/* Calculate the melting temperature of oligo s. See
oligotm.h for documentation of arguments.
*/
double
oligotm(const char *s,
double DNA_nM,
double K_mM,
double divalent_conc,
double dntp_conc,
tm_method_type tm_method,
salt_correction_type salt_corrections)
{
register int dh = 0, ds = 0;
register char c;
double delta_H, delta_S;
double Tm; /* Melting temperature */
double correction;
int len, sym;
const char* d = s;
if(divalent_to_monovalent(divalent_conc, dntp_conc) == OLIGOTM_ERROR)
return OLIGOTM_ERROR;
/** K_mM = K_mM + divalent_to_monovalent(divalent_conc, dntp_conc); **/
if (tm_method != breslauer_auto
&& tm_method != santalucia_auto)
return OLIGOTM_ERROR;
if (salt_corrections != schildkraut
&& salt_corrections != santalucia
&& salt_corrections != owczarzy)
return OLIGOTM_ERROR;
len = (strlen(s)-1);
sym = symmetry(s); /*Add symmetry correction if seq is symmetrical*/
if( tm_method == breslauer_auto ) {
ds=108;
}
else {
if(sym == 1) {
ds+=14;
}
/** Terminal AT penalty **/
if(strncmp("A", s, 1)==0
|| strncmp("T", s, 1)==0) {
ds += -41;
dh += -23;
} else if (strncmp("C", s, 1)==0
|| strncmp("G", s, 1)==0) {
ds += 28;
dh += -1;
}
s+=len;
if(strncmp("T", s, 1)==0
|| strncmp("A", s, 1)==0) {
ds += -41;
dh += -23;
} else if (strncmp("C", s, 1)==0
|| strncmp("G", s, 1)==0) {
ds += 28;
dh += -1;
}
s-=len;
}
/* Use a finite-state machine (DFA) to calucluate dh and ds for s. */
c = *s; s++;
if (tm_method == breslauer_auto) {
if (c == 'A') goto A_STATE;
else if (c == 'G') goto G_STATE;
else if (c == 'T') goto T_STATE;
else if (c == 'C') goto C_STATE;
else if (c == 'N') goto N_STATE;
else goto ERROR;
STATE(A);
STATE(T);
STATE(G);
STATE(C);
STATE(N);
} else {
if (c == 'A') goto A_STATE2;
else if (c == 'G') goto G_STATE2;
else if (c == 'T') goto T_STATE2;
else if (c == 'C') goto C_STATE2;
else if (c == 'N') goto N_STATE2;
else goto ERROR;
STATE2(A);
STATE2(T);
STATE2(G);
STATE2(C);
STATE2(N);
}
DONE: /* dh and ds are now computed for the given sequence. */
delta_H = dh * -100.0; /*
* Nearest-neighbor thermodynamic values for dh
* are given in 100 cal/mol of interaction.
*/
delta_S = ds * -0.1; /*
* Nearest-neighbor thermodynamic values for ds
* are in in .1 cal/K per mol of interaction.
*/
Tm=0; /* Melting temperature */
len=len+1;
/**********************************************/
if (salt_corrections == schildkraut) {
K_mM = K_mM + divalent_to_monovalent(divalent_conc, dntp_conc);
correction = 16.6 * log10(K_mM/1000.0) - T_KELVIN;
Tm = delta_H / (delta_S + 1.987 * log(DNA_nM/4000000000.0)) + correction;
} else if (salt_corrections== santalucia) {
K_mM = K_mM + divalent_to_monovalent(divalent_conc, dntp_conc);
delta_S = delta_S + 0.368 * (len - 1) * log(K_mM / 1000.0 );
if(sym == 1) { /* primer is symmetrical */
/* Equation A */
Tm = delta_H / (delta_S + 1.987 * log(DNA_nM/1000000000.0)) - T_KELVIN;
} else {
/* Equation B */
Tm = delta_H / (delta_S + 1.987 * log(DNA_nM/4000000000.0)) - T_KELVIN;
}
} else if (salt_corrections == owczarzy) {
double gcPercent=0;
double free_divalent; /* conc of divalent cations minus dNTP conc */
int i;
for(i = 0; i <= len && d != NULL && d != '\0';) {
if(*d == 'C' || *d == 'G') {
gcPercent++;
}
d++;
i++;
}
gcPercent = (double)gcPercent/((double)len);
/**** BEGIN: UPDATED SALT BY OWCZARZY *****/
/* different salt corrections for monovalent (Owczarzy et al.,2004)
and divalent cations (Owczarzy et al.,2008)
*/
/* competition bw magnesium and monovalent cations, see Owczarzy et al., 2008 Figure 9 and Equation 16 */
static const double crossover_point = 0.22; /* depending on the value of div_monov_ratio respect
