Executable Code

File name: tables.c

/* Thermodynamic parameters of formation of doublets, 5' to 3'.
   To use these, add them up for each doublet along the sequence.
   A sequence of n nucleotides has n-1 doublets.
 
   Then, add the parameters for helix initiation: 
         DHi = 0
         DSi = -.01677. (derived from Breslauer et. al. '86.)
 
   */
 
/* Enthalpies from Breslauer et. al. '86.
   Average = -8.07 kcal/mol.
   */
 
double doublet_enthalpy[4][4] = {        /* In kcal/mol */
  /*                               */
  /* 1st           2nd base        */
  /* base                          */
  /*          A     C     T     G  */
  /*        ----  ----  ----  ---- */
  {/* A */  -9.1, -6.5, -8.6, -7.8 },
  {/* C */  -5.8,-11.0, -7.8,-11.9 },
  {/* T */  -6.0, -5.6, -9.1, -5.8 },
  {/* G */  -5.6,-11.1, -6.5,-11.0 },
};
 
/* Entropies due to Quartin & Wetmur '89,
   printed in Tijssen '93.
   Average = -.02177 kcal/(mol*kelvin)
   */
 
double doublet_entropy[4][4] = {             /* In kcal/(mol*K) */
  /*                                        */
  /* 1st (5')          2nd (3') base        */
  /* base                                   */
  /*           A       C       T       G    */
  /*        ------  ------  ------  ------  */
  {/* A */  -.02532,-.01710,-.02465,-.02130 },
  {/* C */  -.01560,-.02918,-.02130,-.02968 },
  {/* T */  -.01727,-.01492,-.02532,-.01560 },
  {/* G */  -.01492,-.02817,-.01710,-.02918 },
};
 
/* Average DG0 at 25C = -1.58
                  55C = -0.93
                  72C = -0.55
                  98C = -0.01
 
                  */
 
 
/*
   Thermodynamic parameters of introduction of mismatched base pairs.
   These are from Werntges et. al. '86 except that since we don't know
   the next-nearest-neighbor environments we are averaging the figures
   for X*Y and Y*X.  We will extrapolate to nearest-neighbor
   environments other than TXA*TYA by subtracting (TX*X'A + TY'*YA +
   XA*TX' + Y'A*TY)/2 and adding the corresponding thing for the new
   environment.
 
   These values are overall much more iffy and approximate than the
   matched-base values above.
 
   */
 
#define NA 0 /* Not applicable; Watson-Crick base pair. */
 
double mismatch_enthalpy[4][4] = {
  /*                                       */
  /* 1st           2nd base                */
  /* base                                  */
  /*           A       C       T      G    */
  /*        ------  ------  ------  ------ */
  {/* A */  -13.29, -10.12,     NA, -10.71 },
  {/* C */  -10.12,      0,      0,     NA },
  {/* T */      NA,      0,      0, -10.92 },
  {/* G */  -10.71,     NA, -10.92, -13.62 },
};
 
/* Avg enthalpy = -7.53 */
 
double mismatch_entropy[4][4] = {
  /*                                       */
  /* 1st           2nd base                */
  /* base                                  */
  /*           A       C       T       G   */
  /*        ------  ------  ------  ------ */
  {/* A */  -.0497, -.0407,     NA, -.0401 },
  {/* C */  -.0407, -.0108, -.0079,     NA },
  {/* T */      NA, -.0079, -.0074, -.0387 },
  {/* G */  -.0401,     NA, -.0387, -.0497 },
};
 
/* Avg entropy = -.0310 */
 
/* Avg DG0 at 25C = 1.71
           at 55C = 2.64 */