MELTING - nearest-neighbor computation of nucleic acid hybridation
Marine Dumousseau, William John Gowers
Nicolas Le Novère
n.lenovere@gmail.com
Date: February 2014
The nearest-neighbor approach is based on the fact that the helix-coil
transition works as a zipper. After an initial attachment, the hybridisation
propagates laterally.
The hybridization process depends on the adjacent nucleotides on each strand (the Crick's pairs).
Two duplexes with the same base pairs could have different stabilities, and on the contrary, two
duplexes with different sequences but identical sets of Crick's pairs will have the same
thermodynamics properties (see Sugimoto et al. 1994).
See Wetmur J.G (1991) and Santalucia (1998) for deep reviews on the nucleic acid hybridization
and on the different set of nearest-neighbor parameters.
MELTING computes, for a nucleic acid duplex, the enthalpy and the
entropy of the helix-coil transition, and then its melting temperature. Four
types of hybridisation are possible: DNA/DNA, DNA/RNA, RNA/RNA and 2-O-Methyl RNA/RNA. The program
uses the method of nearest-neighbors. The set of thermodynamic parameters can be
easely changed, for instance following an experimental breakthrough. Melting is
a free program in both sense of the term. It comes with no cost and it is
open-source. In addition it is coded in Java (1.5) and can be compiled on any
operating system.
If you use MELTING, please quote
Le Novère. MELTING, a free tool to compute the
melting temperature of nucleic acid duplex. Bioinformatics, 17: 1226-1227.
Dumousseau M, Rodriguez N, Juty N, Le Novère N. MELTING, a flexible platform to predict the melting temperatures
of nucleic acids. BMC Bioinformatics, 16;13:101, PMID: 22591039.
The options are treated sequentially. If there is a conflict between the value
of two options, the latter normally erases the former.
BE AWARE : The option syntax of MELTING 5 is different from the one of MELTING 4. There
is a space between the option name and the option value. New option names are available
in MELTING 5 to change the default thermodynamic models and default corrections.
There is no interactive mode in MELTING 5 therefore the option '-q' doesn't exist anymore.
You can use the MELTING 4 option syntax, but it doesn't allow the user to change some of
the thermodynamic models and corrections. In addition to that, the user can't enter a formamide or DMSO See the README file to choose the adapted executable.
The MELTING 4 option name '-x' is equivalent to the MELTING 5 option name '-am'.
There is no input file option in MELTING 5 (option '-I') but you can use this option for the compatible executable
of MELTING 5.
The MELTING 4 option names '-N', '-t', '-k', 'G' are replaced by the single option '-E' in MELTING 5.
The MELTING 4 option names '-A', '-D', '-M' are respectively equivalent to '-nn', '-sinDE', '-sinMM' in MELTING 5.
The file names to write with the precedent option are replaced by thermodynamic model names (see below).
The MELTING 4 option name '-K' is replaced by '-ion' in MELTING 5.
- -h
-
Displays a short help and quit.
- -L
-
Prints the legal informations and quit.
- -V
-
Displays the version number and quit.
- -p
-
Return the directory supposed to contain the sets of calorimetric parameters and quit.
If the environment variable NN_PATH is set, it is returned. Otherwise, the value
defined by default during the compilation is returned.
- -S sequence
-
Sequence of one strand of the nucleic
acid duplex, entered 5' to 3'. Important:
Uridine and thymidine are not considered as identical. The bases can be upper or lowercase.
- -C complementary_sequence
-
Enters the complementary sequence, from 3' to 5'. This option is mandatory if
there are mismatches, inosine(s) or hydroxyadenine(s) between the two strands. If it is not used, the program
will compute it as the complement of the sequence entered with the option -S. In case of self complementary sequences,
The program can automatically detect the symmetry and deduce the complementary even though there is (are) dangling
end(s) and it is not necessary to write the complementary sequence with the option -C.
Uridine and thymidine are not considered as identical. The bases can be upper or lowercase.
- -E ion1_name=x.xxe-xx:ion2_name=x.xxe-xx:agent1_name=x.xxe-xx...
