Description of Thermodynamic Parameters

There are nineteen files of free energies for RNA-RNA interactions.  The derivation of these parameters is in Mathews, Disney, Childs, Schroeder, Zuker, and Turner [PNAS. 2004. 101:7287]. Here is a brief summary of what the files contain:
All the parameters used by RNAstructure are for standard free energy at 37° C.  Stack.dat contains the nearest neighbor parameters for stacking in a helix.  Dangle.dat presents the free energy of dangling ends (5’ or 3’).  These energies are used in multibranch and exterior loops.  The loop.dat table contains the entropic penalty for closing hairpin, internal, and bulge loops.  Each has its own penalty based on length.  Tstackh.dat gives the free energy of stacking for a terminal mismatch in a hairpin loop.  Tstacki.dat gives the free energy of stacking for a terminal mismatch in an internal loop.  Tstacki23.dat is used for terminal mismatch stacking in internal loops of size 2x3 unpaired nucleotides (and 3x2).  Tstacki1n.dat is used for terminal mismatch stacking in internal loops of size 1xn nucleotides where n>2.  Tstackm.dat is used for terminal stacking in a multibranch loop.  Tstack.dat is for terminal mismatch stacking in exterior loops, i.e. loops that contain the ends of the sequence.  Miscloop.dat contains miscellaneous loop parameters.  Int21.dat is a lookup table for the free energy of a 2x1 internal loop.  The values presented are the total stability of the loop, including the entropic penalty and the terminal stack bonus.  Int22.dat is a lookup table for the free energy of a 2x2 internal loop analogous to the 2x1 internal loop.  Int11.dat is the lookup table for single mismatches.  Tloop.dat is the tetraloop bonus table.  For hairpin loops with four unpaired nucleotides, this table is consulted.  If the sequence (starting with the 5’ last paired nucleotide and finishing with its 3’ paired nucleotide) appears in the table, the bonus is applied to the hairpin’s stability.  Triloop.dat is a lookup table for hairpin loops of three.  It is applied analogously to the tetraloop table (above).  Also, hexaloop.dat is a lookup table for hairpins of six nucleotides.  Coaxial.dat is the free energy of coaxial stacking for two helixes with no intervening unpaired nucleotides.  When applied, the top nucleotides are the continuous sequence and the bottom nucleotides are interrupted by the rest of the multibranch loop or exterior loop.  Coaxstack.dat is one of the two tables for coaxial stacking with an intervening mismatch.  This is the stack with the open backbone.  Tstackcoax.dat is the second of the tables for coaxial stacking with an intervening mismatch.  This is the stack with the continuous backbone.  


For the Tm calculation in oligo walk, the DH and DS parameters are stored in helix.dat, stack.ds, and stack.dh.

Enthalpy change parameters are also provided to make predictions at temperatures other than 37 °C and were derived in Lu, Turner, Mathews [NAR, 2006. 34: 4912].  These files are similar to those use for free energy change, but are terminated with .dh.

DNA-DNA parameters are used if the DNA option is selected in oligo walk or if DNA is folded.  The DNA files are analogous to the RNA files, but the file names start with the letters dna.  

If the DNA option is selected in OligoWalk or OligoScreen, DNA-RNA parameters are used.  These are contained in stackdr.dat and are derived from Sugimoto, Nakano, Katoh,Matsumura, Nakamuta, Ohmichi, Yoneyama, and Sasaki [Biochemistry. 1995. 34: 11211].
  