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 and Gerhard WIDER

Basic information

Original name

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

Authors

KRÄHENBÜHL, Barbara (756 Switzerland), Peter LUKAVSKY (40 Austria, guarantor, belonging to the institution) and Gerhard WIDER (756 Switzerland)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.141

RIV identification code

RIV/00216224:14740/14:00077315

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000339909200003

Keywords in English

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

Abstract

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 and Gerhard WIDER. Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10. Journal of Biomolecular NMR. Netherlands: Springer Netherlands, 2014, vol. 59, No 4, p. 231-240. ISSN 0925-2738. Available from: 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 and Gerhard WIDER. Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10. \textit{Journal of Biomolecular NMR}. Netherlands: Springer Netherlands, 2014, vol.~59, No~4, p.~231-240. ISSN~0925-2738. Available from: https://dx.doi.org/10.1007/s10858-014-9841-3.

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