-
Enters the different ion (Na, Mg, Tris, K) or agent (dNTP, DMSO, formamide) concentrations. The effect
of ions and denaturing agents on thermodynamic stability of nucleic acid duplexes is complex,
and the correcting functions are at best rough approximations. All the concentrations must be positive numeric
values and in M. There are some exceptions for the DMSO concentrations (in
%) and the formamide concentrations
(in % or M depending on the used correction method). Be aware, the
Tris
is about half of the total tris buffer
concentration.
At least one cation concentration is mandatory, the other agents are optional. See the documentation for the concentration
limits. It depends on the used correction.
- -P x.xxe-xx
-
Concentration of the nucleic acid strand in excess. It must be a strict positive numeric value and it is mandatory. The oligomer
concentration is in mol/L.
- -H hybridisation_type
-
Specifies the hybridisation type. Moreover this parameter determines the nature of the sequences entered by the user.
Possible values are :
- dnadna
- : DNA sequence (option -S) and DNA complementary sequence (option -C)
- rnarna
- : RNA sequence (option -S) and RNA complementary sequence (option -C)
- dnarna
- : DNA sequence (option -S) and RNA complementary sequence (option -C)
- rnadna
- : RNA sequence (option -S) and DNA complementary sequence (option -C)
- mrnarna
- : 2-o-methyl RNA sequence (option -S) and RNA complementary sequence (option -C)
- mrnarna
- : RNA sequence (option -S) and 2-o-methyl RNA complementary sequence (option -C)
This option is mandatory to select the default equations and methods to use.
- -T xxx
-
Size threshold before approximative computation. The nearest-neighbour approach
will be used by default if the length of the sequence is inferior to this threshold,
otherwise it is the approximative approach which will be used by default.
- -v
-
Activates the verbose mode, issuing a lot more information about the current run (try it once
to see if you can get something interesting).
- -nnpath folder_pathway
-
Change the default pathway (Data) where to find the default calorimetric tables (thermodynamic parameters).
The program will look for the file in a directory specified during the installation.
However, if an environment variable NN_PATH is defined, melting will search in this one first.
- -O output_file
-
The output is directed to this file instead of the standard output. The name of the file must be specified.
- -self
-
To precise that the sequence entered with the option -S is self complementary. No complementary sequence is mandatory.
The program automatically can detect a self complementary sequence for perfect matching sequences or sequences with dangling ends.
In these cases, the option -self is not necessary. Otherwise we need to precise that the sequences are self complementary with this option.
examples:
Situation 1 : The sequence ATCGCGAT is self
complementary.
The option -self is not necessary because the program can automatically detect it.
Situation 2 : The sequence -TCGCGAT is self
complementary with a single
dangling end.
The option -self is not necessary because the program
can automatically detect it.
Situation 3 : If the sequence ATCCCGAT is self
complementary with a single mismatch
(C/C)
The option -self is necessary to precise the self
complementarity because the program can't detect it.
- -F factor
-
This is the correction factor used to modulate the effect of the nucleic acid concentration in the computation of the melting temperature.
See section ALGORITHM for details. If the sequences are automatically recognized as self complementary sequences or if the option -self
is used, the factor correction is automatically 1. Otherwise F is 4 if the both strands are present in equivalent amount and 1 if one strand is in excess.
The default factor value is 4.
By default, the approximative mode is used for oligonucleotides longer than 60 bases (the default threshold value), otherwise the nearest
neighbor model is used.
- -am method_name
-
Forces to use a specific approximative formula, based on G+C content. You can use one of the following :
DNA DUPLEXES
- ahs01
- (from von Ahsen et al. 2001)
- che93
- (from Marmur 1962,, Chester and al. 1993)
- che93corr
- (from von Ahsen et al. 2001, Marmur 1962, Chester and al. 1993)
- schdot
- (Marmur-Schildkraut-Doty formula)
- owe69
- (from Owen et al. 1969)
- san98
- (from Allawi and Santalucia. 1998)
- wetdna91
- (from Wetmur 1991) (by default)
RNA DUPLEXES
- wetrna91
- (from Wetmur 1991) (by default)
DNA/RNA DUPLEXES
- wetdnarna91
- (from Wetmur 1991) (by default)
If there is no formula name after the option -am, we will compute the melting temperature with the default approximative formula.
This option has to be used with caution. Note that such a calcul is increasingly incorrect when the length of the duplex
decreases. Moreover, it does not take into account nucleic acid concentration, which is a strong mistake.
examples :
command line 1 : "-am"
if you want to force the approximative approach with the
default formula.
command line 2 : "-am ahs01"
if you want to use the approximative formula from
Ahsen et al. 2001.
