Understanding the Sequence Preference of Recurrent RNA Building
Blocks using Quantum Chemistry: The Intrastrand RNA
Dinucleotide Platform

J 2012

Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

MLÁDEK, Arnošt, Judit ŠPONEROVÁ, Petr KULHÁNEK, Xiang-Jun LU, Wilma K. OLSON et. al.

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

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10610 Biophysics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

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

Abstract

V originále

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 project

Name: CEITEC - central european institute of technology

GD203/09/H046, research and development project

Name: Biochemie na rozcestí mezi in silico a in vitro

Investor: Czech Science Foundation

LC06030, research and development project

Name: 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

Citovat

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, 2012, vol. 8, No 1, p. 335-347. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/ct200712b.

@article{961375,
   author = {Mládek, Arnošt and Šponerová, Judit and Kulhánek, Petr and Lu, XiangandJun and Olson, Wilma K. and Šponer, Jiří},
   article_location = {Washington},
   article_number = {1},
   doi = {http://dx.doi.org/10.1021/ct200712b},
   keywords = {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},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform},
   url = {http://pubs.acs.org/doi/abs/10.1021/ct200712b},
   volume = {8},
   year = {2012}
}

TY  - JOUR
ID  - 961375
AU  - Mládek, Arnošt - Šponerová, Judit - Kulhánek, Petr - Lu, Xiang-Jun - Olson, Wilma K. - Šponer, Jiří
PY  - 2012
TI  - Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform
JF  - Journal of Chemical Theory and Computation
VL  - 8
IS  - 1
SP  - 335-347
EP  - 335-347
PB  - ACS
SN  - 15499618
KW  - WATSON-CRICK/SUGAR-EDGE
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - BASE-PHOSPHATE INTERACTIONS
KW  - DENSITY-FUNCTIONAL THEORY
KW  - NUCLEIC-ACID STRUCTURES
KW  - BASIS-SET CONVERGENCE
KW  - AB-INITIO
KW  - FORCE-FIELD
KW  - TERTIARY INTERACTIONS
KW  - CHEMICAL CALCULATIONS
UR  - http://pubs.acs.org/doi/abs/10.1021/ct200712b
L2  - http://pubs.acs.org/doi/abs/10.1021/ct200712b
N2  - 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.
ER  -

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. \textit{Journal of Chemical Theory and Computation}. Washington: ACS, 2012, vol.~8, No~1, p.~335-347. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct200712b.

Detailed Information on Publication Record