to value of crossover_point Eq 16 (divalent corr, Owczarzy et al., 2008)
or Eq 22 (monovalent corr, Owczarzy et al., 2004) should be used */
double div_monov_ratio;
if(dntp_conc >= divalent_conc) {
free_divalent = 0.00000000001; /* to not to get log(0) */
} else {
free_divalent = (divalent_conc - dntp_conc)/1000.0;
}
static double a = 0,b = 0,c = 0,d = 0,e = 0,f = 0,g = 0;
if(K_mM==0) {
div_monov_ratio = 6.0;
} else {
div_monov_ratio = (sqrt(free_divalent))/(K_mM/1000); /* if conc of monov cations is provided
a ratio is calculated to further calculate
the _correct_ correction */
}
if (div_monov_ratio < crossover_point) {
/* use only monovalent salt correction, Eq 22 (Owczarzy et al., 2004) */
correction
= (((4.29 * gcPercent) - 3.95) * Pow(10,-5) * log(K_mM / 1000.0))
+ (9.40 * Pow(10, -6) * (pow(log(K_mM / 1000.0), 2)));
} else {
/* magnesium effects are dominant, Eq 16 (Owczarzy et al., 2008) is used */
b = -9.11 * Pow(10, -6);
c = 6.26 * Pow(10, -5);
e = -4.82 * Pow(10, -4);
f = 5.25 * Pow(10, -4);
a = 3.92 * Pow(10, -5);
d = 1.42 * Pow(10, -5);
g = 8.31 * Pow(10, -5);
if(div_monov_ratio < 6.0) {
/* in particular ratio of conc of monov and div cations
* some parameters of Eq 16 must be corrected (a,d,g) */
a = 3.92 * Pow(10, -5) * (0.843 - (0.352 * sqrt(K_mM / 1000.0) * log(K_mM / 1000.0)));
d = 1.42 * Pow(10, -5) * (1.279 - 4.03 * Pow(10, -3) * log(K_mM / 1000.0) - 8.03 * Pow(10, -3) * pow(log(K_mM / 1000.0), 2));
g = 8.31 * Pow(10, -5) * (0.486 - 0.258 * log(K_mM / 1000.0) + 5.25 * Pow(10, -3) * pow(log(K_mM / 1000.0), 3));
}
correction = a + (b * log(free_divalent))
+ gcPercent * (c + (d * log(free_divalent)))
+ (1/(2 * (len - 1))) * (e + (f * log(free_divalent))
+ g * (pow((log(free_divalent)),2)));
}
/**** END: UPDATED SALT BY OWCZARZY *****/
if (sym == 1) {
/* primer is symmetrical */
/* Equation A */
Tm = 1/((1/(delta_H
/
(delta_S + 1.9872 * log(DNA_nM/1000000000.0)))) + correction) - T_KELVIN;
} else {
/* Equation B */
Tm = 1/((1/(delta_H
/
(delta_S + 1.9872 * log(DNA_nM/4000000000.0)))) + correction) - T_KELVIN;
}
} /* END else if (salt_corrections == owczarzy) { */
/***************************************/
return Tm;
ERROR: /*
* length of s was less than 2 or there was an illegal character in
* s.
*/
return OLIGOTM_ERROR;
}
double
oligodg(const char *s, /* The sequence. */
int tm_method)
{
register int dg = 0;
register char c;
if (tm_method != breslauer_auto
&& tm_method != santalucia_auto)
return OLIGOTM_ERROR;
/* Use a finite-state machine (DFA) to calucluate dg s. */
c = *s; s++;
if(tm_method != breslauer_auto) {
dg=-1960; /* Initial dG */
if(c == 'A' || c == 'T') {
dg += -50; /* terminal AT penalty */
}
if (c == 'A') goto A_STATE2;
else if (c == 'G') goto G_STATE2;
else if (c == 'T') goto T_STATE2;
else if (c == 'C') goto C_STATE2;
else if (c == 'N') goto N_STATE2;
else goto ERROR;
STATE2(A);
STATE2(T);
STATE2(G);
STATE2(C);
STATE2(N);
} else {
if (c == 'A') goto A_STATE;
else if (c == 'G') goto G_STATE;
else if (c == 'T') goto T_STATE;
else if (c == 'C') goto C_STATE;
else if (c == 'N') goto N_STATE;
else goto ERROR;
STATE(A);
STATE(T);
STATE(G);
STATE(C);
STATE(N);
}
DONE: /* dg is now computed for the given sequence. */
if(tm_method != breslauer_auto) {
int sym;
--s; --s; c = *s;
if(c == 'A' || c == 'T') {
dg += -50; /* terminal AT penalty */
}
sym = symmetry(s);
if(sym==1) {
dg +=-430; /* symmetry correction for dG */
}
}
return dg / 1000.0;
ERROR: /*
* length of s was less than 2 or there was an illegal character in
* s.