- -nn method_name
-
Forces to use a specific nearest neighbor model. You can use one of the following :
DNA DUPLEXES
- all97
- (from Allawi and Santalucia 1997) (by default)
- bre86
- (from Breslauer et al. 1986)
- san04
- (from Hicks and Santalucia 2004)
- san96
- (from Santalucia et al. 1996)
- sug96
- (from Sugimoto et al 1996)
- tan04
- (from Tanaka et al. 2004)
RNA DUPLEXES
- fre86
- (from Freier al. 1986)
- xia98
- (from Xia et al. 1998) (by default)
DNA/RNA DUPLEXES
- sug95
- (from Sugimoto et al. 1995) (by default)
MRNA/RNA DUPLEXES
- tur06
- (from Kierzek et al. 2006) (by default)
If there is no formula name after the option -nn, we will compute the melting temperature with the default nearest neighbor model.
Each nearest neighbor model uses a specific xml file containing the thermodynamic values. If you want to use another file, write the file name or the file pathway preceded by ':' (-nn [optionalname:optionalfile]).
examples:
Command line 1 : "-nn"
if you want to force the nearest neighbor computation with the default model.
Command line 2 : "-nn tan04"
if you want to use the nearest neighbor model from Tanaka et al. 2004 with the
thermodynamic parameters in the default xml file.
Command line 3 : "-nn tan04:fileName"
if you want to use the nearest neighbor model from Tanaka et al. 2004 with the
thermodynamic parameters in the file fileName.
Command line 4 : "-nn :fileName"
if you want to use the default nearest neighbor model with the thermodynamic parameters in the file fileName.
- -sinMM method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of single mismatch to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- allsanpey
- (from Allawi, Santalucia and Peyret 1997, 1998 and 1999) (by default)
DNA/RNA DUPLEXES
- wat10
- (from Watkins et al. 2011) (by default)
RNA DUPLEXES
- tur06
- (from Lu et al. 2006)
- zno07
- (from Davis et al. 2007) (by default)
- zno08
- (from Davis et al. 2008)
To change the file containing the thermodynamic parameters for single mismatch computation, the same syntax as the one for the -nn option is used.
Single mismatches are not taken into account by the approximative mode.
- -GU method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of GU base pairs to the thermodynamic of helix-coil transition.
You can use one of the following :
RNA DUPLEXES
- tur99
- (from Mathews et al. 1999)
- ser12
- (from Serra et al. 2012) (by default)
To change the file containing the thermodynamic parameters for GU base pair computation, the same syntax as the one for the -nn option is used.
GU base pairs are not taken into account by the approximative mode.
- -tanMM method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of tandem mismatches to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- allsanpey
- (from Allawi, Santalucia and Peyret 1997, 1998 and 1999) (by default)
RNA DUPLEXES
- tur99
- (from Mathews et al. 1999) (by default)
To change the file containing the thermodynamic parameters for tandem mismatch computation, the same syntax as the one for the -nn option is used.
Tandem mismatches are not taken into account by the approximative mode. Note that not all the mismatched Crick's pairs have been investigated.
- -intLP method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of internal loop to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- san04
- (from Hicks and Santalucia 2004) (by default)
RNA DUPLEXES
- tur06
- (from Lu et al. 2006) (by default)
- zno07
- (from Badhwar et al. 2007, only for 1x2 loop)
To change the file containing the thermodynamic parameters for internal loop computation, the same syntax as the one for the -nn option is used.
Internal loops are not taken into account by the approximative mode.
- -sinDE method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of single dangling end to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- bom00
- (from Bommarito et al. 2000) (by default)
- sugdna02
- (from Ohmichi et al. 2002, only for polyA dangling ends)
RNA DUPLEXES
- sugrna02
- (from Ohmichi et al. 2002, only for polyA dangling ends)
- ser08
- (from Miller et al. 2008) (by default)
To change the file containing the thermodynamic parameters for single dangling end computation, the same syntax as the one for the -nn option is used.
Single dangling ends are not taken into account by the approximative mode.
