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

Proceedings paper

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

is not subject to a state or trade secret

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

In the original language

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

Cite

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  - CONF
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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