*/
return OLIGOTM_ERROR;
}
/* Calculate the melting temperature of oligo s. See
oligotm.h for documentation of arguments.
*/
double
oligotm(const char *s,
double DNA_nM,
double K_mM,
double divalent_conc,
double dntp_conc,
tm_method_type tm_method,
salt_correction_type salt_corrections)
{
register int dh = 0, ds = 0;
register char c;
double delta_H, delta_S;
double Tm; /* Melting temperature */
double correction;
int len, sym;
const char* d = s;
if(divalent_to_monovalent(divalent_conc, dntp_conc) == OLIGOTM_ERROR)
return OLIGOTM_ERROR;
K_mM = K_mM + divalent_to_monovalent(divalent_conc, dntp_conc);
if (tm_method != breslauer_auto
&& tm_method != santalucia_auto)
return OLIGOTM_ERROR;
if (salt_corrections != schildkraut
&& salt_corrections != santalucia
&& salt_corrections != owczarzy)
return OLIGOTM_ERROR;
len = (strlen(s)-1);
sym = symmetry(s); /*Add symmetry correction if seq is symmetrical*/
if( tm_method == breslauer_auto ) {
ds=108;
}
else {
if(sym == 1) {
ds+=14;
}
/** Terminal AT penalty **/
if(strncmp("A", s, 1)==0
|| strncmp("T", s, 1)==0) {
ds += -41;
dh += -23;
} else if (strncmp("C", s, 1)==0
|| strncmp("G", s, 1)==0) {
ds += 28;
dh += -1;
}
s+=len;
if(strncmp("T", s, 1)==0
|| strncmp("A", s, 1)==0) {
ds += -41;
dh += -23;
} else if (strncmp("C", s, 1)==0
|| strncmp("G", s, 1)==0) {
ds += 28;
dh += -1;
}
s-=len;
}
/* Use a finite-state machine (DFA) to calucluate dh and ds for s. */
c = *s; s++;
if (tm_method == breslauer_auto) {
if (c == 'A') goto A_STATE;
else if (c == 'G') goto G_STATE;
else if (c == 'T') goto T_STATE;
else if (c == 'C') goto C_STATE;
else if (c == 'N') goto N_STATE;
else goto ERROR;
STATE(A);
STATE(T);
STATE(G);
STATE(C);
STATE(N);
} else {
if (c == 'A') goto A_STATE2;
else if (c == 'G') goto G_STATE2;
else if (c == 'T') goto T_STATE2;
else if (c == 'C') goto C_STATE2;
else if (c == 'N') goto N_STATE2;
else goto ERROR;
STATE2(A);
STATE2(T);
STATE2(G);
STATE2(C);
STATE2(N);
}
DONE: /* dh and ds are now computed for the given sequence. */
delta_H = dh * -100.0; /*
* Nearest-neighbor thermodynamic values for dh
* are given in 100 cal/mol of interaction.
*/
delta_S = ds * -0.1; /*
* Nearest-neighbor thermodynamic values for ds
* are in in .1 cal/K per mol of interaction.
*/
Tm=0; /* Melting temperature */
len=len+1;
if (salt_corrections == schildkraut) {
double correction=- 273.15 + 16.6 * log10(K_mM/1000.0);
Tm = delta_H / (delta_S + 1.987 * log(DNA_nM/4000000000.0)) + correction;
} else if (salt_corrections== santalucia) {
delta_S = delta_S + 0.368 * (len - 1) * log(K_mM / 1000.0 );
if(sym == 1) { /* primer is symmetrical */
/* Equation A */
Tm = delta_H / (delta_S + 1.987 * log(DNA_nM/1000000000.0)) - 273.15;
} else {
/* Equation B */
Tm = delta_H / (delta_S + 1.987 * log(DNA_nM/4000000000.0)) - 273.15;
}
} else if (salt_corrections == owczarzy) {
double gcPercent=0;
int i;
for(i=0; i<=len && d != NULL && d != '\0';) {
if(*d == 'C' || *d == 'G') {
gcPercent++;
}
d++;
i++;
}
gcPercent = (double)gcPercent/((double)len);
/* double */ correction
= (((4.29 * gcPercent) - 3.95) * pow(10,-5) * log(K_mM / 1000.0))
+ (9.40 * pow(10,-6) * (pow(log(K_mM / 1000.0),2)));
if (sym == 1) { /* primer is symmetrical */
/* Equation A */
Tm
= (1/((1/(delta_H
/
(delta_S + 1.9872 * log(DNA_nM/1000000000.0)))) + correction))
- 273.15;
} else {
/* Equation B */
Tm
= (1/((1/(delta_H
/
(delta_S + 1.9872 * log(DNA_nM/4000000000.0)))) + correction))
- 273.15;
}
}
return Tm;
ERROR: /*
* length of s was less than 2 or there was an illegal character in
* s.
*/
return OLIGOTM_ERROR;
}
