Data on properties of phosphoramide benzoazole oligonucleotides
Description
The data include: 1) temperature series of circular dichroism spectra of the native and modified duplexes (folders: CD and CD_melting); 2) data from singular value decomposition of UV-Vis used for pKa determination of the phosphoramidate N-benzazole moiety (folders: UV-Vis_thiazole and pKa_SVD_analysis); 3) values of thermodynamic parameters (changes in enthalpy, entropy, Gibbs free energy and melting temperature) of DNA/DNA and PABAO/DNA duplexes (folder: thermodynamic parameters); 4) partial atomic charges of the phosphoramidate N-benzazole moiety (folder: patial_charges); 5) structures of DNA/DNA and PABAO/DNA duplexes obtained using k-means cluster analysis of molecular dynamics trajectories (folder: molecular_dynamics_structures).
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Steps to reproduce
Detailed description of the methods for data curation described in "Data for properties of phosphoramidate benzoazole oligonucleotides" by I.I. Yushin, V.M. Golyshev, E.E. Baranovskaya and A.A. Lomzov, Data in Brief. In brief, UV‑Vis spectra were recorded and UV‑melting experiments were carried out using a Cary 3500 spectrophotometer (Agilent, USA) equipped with a multizone Peltier holder. Measurements were performed in quartz cuvettes with a 2 mm optical path length across a wavelength range of 200–800 nm. Thermodynamic parameters were calculated using a two‑state model by nonlinear fitting of denaturation and renaturation curves. CD spectra were recorded on a JASCO J‑600 spectropolarimeter (JASCO, Japan) in the wavelength range of 200–330 nm and over a temperature range of 5–95 °C using a quartz cell with a 1 cm light path. Atomic partial charges were calculated in Gaussian 09 based on optimized structures via single‑point calculations at the HF/6‑31G//B3LYP/6‑31G++(3df,3pd) level, followed by ESP fitting using PyRESP software. Molecular dynamics simulations were performed in explicit solvent using the OPC water model, the OL21 force field for DNA, and GAFF2 parameters for the modified phosphate residues. All simulations and analyses were conducted using AMBER 23. A 300 ns trajectory was obtained for each complex. Representative structures were derived from the MD trajectories via k‑means cluster analysis.
Institutions
- Institute khimicheskoi biologii i fundamental'noi meditsiny