NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA
Hairpin Tetraloop

J 2007

NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop

TRANTÍREK, Lukáš, Erik CAHA, Pavel KADEŘÁVEK and Radovan FIALA

Basic information

Original name

NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop

Name in Czech

Studium dynamiky bazí a cukrů v RNA smyčce GCAA pomocí NMR relaxace C-13

Authors

TRANTÍREK, Lukáš (203 Czech Republic), Erik CAHA (203 Czech Republic), Pavel KADEŘÁVEK (203 Czech Republic) and Radovan FIALA (203 Czech Republic, guarantor)

Edition

Journal of Biomolecular Structure and Dynamics, GUILDERLAND, Adenine Press, 2007, 0739-1102

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 1.413

RIV identification code

RIV/00216224:14310/07:00020606

Organization unit

Faculty of Science

UT WoS

000250986500004

Keywords in English

RNA; nucleic acid; dynamics; internal motion; NMR; C-13

Abstract

ORIG CZ

V originále

Intramolecular dynamics of a 14-mer RNA hairpin including GCAA tetraloop was investigated by 13C NMR relaxation. R1 and R1rho relaxation rates were measured for all protonated base carbons as well as for C1' carbons of ribose sugars at several magnetic field strengths. The data has been interpreted in the framework of modelfree analysis (G. Lipari and A. Szabo, J. Am. Chem. Soc. 104, 4546-4559 (1982); G. Lipari and A. Szabo, J. Am. Chem. Soc. 104, 4559-4570 (1982)) characterizing the internal dynamics of the molecule by order parameters and correlation times for fast motions on picosecond to nanosecond time scale and by contributions of the chemical exchange. The fast dynamics reveals a rather rigid stem and a significantly more flexible loop. The cytosine and the last adenine bases in the loop as well as all the loop sugars exhibit a significant contribution of conformational equilibrium on microsecond to millisecond time scale. The high R1rho values detected on both base and sugar moieties of the loop indicate coordinated motions in this region. A semiquantitative analysis of the conformational equilibrium suggests the exchange rates on the order of 10000/s. The results are in general agreement with dynamics studies of GAAA loops by NMR relaxation and fluorescent spectroscopy and support the data on the GCAA loop dynamics obtained by MD simulations.

In Czech

Práce popisuje výsledky studia intramolekulární dynamiky RNA vlásenky sestávající ze 14 nukleotidů a obsahující smyčku GCAA pomocí NMR relaxace jader C-13.

Links

GA203/99/0311, research and development project

Name: Studium dynamiky oligonukleotidů pomocí NMR spektroskopie

Investor: Czech Science Foundation, Nuclear magnetic resonance studies of oligonucleotide dynamics

LC06030, research and development project

Name: Biomolekulární centrum

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre

Citovat

TRANTÍREK, Lukáš, Erik CAHA, Pavel KADEŘÁVEK and Radovan FIALA. NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop. Journal of Biomolecular Structure and Dynamics. GUILDERLAND: Adenine Press, 2007, vol. 25, No 3, p. 307-326, 19 pp. ISSN 0739-1102.

@article{728047,
   author = {Trantírek, Lukáš and Caha, Erik and Kadeřávek, Pavel and Fiala, Radovan},
   article_location = {GUILDERLAND},
   article_number = {3},
   keywords = {RNA; nucleic acid; dynamics; internal motion; NMR; C-13},
   language = {eng},
   issn = {0739-1102},
   journal = {Journal of Biomolecular Structure and Dynamics},
   title = {NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop},
   url = {http://www.jbsdonline.com/},
   volume = {25},
   year = {2007}
}

TY  - JOUR
ID  - 728047
AU  - Trantírek, Lukáš - Caha, Erik - Kadeřávek, Pavel - Fiala, Radovan
PY  - 2007
TI  - NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop
JF  - Journal of Biomolecular Structure and Dynamics
VL  - 25
IS  - 3
SP  - 307-326
EP  - 307-326
PB  - Adenine Press
SN  - 07391102
KW  - RNA
KW  - nucleic acid
KW  - dynamics
KW  - internal motion
KW  - NMR
KW  - C-13
UR  - http://www.jbsdonline.com/
N2  - Intramolecular dynamics of a 14-mer RNA hairpin including GCAA tetraloop was investigated by 13C NMR relaxation. R1 and R1rho relaxation rates were measured for all protonated base carbons as well as for C1' carbons of ribose sugars at several magnetic field strengths. The data has been interpreted in the framework of modelfree analysis (G. Lipari and A. Szabo, J. Am. Chem. Soc. 104, 4546-4559 (1982); G. Lipari and A. Szabo, J. Am. Chem. Soc. 104, 4559-4570 (1982)) characterizing the internal dynamics of the molecule by order parameters and correlation times for fast motions on picosecond to nanosecond time scale and by contributions of the chemical exchange. The fast dynamics reveals a rather rigid stem and a significantly more flexible loop. The cytosine and the last adenine bases in the loop as well as all the loop sugars exhibit a significant contribution of conformational equilibrium on microsecond to millisecond time scale. The high R1rho values detected on both base and sugar moieties of the loop indicate coordinated motions in this region. A semiquantitative analysis of the conformational equilibrium suggests the exchange rates on the order of 10000/s. The results are in general agreement with dynamics studies of GAAA loops by NMR relaxation and fluorescent spectroscopy and support the data on the GCAA loop dynamics obtained by MD simulations.
ER  -

TRANTÍREK, Lukáš, Erik CAHA, Pavel KADEŘÁVEK and Radovan FIALA. NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop. \textit{Journal of Biomolecular Structure and Dynamics}. GUILDERLAND: Adenine Press, 2007, vol.~25, No~3, p.~307-326, 19 pp. ISSN~0739-1102.

Detailed Information on Publication Record