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Are the Hydrogen Bonds of RNA (A⋅U) Stronger Than those of DNA (A⋅T)? A Quantum Mechanics Study
Author(s) -
Pérez Alberto,
Sponer Jiri,
Jurecka Petr,
Hobza Pavel,
Luque F. Javier,
Orozco Modesto
Publication year - 2005
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.200500255
Subject(s) - hydrogen bond , solvation , stacking , dna , base pair , rna , chemistry , hydrogen , chemical physics , molecular dynamics , quantum , reactivity (psychology) , thermodynamics , crystallography , computational chemistry , physics , molecule , quantum mechanics , organic chemistry , pathology , biochemistry , gene , medicine , alternative medicine
The intrinsic stability of Watson–Crick d(A⋅T) and r(A⋅U) hydrogen bonds was analyzed by employing a variety of quantum‐mechanical techniques, such as energy calculations, determination of reactivity indexes, and analysis of electron density topology. The analyses were performed not only for equilibrium gas‐phase geometries, but also on hundreds of conformations derived from molecular dynamics (MD) and database analysis. None of our results support the idea that r(A⋅U) hydrogen bonds are intrinsically more stable than those of d(A⋅T). Instead, our data are in accordance with the traditional view that the greater stability of RNA relative to DNA is attributable to a variety of effects (e.g., stacking, sugar puckering, solvation) rather than to a significant difference in the hydrogen bonding of DNA and RNA base pairs.