Ru[(bpy)2(dppz)]²âº and Rh[(bpy)2(chrysi)]³âº targeting double strand DNA: the shape of the intercalating ligand tunes the free energy landscape of deintercalation.

Octahedral metal complexes can bind to double strand (ds) DNA either by intercalation or by insertion, this latter mechanism being observed in the case of mismatched base pairs (bps). In this work we modeled the process of deintercalation from the major groove for Δ-Ru[(bpy)2(dppz)](2+) (1) and Δ-Rh[(bpy)2(chrysi)](3+) (2), prototypical examples of metallo-intercalators and metallo-insertors, respectively. By using advanced sampling techniques, we show that the two complexes have comparable deintercalation barriers and that in both systems the main cost of deintercalation is due to disruption of π-π stacking interactions between the intercalating moiety and the bps flanking the binding site. A striking difference between dppz and chrysi is found in their intercalation modes, being their longest axes, respectively, perpendicular and parallel to the P-P direction between opposite DNA strands. This leads the two ligands to deintercalate from the DNA through different mechanisms. Compound 1 goes through the formation of a metastable short-lived intermediate, with an overall free energy barrier of ~14.5 kcal/mol, in line with experimental findings. Due to the length of the dppz intercalating moiety, an extended plateau appears in the free energy landscape at ~3 kcal/mol above the most stable minimum. Compound 2 must cross a similar barrier (~15.5 kcal/mol), but does not form intermediates along the deintercalation path, and the deintercalation profile is steeper than that found for 1. Thus, the shape of the intercalating moiety affects the deintercalation mechanism of these inorganic molecules. This work is a first step to rationalize from a computational perspective the factors tuning the preferential binding mode of inorganic molecules (such as diagnostic probes, therapeutic agents, or regulators of DNA expression) to ds DNA.

Structural role of uracil DNA glycosylase for the recognition of uracil in DNA duplexes. Clues from atomistic simulations.

In the first stage of the base excision repair pathway the enzyme uracil DNA glycosylase (UNG) recognizes and excises uracil (U) from DNA filaments. U repair is believed to occur via a multistep base-flipping process, through which the damaged U base is initially detected and then engulfed into the enzyme active site, where it is cleaved. The subtle recognition mechanism by which UNG discriminates between U and the other similar pyrimidine nucleobases is still a matter of active debate. Detailed structural information on the different steps of the base-flipping pathway may provide insights on it. However, to date only two intermediates have been trapped crystallographically thanks to chemical modifications of the target and/or of its complementary base. Here, we performed force-field based molecular dynamics (MD) simulations to explore the structural and dynamical properties of distinct UNG/dsDNA adducts, containing A:U, A:T, G:U, or G:C base pairs, at different stages of the base-flipping pathway. Our simulations reveal that if U is present in the DNA sequence a short-lived extra-helical (EH) intermediate exists. This is stabilized by a water-mediated H-bond network, which connects U with His148, a residue pointed out by mutational studies to play a key role for U recognition and catalysis. Moreover, in this EH intermediate, UNG induces a remarkable overall axis bend to DNA. We believe this aspect may facilitate the flipping of U, with respect to other similar nucleobases, in the latter part of the base-extrusion process. In fact, a large DNA bend has been demonstrated to be associated with a lowering of the free energy barrier for base-flipping. A detailed comparison of our results with partially flipped intermediates identified crystallographically or computationally for other base-flipping enzymes allows us to validate our results and to formulate hypothesis on the recognition mechanism of UNG. Our study provides a first ground for a detailed understanding of the UNG repair pathway, which is necessary to devise new pharmaceutical strategies for targeting DNA-related pathologies.

Theoretical studies of homogeneous catalysts mimicking nitrogenase.

The conversion of molecular nitrogen to ammonia is a key biological and chemical process and represents one of the most challenging topics in chemistry and biology. In Nature the Mo-containing nitrogenase enzymes perform nitrogen 'fixation' via an iron molybdenum cofactor (FeMo-co) under ambient conditions. In contrast, industrially, the Haber-Bosch process reduces molecular nitrogen and hydrogen to ammonia with a heterogeneous iron catalyst under drastic conditions of temperature and pressure. This process accounts for the production of millions of tons of nitrogen compounds used for agricultural and industrial purposes, but the high temperature and pressure required result in a large energy loss, leading to several economic and environmental issues. During the last 40 years many attempts have been made to synthesize simple homogeneous catalysts that can activate dinitrogen under the same mild conditions of the nitrogenase enzymes. Several compounds, almost all containing transition metals, have been shown to bind and activate N2 to various degrees. However, to date Mo(N2)(HIPTN)3N with (HIPTN)3N= hexaisopropyl-terphenyl-triamidoamine is the only compound performing this process catalytically. In this review we describe how Density Functional Theory calculations have been of help in elucidating the reaction mechanisms of the inorganic compounds that activate or fix N2. These studies provided important insights that rationalize and complement the experimental findings about the reaction mechanisms of known catalysts, predicting the reactivity of new potential catalysts and helping in tailoring new efficient catalytic compounds.