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@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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