Application of multi dimensional NMR experiments to VBS RNAs of Yeast Saccaromyces cerevisiae virus

Abstract

The structures of two VBS (viral binding site) RNAs, SL1 and SL2, of Yeast Saccharomyces cerevisiae virus have been studied by 2D and 3D NMR experiments. VBSs play a crucial role in viral particle binding to the plus strand and packaging of the RNA. The secondary structures of the two VBS RNAs share a common feature of the stem-internal loop-stem-hairpin loop structure although the size of the internal loops of SL1 and SL2 differs. 2D experiments were sufficient for full assignments of SL1. However, isotope labeling of the sample and multidimensional experiments were required for 28-nucleotide-long SL2 due to the spectral overlap. Several 3D HCCH experiments have accomplished full assignment of SL2 RNA.