Last modified on 18 April 2012.

Literature Reference:

Wu J.C., Gardner D.P., Ozer S., Gutell R.R., and Ren P. (2009).
Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding.
Journal of Molecular Biology, 391:769-783.

Manuscript Figures and Tables:

Figure 1. Illustrations of four secondary structures.
  1. An example of a base-pair stack that is denoted UA/CG.
  2. An example of a basepair stack that is denoted CG/UA.
  3. An example of a hairpin flank that is denoted GC/CA.
  4. An example of an internal loop that is denoted GC/CG/AG/AA.
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Figure 2.
  1. Base-pair stack statistical energy (SE) derived from all-sequence dataset.
  2. Bacterial 16 S rRNA.
  3. Bacterial 5 S rRNA.
  4. Eukaryotic 5 S rRNA.
  5. tRNA versus free energy obtained experimentally for a given basepair stack.
  6. PDB-derived statistical potentials versus free energy obtained experimentally.29 Experimental values are in kcal/mol.
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Figure 3.
  1. Base-pair statistical energy versus base-pair stack statistical energy with a correlation coefficient of 0.8582.
  2. Stacking statistical energy versus base-pair stack statistical energy with a correlation coefficient of 0.1790.
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Figure 4. Each group of bars represents folding accuracy of (from left to right) tRNA, eukaryotic 5 S rRNA, bacterial 5 S rRNA, and bacterial 16 S rRNA. Within each group, each bar represents (from left to right) unmodified Mfold, base-pair stack SE derived using tRNA, eukaryotic 5 S rRNA, bacterial 5 S rRNA, bacterial 16 S rRNA, and all-sequence dataset. PNG
Figure 5. Each group of bars represents the folding accuracy of (from left to right) tRNA, eukaryotic 5 S rRNA, bacterial 5 S rRNA, and bacterial 16 S rRNA.Within each group, each bar represents (from left to right) unmodified Mfold, base-pair stack SE, hairpin flank SE, internal loop SE, and all available SE (base-pair stack, hairpin flank, and internal loops). PNG
Figure 6. Each group of bars represents folding accuracy of (from left to right) tRNA, eukaryotic 5 S rRNA, bacterial 5 S rRNA, and bacterial 16 S rRNA. Within each group, each bar represents (from left to right) unmodified Mfold, base-pair stack, hairpin flank, and internal loop SEs derived using tRNA, eukaryotic 5 S rRNA, bacterial 5 S rRNA, bacterial 16 S rRNA, and all-sequence dataset. PNG
Table 1. Statistical energy derived from sequences of each specified molecule. HTML
Table 2. Base-pair stack statistics. HTML