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 a Radovan FIALA

Základní údaje

Originální název

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

Název česky

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

Autoři

TRANTÍREK, Lukáš (203 Česká republika), Erik CAHA (203 Česká republika), Pavel KADEŘÁVEK (203 Česká republika) a Radovan FIALA (203 Česká republika, garant)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 1.413

Kód RIV

RIV/00216224:14310/07:00020606

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000250986500004

Klíčová slova anglicky

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

Štítky

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

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 21. 11. 2007 11:05, doc. RNDr. Radovan Fiala, CSc.

Anotace

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.

Česky

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

Návaznosti

GA203/99/0311, projekt VaV

Název: Studium dynamiky oligonukleotidů pomocí NMR spektroskopie

Investor: Grantová agentura ČR, Studium dynamiky oligonukleotidů pomocí NMR spektroskopie

LC06030, projekt VaV

Název: Biomolekulární centrum

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

Citovat

TRANTÍREK, Lukáš, Erik CAHA, Pavel KADEŘÁVEK a 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, roč. 25, č. 3, s. 307-326, 19 s. 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 a 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, roč.~25, č.~3, s.~307-326, 19 s. ISSN~0739-1102.

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