- -secDE method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of double dangling end to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- sugdna02
- (from Ohmichi et al. 2002, only for polyA dangling ends) (by default)
RNA DUPLEXES
- sugrna02
- (from Ohmichi et al. 2002, only for polyA dangling ends)
- ser05
- (from O'toole et al. 2005)
- ser06
- (from O'toole et al. 2006) (by default)
To change the file containing the thermodynamic parameters for double dangling end computation, the same syntax as the one for the -nn option is used.
Double dangling ends are not taken into account by the approximative mode.
- -longDE method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of long dangling end to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- sugdna02
- (from Ohmichi et al. 2002, only for polyA dangling ends) (by default)
RNA DUPLEXES
- sugrna02
- (from Ohmichi et al. 2002, only for polyA dangling ends)
To change the file containing the thermodynamic parameters for long dangling end computation, the same syntax as the one for the -nn option is used.
Long dangling ends are not taken into account by the approximative mode.
- -sinBU method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of single bulge loop to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- san04
- (from Santalucia 2004)
- tan04
- (from Tanaka et al. 2004) (by default)
RNA DUPLEXES
- ser07
- (from Blose et al. 2007)
- tur06
- (from Lu et al. 1999 and 2006) (by default)
To change the file containing the thermodynamic parameters for single bulge loop computation, the same syntax as the one for the -nn option is used.
Single bulge loops are not taken into account by the approximative mode.
- -lonBU method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of long bulge loop to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- san04
- (from Hicks and Santalucia 2004) (by default)
RNA DUPLEXES
- tur06
- (from Mathews et al. 1999 and Lu et al 2006) (by default)
To change the file containing the thermodynamic parameters for long bulge loop computation, the same syntax as the one for the -nn option is used.
Long bulge loops are not taken into account by the approximative mode.
- -CNG method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of CNG repeats to the thermodynamic of helix-coil transition.
N represents a single mismatch of type N/N.
You can use one of the following :
RNA DUPLEXES
- bro05
- (from Magdalena et al. 2005) (by default)
To change the file containing the thermodynamic parameters for CNG repeats computation, the same syntax as the one for the -nn option is used.
CNG repeats are not taken into account by the approximative mode.
Be aware : Melting can compute the contribution of CNG repeats to the thermodynamic of helix-coil transition for only 2 to 7 CNG repeats.
- -ino method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of inosine bases (I) to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- san05
- (from Watkins and Santalucia 2005) (by default)
RNA DUPLEXES
- zno07
- (from Wright et al. 2007, only IU base pairs) (by default)
To change the file containing the thermodynamic parameters for inosine bases computation, the same syntax as the one for the -nn option is used.
Inosine bases (I) are not taken into account by the approximative mode.
- -ha method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of hydroxyadenine bases (A*) to the thermodynamic of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- sug01
- (from Kawakami et al. 2001) (by default)
To change the file containing the thermodynamic parameters for hydroxyadenine bases computation, the same syntax as the one for the -nn option is used.
Hydroxyadenine bases (A*) are not taken into account by the approximative mode.
- -azo method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of azobenzenes (X_T for trans azobenzenes and X_C for cis azobenzenes) to the thermodynamic
of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- asa05
- (from Asanuma et al. 2005)(by default)
To change the file containing the thermodynamic parameters for azobenzene computation, the same syntax as the one for the -nn option is used.
Azobenzenes (X_T for trans azobenzenes and X_C for cis azobenzenes) are not taken into account by the approximative mode.
- -lck method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of single locked nucleic acids (AL, GL, TL and CL) to the thermodynamic
of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- mct04
- (from McTigue et al. 2004)
- owc11
- (from Owczarzy et al. 2011) (by default)
To change the file containing the thermodynamic parameters for single locked nucleic acids computation, the same syntax as the one for the -nn option is used.
Locked nucleic acids (AL, GL, TL and CL) are not taken into account by the approximative mode.
- -tanLck method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of consecutive locked nucleic acids (AL, GL, TL and CL) to the thermodynamic
of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- owc11
- (from Owczarzy et al. 2011) (by default)
To change the file containing the thermodynamic parameters for consecutive locked nucleic acids computation, the same syntax as the one for the -nn option is used.
Locked nucleic acids (AL, GL, TL and CL) are not taken into account by the approximative mode.
