscopy (SNIFTIRS) was applied to study (bi)sulfate adsorption on a Pt(111) surface in solutions of variable pH while maintaining a constant total bisulfate/sulfate ((bi)sulfate) concentration without the addition of an inert supporting electrolyte. The spectra were recorded for both the p- and s-polarizations of the IR radiation in order to differentiate between the IR bands of the (bi)sulfate species adsorbed on the electrode surface from those species located in the thin layer of electrolyte. The spectra recorded with p-polarized light consist of the IR bands from both the species adsorbed at the electrode surface and those present in the thin layer of electrolyte between the electrode surface and ZnSe window whereas the s-polarized spectra contain only the IR bands from the species located in the thin layer of electrolyte. A new procedure was developed to calculate the angle of incidence and thickness of the electrolyte between the Pt(111) electrode surface and the ZnSe IR transparent window. By combining these values with the knowledge of the optical constants for Pt, H(2)O and ZnSe, the mean square electric field strength (MSEFS) at the Pt(111) electrode surface and for thin layer of solution were accurately calculated. The spectra recorded using s-polarization were multiplied by the ratio of the average MSEFS for p- and s-polarizations and subtracted from the spectra recorded using p-polarization in order to remove the IR bands that arise from the species present within the thin layer cavity. In this manner, the resulting IR spectra contain only the IR bands for the anions adsorbed on the Pt(111) electrode surface. The spectra of adsorbed anions show little change with respect to the pH ranging from 1 to 5.6. This behavior indicates that the same species is predominantly adsorbed on the metal surface for this broad range of pH values and the results suggest that sulfate is the most likely candidate for this adsorbate.     

Reactions of (η5-C5H5)Fe(CO)2(η1-C5H5) with phosphorus donor ligands

The course of the reaction of (η⁵-C₅H₅)Fe(CO)₂(η¹-C₅H₅) with phosphorus donor ligands depends strongly on the nature of the ligand; products derived from an Arbuzov-like rearrangement or from reduction have been found as well as the expected simple substitution product. The dynamic PMR behavior of (η⁵-C₅H₅)Fe(CO) (P(OPh)₃) (η¹-C₅H₅) has been examined.