Effect of Single Strand Constraints on the Conformation Space of tRNA Asp 7.

The sequence for human tRNA Asp 7 [26] was folded using the Wuchty algorithm with the no lonely slow option and 2004 thermodynamic parameters and the largest possible window size in a 48-hour computing time. Hard single strand constraints require the nucleotide to be unpaired. Context-dependent single strand constraints allow nucleotide pairing at the end of helix, adjacent to loops, and adjacent to GU pairs. The maximum and average base pair distance values are calculated using the rna_distance function in the Vienna Package. The base pair distance is a count of how many base pairs exist in one structure and not another when comparing two RNA secondary structures. All computed structures were compared to the MFE structure in the rna distance calculations. Note: this use of “base pair distance” is not to be confused with the constraint (not used in these RNA structure predictions) that limits how far away a nucleotide can pair with another nucleotide within a single structure.
Effect of Single Strand Constraints on the Conformation Space of tRNA Asp 7.