Molecular Mechanism of Phosphate Steering for DNA Binding, Cleavage Localization, and Substrate Release in Nucleases

Structure-specific endonucleases (SSEs) cleave the DNA substrate in a precise position based on the specific DNA 3D structure. Human flap endonuclease 1 (hFEN1) is a 5′ SSE that prevents DNA instability by processing Okazaki fragment 5′-flaps with remarkable efficiency and selectivity using two-metal-ion catalysis. Recent structural and mutagenesis data of hFEN1 suggest that phosphate steering favors specificity and catalysis. Here, we investigate the phosphate steering mechanism at the atomistic level using microsecond-long molecular dynamics and well-tempered metadynamics simulations of wild-type and mutant systems of hFEN1. We show how positively charged second and third-shell residues operate the phosphate steering mechanism to promote catalysis through (i) substrate recruitment; (ii) precise cleavage localization; and (iii) substrate release, thus actively preventing the off-target incision of the substrate. Importantly, structural comparisons of hFEN1 and other nuclease enzymes suggest that phosphate steering may also serve the structure-based selection of the specific DNA substrate by other 5′ structure-specific nucleases

Deuterium Isotope Effects in A:T and A:U Base Pairs: A Computational NMR Study

Abstract:Recent measurements of trans-hydrogen bond deuterium isotope effects (DIEs) on 13C chemical shifts in nucleic acids (Vakonakis, I.; LiWang, A. C. J. Biomol. NMR2004, 29, 65; J. Am. Chem. Soc. 2004, 126, 5688) have led to intriguing results: (i) the DIEs of A:T pairs in DNA are about 5 ppb smaller than those of A:U in RNA and (ii) A:T DIEs vary by as much as 13 ppb among the oligonucleotides. The first observation suggests that inter-base H-bonds in RNA may be stronger than those in DNA, while the second indicates that the conformation of the base pair modulates the transmission of the isotope effect across the hydrogen bond. In an effort at providing a rationale s so far unknown s for the observed DIEs in nucleic acids, density functional theory and hybrid Car Parrinello/molecular mechanical calculations DIEs on nucleosides and nucleotides in the gas phase and in aqueous solution have been performed. The calculations suggest that (i) the DIE in an isolated A:T base pair differs from that in an A:U base pair because of the changes in the magnetic properties caused by the replacement of a methyl group on passing from U to T, (ii) the DIEs depend crucially on the conformation of the base pairs, and (iii) the DIEs are strongly affected by magnetic and electrostatic interactions with the surrounding environment

Selective synthesis of tetrasubstituted olefins by copper-mediated acetoxythiolation of internal alkynes: Scope and mechanistic studies

The Cu-mediated synthesis of tetrasubstituted olefins by the addition of an acetate group and a thiolate to an unactivated internal alkyne is described. The reaction is fully stereoselective, because only the E alkene is obtained. If the alkyne is asymmetric, the reaction also shows a very high degree of regioselectivity. The mechanism of the reaction is elucidated by DFT methods, which show that it takes place through Cu-stabilized radical species. Calculations highlight the crucial role of the dimeric copper(II) diacetate in the process, as it generates the active species in which the sulfur center has an incipient thiyl radical character and accepting, through a series of changes in the oxidation states of the two copper centers, the two electrons released in the addition of two nucleophiles to the alkyne.Funding by the Ministerio de Economìa y Competitividad (MINECO) (Spain, Project CTQ2017‐87889‐P) and Gobierno de Aragón (Spain, research group: Activación Molecular a través de Organometálicos, E97) is gratefully acknowledged. S.R. thanks Gobierno de Aragón‐Fondo Social Europeo (Spain) for a Ph.D. grant and Universidad de Zaragoza, Fundación Bancaria Ibercaja and Fundación CAI for a mobility grant.Peer reviewe

Isolation of a Cationic Platinum(II) s-Silane Complex

The platinum complex [Pt(ItBuiPr¿)(ItBuiPr)][BArF] interacts with tertiary silanes to form stable (<0 C) mononuclear PtII sigma-SiH complexes [Pt(ItBuiPr¿)(ItBuiPr)(eta1-HSiR3)][BArF]. These compounds have been fully characterized, including X-ray diffraction methods, as the first examples for platinum. DFT calculations (including electronic topological analysis) support the interpretation of the coordination as an unusual eta1-SiH. However, the energies required for achieving a eta2-SiH mode are rather low, and is consistent with the propensity of these derivatives to undergo Si-H cleavage leading to the more stable silyl species [Pt(SiR3)(ItBuiPr)2]- [BArF] at room temperature.Peer Reviewe

INTERNET, GUERRA Y PAZ EN COLOMBIA: CONFLICTO, NARRATIVAS E IDENTIDADES

El texto presenta una síntesis del componente tecnológico de la investigación interinstitucional “Internet, guerra y paz en Colombia”. Para tal fin, se hace un seguimiento a las nociones de innovación tecnológica, su uso y la construcción de la paz. En primer lugar, se reconstruye la discusión en torno a Internet en tanto objeto de estudio; posteriormente, se hace énfasis en el uso como apropiación comunicativa del medio y, finalmente, se realizan algunas anotaciones en términos de la transformación de los espacios comunicativos públicos en relación con el conflicto armado