- -sinMMLck method_name
-
Forces to use a specific nearest neighbor model to compute the contribution of single mismatch in consecutive locked nucleic acids (AL, GL, TL and CL) to the thermodynamic
of helix-coil transition.
You can use one of the following :
DNA DUPLEXES
- owc11
- (from Owczarzy et al. 2011) (by default)
To change the file containing the thermodynamic parameters for single mismatch in consecutive locked nucleic acids computation, the same syntax as the one for the -nn option is used.
Locked nucleic acids (AL, GL, TL and CL) are not taken into account by the approximative mode.
- -ion method_name
-
Forces to use a specific ion correction. You can use one of the following corrections :
Sodium corrections
DNA DUPLEXES
- ahs01
- (from von Ahsen et al. 2001)
- kam71
- (from Frank-Kamenetskii 2001)
- owc1904
- (equation 19 from Owczarzy et al. 2004)
- owc2004
- (equation 20 from Owczarzy et al. 2004)
- owc2104
- (equation 21 from Owczarzy et al. 2004)
- owc2204
- (equation 21 from Owczarzy et al. 2004) (by default)
- san96
- (from Santalucia et al. 1996)
- san04
- (from Santalucia et al. 1998, 2004)
- schlif
- (from Schildkraut and Lifson 1965)
- tanna06
- (from Tan et al. 2006)
- wetdna91
- (from wetmur 1991)
RNA DUPLEXES OR MRNA/RNA DUPLEXES
- tanna07
- (from Tan et al. 2007) (by default)
- wetrna91
- (from wetmur 1991)
DNA/RNA DUPLEXES
- wetdnarna91
- (from wetmur 1991)
Magnesium corrections
DNA DUPLEXES
- owcmg08
- (from Owczarzy et al. 2008) (by default)
- tanmg06
- (from Tan et al. 2006)
RNA DUPLEXES OR MRNA/RNA DUPLEXES
- tanmg07
- (from Tan et al. 2007) (by default)
Mixed Na Mg corrections
DNA DUPLEXES
- owcmix08
- (from Owczarzy et al. 2008) (by default)
- tanmix07
- (from Tan et al. 2007)
RNA DUPLEXES OR MRNA/RNA DUPLEXES
- tanmix07
- (from Tan et al. 2007) (by default)
The effect of ions on thermodynamic stability of nucleic acid duplexes is complex, and the correcting
functions are at best rough approximations.
By default, the program use the algorithm from Owczarzy et al 2008 : ratio =
Mg
and monovalent = Na + Tris + K
if monovalent = 0, a magnesium correction is used.
if ratio < 0.22, a sodium correction is used.
if 0.22 <= ratio < 6, a mixed Na Mg correction is used.
if ratio >= 6, a magnesium correction is used.
example :
Command line : "-ion owcmg08"
if you want to force the use of the magnesium correction from Owczarzy et al 2008. This correction will be used
independently of the cations present in the solution.
- -naeq method_name
-
Forces to use a specific ion correction which gives a sodium equivalent concentration if other cations are present.
You can use one of the following :
DNA DUPLEXES
- ahs01
- (from von Ahsen et al 2001) (by default)
- mit96
- (from Mitsuhashi et al. 1996)
- pey00
- (from Peyret 2000)
For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.
If there are other cations when an approximative approach is used, a sodium equivalence is automatically computed.
The correcting functions are at best rough approximations.
example :
Command line 1 : "-naeq ahs01"
if you want to force the use of the sodium equivalence from Ahsen et al 2001. This sodium equivalence
will be used in case of approximative approach. In case of nearest neighbor approach, the sodium equivalence
will be used only if a sodium correction is selected by the user.
Command line 2 : "-naeq ahs01 -ion san04"
it means that the sodium equivalence computed by the method ahs01 (from Ahsen et al 2001) will be combined with the
sodium correction san04 (from Santalucia 2004).
- -DMSO method_name
-
Forces to use a specific DMSO correction (DMSO is always in %).
You can use one of the following :
DNA DUPLEXES
- ahs01
- (from von Ahsen et al 2001) (by default)
- mus81
- (from Musielski et al. 1981)
- cul76
- (from Cullen et al. 1976)
- esc80
- (from Escara et al. 1980)
For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.
If there are DMSO when an approximative approach is used, a DMSO correction is automatically computed.
