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.

Základní údaje

Originální název

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

Autoři

MLÁDEK, Arnošt (203 Česká republika), Judit ŠPONEROVÁ (348 Maďarsko, domácí), Petr KULHÁNEK (203 Česká republika, domácí), Xiang-Jun LU (156 Čína), Wilma K. OLSON (840 Spojené státy) a Jiří ŠPONER (203 Česká republika, garant, domácí)

Vydání

Journal of Chemical Theory and Computation, Washington, ACS, 2012, 1549-9618

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10610 Biophysics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.389

Kód RIV

RIV/00216224:14740/12:00057217

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/ct200712b

UT WoS

000298908500035

Klíčová slova anglicky

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

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 7. 4. 2013 14:46, Olga Křížová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GD203/09/H046, projekt VaV

Název: Biochemie na rozcestí mezi in silico a in vitro

Investor: Grantová agentura ČR, Biochemie na rozcestí mezi in silico a in vitro

LC06030, projekt VaV

Název: Biomolekulární centrum

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

MSM0021622413, záměr

Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím

Citovat

MLÁDEK, Arnošt, Judit ŠPONEROVÁ, Petr KULHÁNEK, Xiang-Jun LU, Wilma K. OLSON a 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, roč. 8, č. 1, s. 335-347. ISSN 1549-9618. Dostupné z: 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 a 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, roč.~8, č.~1, s.~335-347. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct200712b.

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