Strategy for automated NMR resonance assignment of RNA:
application to 48-nucleotide K10

J 2014

Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10

KRÄHENBÜHL, Barbara, Peter LUKAVSKY a Gerhard WIDER

Základní údaje

Originální název

Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10

Autoři

KRÄHENBÜHL, Barbara (756 Švýcarsko), Peter LUKAVSKY (40 Rakousko, garant, domácí) a Gerhard WIDER (756 Švýcarsko)

Vydání

Journal of Biomolecular NMR, Netherlands, Springer Netherlands, 2014, 0925-2738

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.141

Kód RIV

RIV/00216224:14740/14:00077315

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1007/s10858-014-9841-3

UT WoS

000339909200003

Klíčová slova anglicky

Nucleic acids; NMR; Projection spectroscopy; APSY; Automated assignment; FLYA; Novel sampling methods

Štítky

kontrola MP, MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 14. 11. 2014 12:38, Martina Prášilová

Anotace

V originále

A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [C-13, N-15]-labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3 mM sample of an RNA stem-loop with 48 nucleotides, K10, which is responsible for dynein-mediated localization of Drosophila fs(1)K10 mRNA transcripts. The automated analysis of the APSY data led to highly accurate and precise 3- to 4-dimensional peak lists. They provided a reliable basis for the subsequent sequence-specific resonance assignment with the algorithm FLYA and resulted in the fully automated resonance assignment of more than 80 % of the resonances of the C-13-H-1 moieties at the 1', 2', 5, 6, and 8 positions in the nucleotides. The procedure was robust with respect to numerous impurity peaks, low concentration of this for NMR comparably large RNA, and structural features such as a loop, single-nucleotide bulges and a non-Watson-Crick wobble base pairs. Currently, there is no precise chemical shift statistics (as used by FLYA) for RNA regions which deviate from the regular A-form helical structure. Reliable and precise peak lists are thus required for automated sequence-specific assignment, as provided by APSY.

Citovat

KRÄHENBÜHL, Barbara, Peter LUKAVSKY a Gerhard WIDER. Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10. Journal of Biomolecular NMR. Netherlands: Springer Netherlands, 2014, roč. 59, č. 4, s. 231-240. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-014-9841-3.

@article{1206002,
   author = {Krähenbühl, Barbara and Lukavsky, Peter and Wider, Gerhard},
   article_location = {Netherlands},
   article_number = {4},
   doi = {http://dx.doi.org/10.1007/s10858-014-9841-3},
   keywords = {Nucleic acids; NMR; Projection spectroscopy; APSY; Automated assignment; FLYA; Novel sampling methods},
   language = {eng},
   issn = {0925-2738},
   journal = {Journal of Biomolecular NMR},
   title = {Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10},
   url = {http://link.springer.com/article/10.1007%2Fs10858-014-9841-3},
   volume = {59},
   year = {2014}
}

TY  - JOUR
ID  - 1206002
AU  - Krähenbühl, Barbara - Lukavsky, Peter - Wider, Gerhard
PY  - 2014
TI  - Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10
JF  - Journal of Biomolecular NMR
VL  - 59
IS  - 4
SP  - 231-240
EP  - 231-240
PB  - Springer Netherlands
SN  - 09252738
KW  - Nucleic acids
KW  - NMR
KW  - Projection spectroscopy
KW  - APSY
KW  - Automated assignment
KW  - FLYA
KW  - Novel sampling methods
UR  - http://link.springer.com/article/10.1007%2Fs10858-014-9841-3
L2  - http://link.springer.com/article/10.1007%2Fs10858-014-9841-3
N2  - A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [C-13, N-15]-labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3 mM sample of an RNA stem-loop with 48 nucleotides, K10, which is responsible for dynein-mediated localization of Drosophila fs(1)K10 mRNA transcripts. The automated analysis of the APSY data led to highly accurate and precise 3- to 4-dimensional peak lists. They provided a reliable basis for the subsequent sequence-specific resonance assignment with the algorithm FLYA and resulted in the fully automated resonance assignment of more than 80 % of the resonances of the C-13-H-1 moieties at the 1', 2', 5, 6, and 8 positions in the nucleotides. The procedure was robust with respect to numerous impurity peaks, low concentration of this for NMR comparably large RNA, and structural features such as a loop, single-nucleotide bulges and a non-Watson-Crick wobble base pairs. Currently, there is no precise chemical shift statistics (as used by FLYA) for RNA regions which deviate from the regular A-form helical structure. Reliable and precise peak lists are thus required for automated sequence-specific assignment, as provided by APSY.
ER  -

KRÄHENBÜHL, Barbara, Peter LUKAVSKY a Gerhard WIDER. Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10. \textit{Journal of Biomolecular NMR}. Netherlands: Springer Netherlands, 2014, roč.~59, č.~4, s.~231-240. ISSN~0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-014-9841-3.

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