Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1- and 2-Bond Residual Dipolar Couplings

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Authors

NOVÁK Petr ŽÍDEK Lukáš PADRTA Petr SKLENÁŘ Vladimír

Year of publication 2004
Type Article in Proceedings
Conference 19th NMR Valtice
MU Faculty or unit

Faculty of Science

Citation
Field Biochemistry
Keywords NMR; Residual dipolar couplings; RNA; structure;
Description 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.
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