MORGADO, Claudio A, Daniel SVOZIL, Douglas H TURNER and Jiří ŠPONER. Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2012, vol. 14, No 36, p. 12580-12591. ISSN 1463-9076. doi:10.1039/c2cp40556c.
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Basic information
Original name Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes
Authors MORGADO, Claudio A (152 Chile), Daniel SVOZIL (203 Czech Republic), Douglas H TURNER (840 United States of America) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution).
Edition Physical Chemistry Chemical Physics, CAMBRIDGE, ROYAL SOC CHEMISTRY, 2012, 1463-9076.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10610 Biophysics
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 3.829
RIV identification code RIV/00216224:14740/12:00057881
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1039/c2cp40556c
UT WoS 000307900800018
Keywords in English DENSITY-FUNCTIONAL THEORY; GAUSSIAN-BASIS SETS; DOT-A MISMATCHES; MAGNETIC-RESONANCE-SPECTROSCOPY; RELAXATION MATRIX APPROACH; EMPIRICAL DISPERSION TERM; UNIQUE DINUCLEOTIDE STEPS; MOLECULAR-ORBITAL METHODS; LARGE SUBUNIT 23S-LIKE; PROTEIN DATA-BANK
Tags ok, rivok
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 6. 4. 2013 17:36.
Abstract
Preceding NMR experiments show that the conformation of tandem GA base pairs, an important recurrent non-canonical building block in RNA duplexes, is context dependent. The GA base pairs adopt "sheared" N3(G)-N6(A), N2(G)-N7(A) geometry in the r(CGAG)(2) and r(iGGAiC)(2) contexts while switching to "imino" N1(G)-N1(A), O6(G)-N6(A) geometry in the r(GGAC)(2) and r(iCGAiG)(2) contexts (iC and iG stand for isocytosine and isoguanine, respectively). As base stacking is likely to be one of the key sources of the context dependence of the conformation of GA base pairs, we calculated base stacking energies in duplexes containing such base pairs, to see if this dependence can be predicted by stacking energy calculations. When investigating the context dependence of the GA geometry two different conformations of the same duplex were compared (imino vs. sheared). The geometries were generated via explicit solvent MD simulations of the respective RNA duplexes, while the subsequent QM energy calculations focused on base stacking interactions of the four internal base pairs. Geometrical relaxation of nucleobase atoms prior to the stacking energy computations has a non-negligible effect on the results. The stacking energies were derived at the DFT-D/6-311++G(3df,3pd) level. We show a rather good correspondence between the intrinsic gas-phase stacking energies and the NMR-determined GA geometries. The conformation with more favorable gas-phase stacking is in most cases the one observed in experiments. This correlation is not improved when including solvent effects via the COSMO method. On the other side, the stacking calculations do not predict the relative thermodynamic stability of duplex formation for different sequences.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
GBP305/12/G034, research and development projectName: Centrum biologie RNA
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