Analysis of local convergence in NMR structure calculation for RNA by a classification system for nucleic acid structure (CSNA)

We are developing a program system, CSNA, to classify a set of structures into groups sharing similar structural characters. In the present study, CSNA was applied to the analysis of NMR structures obtained by the simulated annealing calculation to elucidate local convergences. A 34-mer RNA, U6-34, having a bulge-out region that is derived from the human U6 snRNA is used as a target molecule in the present study. Although the structure calculation was not converged with the conventional method, it was found by the CSNA analysis that the two stem regions in the molecule were converged well. Furthermore, one strand of the bulge-out region (A7-A11) was found to form a continuously stacked structure in two-thirds of calculated structures. In conclusion, CSNA can be a novel tool to elucidate the local convergence of the NMR structure calculations.