How Flexible are DNA Constituents? The Quantum-Mechanical Study

Abstract

Relaxed force constants (RFCs) and vibrational root-mean-square deviations have been evaluated by the original calculation method for conformational parameters of the DNA structural units and their constituents: nucleic acid bases (uracile, thymine, cytosine, adenine and guanine) and their 'building blocks' (benzene, pyrimidine, imidazole and purine molecules), as well as the DNA backbone structural units: tetrahydrofuran, 1,2-dideoxyribose, methanol and orthophosphoric acid. It has been found that the RFCs for nomenclature torsions beta, gamma, epsilon; and sugar pseudorotation angle P in 1,2-dideoxyribose are sensible to the molecule conformation and their values are in the range of 1-25 kcal/(mole·rad²) obeying the inequality K(γ)> K(ε) > K(ρ) > K(β). The RFCs values for endocyclic torsions of nucleic acid bases six-member rings lie within 15-45 kcal/(mole·rad²) in pyrimidines and within 20-60 kcal/(mole·rad²) in purines. It is shown that the quantum zero-point motion effectively neglects the amino group non-planarity in cytosine, adenine and partially in guanine.

A novel conception for spontaneous transversions caused by homo-pyrimidine DNA mismatches: a QM/QTAIM highlight

“…Thus, we have shown for the first time that plane-symmetric (C s ) Т·Т(w) mismatch, that in fact is observed in the DNA double helix under physiological conditions [25][26][27], stays in slow tautomeric equilibrium with two Т·Т*(WC) [20] and Т* O2 ·Т(WC) mispairs representing itself propeller-like and structurally non-rigid complexes [39,40] (Figs. 1, S1 and Tables 1, S1, S4).…”

A computational study of dsDNA pairs and vibrational resonance in separating water

“…Recent research indicates that low-frequency vibrational modes of nucleotides occur from two primary sources: the structural flexibility of the molecules themselves (Nikolaienko et al 2011), and the occurrence of weak CHÁÁÁO/N H-bonds between the molecules (Brovarets' et al 2013;Yurenko et al 2011). That these vibrational modes and relaxed force constants vary per nucleotide, and even per conformation, further strengthens prior sequence-dependent DNA mechanics research (Miyamoto et al 2005;Rief et al 1999;Ten et al 2009).…”

X-ray structure and conformational study of tris(2-(dimethylamino)phenyl)methanol salt derivatives: Roles of anions and hydrogen bond

“…The calculated energy of E' is higher than that of E. Except that, the H-bond structure of E' shows a non-binding dimethylamino group. And because of the steric hindrance induced by the attached methyl groups, this nitrogen atom would also take a tetrahedral configuration, instead of planar configuration [35,36]. However, as a weakacid-strong-base salt, the generated Na 2 SO 3 salt was thought to be something not so compatible with the formed [LH] þ cation salt.…”