MLÁDEK, Arnošt, Judit ŠPONEROVÁ, Petr KULHÁNEK, Xiang-Jun LU, Wilma K. OLSON and Jiří ŠPONER. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. Journal of Chemical Theory and Computation. Washington: ACS, vol. 8, No 1, p. 335-347. ISSN 1549-9618. doi:10.1021/ct200712b. 2012.
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Basic information
Original name Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform
Authors MLÁDEK, Arnošt (203 Czech Republic), Judit ŠPONEROVÁ (348 Hungary, belonging to the institution), Petr KULHÁNEK (203 Czech Republic, belonging to the institution), Xiang-Jun LU (156 China), Wilma K. OLSON (840 United States of America) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution).
Edition Journal of Chemical Theory and Computation, Washington, ACS, 2012, 1549-9618.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10610 Biophysics
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 5.389
RIV identification code RIV/00216224:14740/12:00057217
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1021/ct200712b
UT WoS 000298908500035
Keywords in English WATSON-CRICK/SUGAR-EDGE; MOLECULAR-DYNAMICS SIMULATIONS; BASE-PHOSPHATE INTERACTIONS; DENSITY-FUNCTIONAL THEORY; NUCLEIC-ACID STRUCTURES; BASIS-SET CONVERGENCE; AB-INITIO; FORCE-FIELD; TERTIARY INTERACTIONS; CHEMICAL CALCULATIONS
Tags ok, rivok
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 7/4/2013 14:46.
Abstract
Folded RNA molecules are shaped by an astonishing variety of highly conserved non-canonical molecular interactions and backbone topologies. The dinucleotide platform is a widespread recurrent RNA modular building submotif formed by the side-by-side pairing of bases from two consecutive nucleotides within a single strand, with highly specific sequence preferences. This unique arrangement of bases is cemented by an intricate network of noncanonical hydrogen bonds and facilitated by a distinctive backbone topology. The present study investigates the gas-phase intrinsic stabilities of the three most common RNA dinucleotide platforms, 5'-GpU-3', ApA, and UpC, via state-of-the-art quantum-chemical (QM) techniques. The mean stability of base-base interactions decreases with sequence in the order GpU > ApA > UpC. Bader’s atoms-in-molecules analysis reveals that the N2(G)...O4(U) hydrogen bond of the GpU platform is stronger than the corresponding hydrogen bonds in the other two platforms. The mixed-pucker sugar-phosphate backbone conformation found in most GpU platforms, in which the 5'-ribose sugar (G) is in the C2'-endo form and the 3'-sugar (U) in the C3'-endo form, is intrinsically more stable than the standard A-RNA backbone arrangement, partially as a result of a favorable O2'...O2P intra-platform interaction. Our results thus validate the hypothesis of Lu et al. (Lu Xiang-Jun, et al. Nucleic Acids Res. 2010, 38, 4868-4876), that the superior stability of GpU platforms is partially mediated by the strong O2'...O2P hydrogen bond. In contrast, ApA and especially UpC platform-compatible backbone conformations are rather diverse and do not display any characteristic structural features. The average stabilities of ApA and UpC derived backbone conformers are also lower than those of GpU platforms. Our work also gives methodological insights into QM calculations of experimental RNA backbone geometries.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
GD203/09/H046, research and development projectName: Biochemie na rozcestí mezi in silico a in vitro
Investor: Czech Science Foundation
LC06030, research and development projectName: Biomolekulární centrum
Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre
MSM0021622413, plan (intention)Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment
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