MARDIGRAS distance restraints

Since coupling constant-derived torsion anlges constrain the ribose moieties more precisely and efficiently, all intra-ribose distance restraints were omitted in the refinement calculations. On a per-nucleotide basis, our list contained 7.5 MARDIGRAS distance restraints and 4.4 semiquantitative distance restraints. For the internal loop, comprising residues U5-G9 and A20-G24, the list had 7.3 MARDIGRAS distance restraints and 5.3 semiquantitative distance restraints. 

To date, only two applications of complete relaxation matrix derived distance restraints have been reported for RNA. MARDIGRAS provided "precise" distance restraints for the structure determination of a 17mer RNA with a flexible loop (26) and a 31mer hairpin with a large internal loop (18). For the latter, assignments and NOE volume extraction was made feasible through deuteration of all cytosines. 

The preliminary NMR structure of SRP 28mer is shown in Figure 8. We are currently performing the final rMD refinement simulations with improved MARDIGRAS-derived distance restraints where the preliminary NMR structure was used as a starting model for the MARDIGRAS calculations. Therefore, we refrain from a detailed discussion of the structure of the SRP 28mer in this article and refer to future publications. 

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