Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations

0370405 - BFÚ 2012 RIV US eng J - Journal Article
Zgarbová, M. - Jurečka, P. - Banáš, P. - Otyepka, M. - Šponer, Judit E. - Leontis, N.B. - Zirbel, C.L. - Šponer, Jiří
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.
Journal of Physical Chemistry A. Roč. 115, č. 41 (2011), s. 11277-11292. ISSN 1089-5639. E-ISSN 1520-5215
R&D Projects: GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GD203/09/H046; GA MŠMT(CZ) LC06030; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822
Grant - others:GA ČR(CZ) GAP208/10/1742; GA ČR(CZ) GPP301/11/P558
Program: GA; GP
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : density-functional theory * large ribosomal-subunit * gaussian-basis sets
Subject RIV: BO - Biophysics
Impact factor: 2.946, year: 2011

RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects.
Permanent Link: http://hdl.handle.net/11104/0006782