Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1-
and 2-Bond Residual Dipolar Couplings

D 2004

Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1- and 2-Bond Residual Dipolar Couplings

NOVÁK, Petr, Lukáš ŽÍDEK, Petr PADRTA and Vladimír SKLENÁŘ

Basic information

Original name

Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1- and 2-Bond Residual Dipolar Couplings

Name in Czech

Rafinace struktury Trypanosoma U6 RNA s využitím jedno- a dvouvazebných zbytkových dipolárních interakcí

Authors

NOVÁK, Petr (203 Czech Republic), Lukáš ŽÍDEK (203 Czech Republic), Petr PADRTA (203 Czech Republic) and Vladimír SKLENÁŘ (203 Czech Republic, guarantor)

Edition

Brno, 19th NMR Valtice, p. 30-30, 1 pp. 2004

Publisher

Masarykova universita v Brně

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14310/04:00011133

Organization unit

Faculty of Science

ISBN

80-210-3352-5

Keywords in English

NMR; Residual dipolar couplings; RNA; structure;

Abstract

ORIG CZ

V originále

The spliceosome is a complex of proteins and small nuclear RNAs (snRNAs) responsible for the removal of introns from pre-mRNA in eukaryotes. U6 snRNA has been demonstrated to be a vital element in splicing and its sequence is the most conserved of all snRNAs[1]. U6 snRNA from trypanosoma was our study. Determination of the solution structure of nucleic acid fragments is significantly improved if residual dipolar are measured. This data provides us additional long-range and local geometry restraints using a small degree of molecular alignment with the static magnetic field. We wanted to test polyethylenglycol (PEG) as a alignment medium for measuring the residual dipolar couplings (RDCs). PEG is a stable and unexpensive organic polymer that does not require a complex biochemical preparation like the most often used bacteriophage Pf1. In our study, applicability of PEG to several spin-state-selective E.COSY experiments was investigated. Measured RDCs were tested for internal consistency as refered in [2] in order to check the reliability of the values obtained in the PEG-aligned samples.

In Czech

Rafinace struktury Trypanosoma U6 RNA s využitím jedno- a dvouvazebných zbytkových dipolárních interakcí.

Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM

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

Citovat

NOVÁK, Petr, Lukáš ŽÍDEK, Petr PADRTA and Vladimír SKLENÁŘ. Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1- and 2-Bond Residual Dipolar Couplings. In 19th NMR Valtice. Brno: Masarykova universita v Brně, 2004, p. 30-30. ISBN 80-210-3352-5.

@inproceedings{571832,
   author = {Novák, Petr and Žídek, Lukáš and Padrta, Petr and Sklenář, Vladimír},
   address = {Brno},
   booktitle = {19th NMR Valtice},
   keywords = {NMR; Residual dipolar couplings; RNA; structure;},
   language = {eng},
   location = {Brno},
   isbn = {80-210-3352-5},
   pages = {30-30},
   publisher = {Masarykova universita v Brně},
   title = {Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1- and 2-Bond Residual Dipolar Couplings},
   year = {2004}
}

TY  - JOUR
ID  - 571832
AU  - Novák, Petr - Žídek, Lukáš - Padrta, Petr - Sklenář, Vladimír
PY  - 2004
TI  - Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1- and 2-Bond Residual Dipolar Couplings
PB  - Masarykova universita v Brně
CY  - Brno
SN  - 8021033525
KW  - NMR
KW  - Residual dipolar couplings
KW  - RNA
KW  - structure;
N2  - The spliceosome is a complex of proteins and small nuclear RNAs (snRNAs) responsible for the removal of introns from pre-mRNA in eukaryotes. U6 snRNA has been demonstrated to be a vital element in splicing and its sequence is the most conserved of all snRNAs[1]. U6 snRNA from trypanosoma was our study. Determination of the solution structure of nucleic acid fragments is significantly improved if residual dipolar are measured. This data provides us additional long-range and local geometry restraints using a small degree of molecular alignment with the static magnetic field. We wanted to test polyethylenglycol (PEG) as a alignment medium for measuring the residual dipolar couplings (RDCs). PEG is a stable and unexpensive organic polymer that does not require a complex biochemical preparation like the most often used bacteriophage Pf1. In our study, applicability of PEG to several spin-state-selective E.COSY experiments was investigated. Measured RDCs were tested for internal consistency as refered in [2] in order to check the reliability of the values obtained in the PEG-aligned samples.
ER  -

NOVÁK, Petr, Lukáš ŽÍDEK, Petr PADRTA and Vladimír SKLENÁŘ. Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1- and 2-Bond Residual Dipolar Couplings. In \textit{19th NMR Valtice}. Brno: Masarykova universita v Brně, 2004, p.~30-30. ISBN~80-210-3352-5.

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