The correcting functions are at best rough approximations.
example :
Command line : "-DMSO ahs01"
if you want to force the use of the DMSO correction from Ahsen et al 2001. This DMSO correction will be used if there is
DMSO present in the solutions in case of nearest neighbor approach and approximative approach.
- -for method_name
-
Forces to use a specific formamide correction.
You can use one of the following :
DNA DUPLEXES
- bla96
- (from Blake 1996) with formamide concentration in mol/L (by default)
- lincorr
- (linear correction) with a % of formamide volume
For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.
If there are formamide when an approximative approach is used, a formamide correction is automatically computed.
The correcting functions are at best rough approximations.
example :
Command line : "-for lincorr"
if you want to force the use of the linear formamide correction. This formamide correction will be used if there is formamide
present in the solutions in case of nearest neighbor approach and approximative approach.
The nearest-neighbor approach is based on the fact that the helix-coil
transition works as a zipper. After an initial attachment, the hybridisation
propagates laterally. This program first computes the hybridisation enthalpy
and entropy for each structure in the duplex. (see later for the different possible
structures recognized by Melting). If the sequences are self complementary, a
symmetry correction will be added to the initiation energy.
Example :
Sequence with a single mismatch
ATCGGCTA
TAGACGAT
where :
structure1 = perfectly matching sequences ATC/TAG
structure2 = single mismatch G/A
structure 3 = perfectly matching sequences GCTA/CGAT
The hybridization process depends on the adjacent nucleotides on each strand (the Crick's pairs).
Two duplexes with the same base pairs could have different stabilities, and on the contrary, two
duplexes with different sequences but identical sets of Crick's pairs will have the same
thermodynamics properties. This program first computes the hybridisation enthalpy
and entropy from the elementary parameters of each Crick's pair.
The initiation computation is not the same for each following model.
model |
limits |
Article |
all97 |
DNA |
Allawi and SantaLucia (1997) |
|
|
Biochemistry 36 : 10581-10594 |
bre86 |
DNA |
Breslauer et al. (1986) |
|
|
Proc Natl Acad Sci USA 83 : 3746-3750 |
san04 |
DNA |
Santalucia and Hicks (2004) |
|
|
Annu. Rev. Biophys. Biomol. Struct 33 : 415-440 |
san96 |
DNA |
SantaLucia et al.(1996) |
|
|
Biochemistry 35 : 3555-3562 |
sug96 |
DNA |
Sugimoto et al. (1996) |
|
|
Nuc Acids Res 24 : 4501-4505 |
tan04 |
DNA |
Tanaka et al (2004) |
|
|
Biochemistry 43 : 7143-7150 |
fre86 |
RNA |
Freier et al (1986) |
|
|
Proc Natl Acad Sci USA 83: 9373-9377 |
xia98 |
RNA |
Xia et al (1998) |
|
|
Biochemistry 37: 14719-14735 |
sug95 |
DNA/RNA |
SantaLucia et al.(1996) |
|
|
Biochemistry 35 : 3555-3562 |
tur06 |
mRNA/RNA |
Kierzeck et al (2006) |
|
A sodium |
Nucleic acids research 34: 3609-3614 |
|
correction (san04) |
|
|
is automatically |
|
|
applied to |
|
|
the computed |
|
|
entropy to |
|
|
convert the |
|
|
entropy (Na = 0.1M) |
|
|
into the |
|
|
entropy (Na=1M) |
|
Example :
(The same computation is performed for
)
Figure:
Comparison of experimental and computed Tm for various sets of
DNA nearest-neighbor parameters.
Na
M,
nucleic acid
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of
RNA nearest-neighbor parameters.
Na
M,
nucleic acid
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of
DNA/RNA nearest-neighbor parameters.
Na
M,
nucleic acid
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of
2-O-methyl RNA nearest-neighbor parameters.
Na
M,
nucleic acid
M
 |
If the sequence (sens 5'3') is a sequence of type G(CNG)xC where x is the number of CNG repeats in
the sequence and N a unique nucleic acid which will get bound to itself, we can use specific
experimental parameters to compute the enthalpy and entropy of the duplex formation. These parameters can be used
only for sequences composed from 2 to 7 CNG repeats and the initiation is already included.
