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@article{1076042,
author = {Morgado, Claudio A and Svozil, Daniel and Turner, Douglas H and Šponer, Jiří},
article_location = {CAMBRIDGE},
article_number = {36},
doi = {http://dx.doi.org/10.1039/c2cp40556c},
keywords = {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},
language = {eng},
issn = {1463-9076},
journal = {Physical Chemistry Chemical Physics},
title = {Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22722325},
volume = {14},
year = {2012}
}
TY - JOUR
ID - 1076042
AU - Morgado, Claudio A - Svozil, Daniel - Turner, Douglas H - Šponer, Jiří
PY - 2012
TI - Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes
JF - Physical Chemistry Chemical Physics
VL - 14
IS - 36
SP - 12580-12591
EP - 12580-12591
PB - ROYAL SOC CHEMISTRY
SN - 14639076
KW - DENSITY-FUNCTIONAL THEORY
KW - GAUSSIAN-BASIS SETS
KW - DOT-A MISMATCHES
KW - MAGNETIC-RESONANCE-SPECTROSCOPY
KW - RELAXATION MATRIX APPROACH
KW - EMPIRICAL DISPERSION TERM
KW - UNIQUE DINUCLEOTIDE STEPS
KW - MOLECULAR-ORBITAL METHODS
KW - LARGE SUBUNIT 23S-LIKE
KW - PROTEIN DATA-BANK
UR - http://www.ncbi.nlm.nih.gov/pubmed/22722325
L2 - http://www.ncbi.nlm.nih.gov/pubmed/22722325
N2 - 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.
ER -
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. \textit{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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