RESUMEN
Why are DNA bases stacked in a double helix structure? We combined three theoretical approaches to demonstrate how one core concept derived from quantum mechanics (Pauli repulsion) annihilates the contribution of dispersion to the π-π stacking. The helical architecture is governed by a combination of exchange and electrostatic forces, a result that is interpreted from both a computational and a biological perspective.
Asunto(s)
ADN , Conformación de Ácido Nucleico , Teoría Cuántica , ADN/química , Electricidad EstáticaRESUMEN
The aim of the present study is to provide computational insight using dispersion-corrected density-functional calculations into the reactivity properties of modified cytosine in the gas phase and in aqueous solution, whereby special emphasis is put on systems that are obtained through demethylation and methylation. Since this field is relatively incipient, our goal is to identify relationships between reactivity and stability for the modified compounds to understand their biological functionalities. Our results show that addition of a methyl, hydroxylmethyl, formyl, or carboxyl group reduces the length of the nearest hydrogen bond between the cytosine-guanine (CG) base pair and increases the length of the longest hydrogen bond of the DNA base pair. © 2017 Wiley Periodicals, Inc.
Asunto(s)
Citosina/análogos & derivados , ADN/química , Guanina/química , Emparejamiento Base , Citosina/química , Metilación de ADN , Gases/química , Enlace de Hidrógeno , Metilación , Modelos Moleculares , Teoría Cuántica , Soluciones/química , TermodinámicaRESUMEN
We report a straightforward synthesis of 8-ethynyl-BODIPY derivatives and their potential as fluorescent labeling compounds using an alkyne-azide click chemistry approach. The ethynyl substituted BODIPY dyes at the meso-position were reacted under Cu(+) catalysis and mild physiological conditions in organic and biological model systems using benzyl azide and a Barstar protein which was selectively modified by a single amino acid substituted methionine at the N-terminus (Met1) â azidohomoalanine (Aha). Conjugation with the protein and the model azide was indicated by a significant blue shift upon formation of the triazole moiety system, which allowed easy distinction between free and coupled dyes. This blue shift was rationalized by the perpendicular orientation of the triazole relative to the chromophore using time dependent density functional theory (TDDFT) calculations. A full spectroscopic and thermodynamic characterization of the protein revealed that a fluorophore was incorporated without the cross influence of protein stability and functional integrity. Furthermore, model reactions of 8-ethynyl-BODIPY derivatives with benzyl azide under copper-free conditions indicate second order kinetics with high rate constants comparable with those found for the strain-promoted azide-alkyne cycloaddition (SPAAC). In this way, we establish a unique and highly efficient method to introduce alkyne-BODIPY into a protein scaffold potentially useful for diverse applications in areas ranging from fundamental protein dynamics studies to biotechnology or cell biology.