Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry

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This paper reports the largest previously unpublished RNA structure determined ab initio from native data alone by direct methods using the program SIR2014. This is also the first structure determination of an RNA by direct methods in the presence of translational pseudosymmetry (TPS). TPS is known to hinder structure determination. Molecular TPS is common in dsRNAs longer than one helical turn. This RNA has almost three helical turns and had TPS between helical turns 1 and 2, 2 and 3, and 1 and 3. I did hundreds of phasing experiments to probe the effect of TPS on success at structure determination by direct methods. Much more computing time was required to determine this structure than the structure of a hairpin RNA of similar size.

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