Other formats:
BibTeX
LaTeX
RIS
@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.
|