For further information, see the referenced article.
model |
limits |
Article |
bro05 |
RNA |
Magdalena et al (2005) |
|
Self complementary sequences |
Biochemistry 44: 10873-10882 |
|
2 to 7 CNG repeats |
|
Example :
GCAGCAGCAGC
CGACGACGACG
(The same computation is performed for
)
Figure:
Comparison of experimental and computed Tm for various sets of
RNA sequences composed of CNG repeats.
Na
M,
nucleic acid
M
 |
Be aware : The results for sequences composed of 4 or 5 CCG repeats is not reliable. (the figure shows two values
far from the expected temperature). This might be due to a majority of hairpin loop formation. See the article
above for further informations.
The single mismatches are taken into account but the two first and positions cannot
be mismatched. in such a case, the result is unpredictable, and all cases are
possible. for instance (see Allawi and SanLucia 1997), the duplex
A T
GTGAGCTCAT
TACTCGAGTG
T A
is more stable than
AGTGAGCTCATT
TTACTCGAGTGA
For DNA duplexes, this program computes the hybridisation enthalpy and entropy from the elementary
parameters of each Crick's pair containing the single mismatch.
Example :
(The same computation is performed for
)
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing one single mismatch.
Na
M,
nucleic acid
M
 |
For DNA/RNA duplexes, the same model is used, taking parameters from Watkins
et al. (2011). The only mismatches permitted are dA/rA,
dT/rU, dC/rC and dG/rG.
Example :
(The same computation is performed for
)
Figure:
Comparison of experimental and computed Tm for various sets of
DNA/RNA sequences containing one single mismatch.
Na
M,
nucleic acid
M
 |
For RNA duplexes, the different models to computes the thermodynamic contribution of single mismatch to the helix coil
stability are more complex.
Where :
accounts for the identity of the single mismatch nucleotides.
accounts for the interaction between the mismatch nucleotides and
the nearest neighbors. (R purine, Y pyrimidine)
accounts for AU or GU nearest neighbors.
Example :
(The same computation is performed for
)
Where :
accounts for the initiation of a single non canonical pair.
accounts for a GG single mismatch.
accounts for a 5'RU/3'YU stack with R a purine and Y a pyrimidine.
accounts for AU or GU nearest neighbors.
Example :
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
allsanpey |
DNA |
Allawi and SantaLucia (1997) |
|
|
Biochemistry 36: 10581-10594 |
|
|
Allawi and SantaLucia (1998) |
|
|
Biochemistry 37: 2170-2179 |
|
|
Allawi and SantaLucia (1998) |
|
|
Nuc Acids Res 26: 2694-2701 |
|
|
Allawi and SantaLucia (1998) |
|
|
Biochemistry 37: 9435-9444 |
|
|
Peyret et al. (1999) |
|
|
Biochemistry 38: 3468-3477 |
wat11 |
DNA/RNA |
Watkins et al. (2011) |
tur06 |
RNA |
Lu et al (2006) |
|
|
Nucleic Acids Research 34: 4912-4924 |
zno07 |
RNA |
Davis and Znosko (2007) |
|
|
Biochemistry 46: 13425-13436 |
zno08 |
RNA |
Davis and Znosko (2008) |
|
at least |
Biochemistry 47: 10178-10187 |
|
one adjacent |
|
|
GU base pair |
|
Figure:
Comparison of experimental and computed Tm for various sets of
RNA sequences containing one single mismatch.
Na
M,
nucleic acid
M
 |
The tandem mismatches (two adjacent mismatches) are taken into account but the two first and positions cannot
be mismatched. Moreover the thermodynamic parameters are still not available for every possible cases.
In such a case, the program, unable to compute any relevant result, will quit with a warning.
For DNA duplexes, this program computes the hybridisation enthalpy and entropy from the elementary
parameters of each Crick's pair containing the mismatch(es).
Example :
(The same computation is performed for
)
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing one tandem mismatch.
Na
M,
nucleic acid
M
 |
For RNA duplexes, the different models to computes the thermodynamic contribution of tandem mismatch to the helix coil
stability are more complex.
Where :
accounts for the identity of the double mismatch nucleotides and the identity of the base pairs
adjacent to the tandem mismatches.
Example :
(The same computation is performed for
)
Where :
accounts for the enthalpy of a symmetric tandem mismatch composed of
the first closing base pair and the first mismatch nucleotides.
accounts for the enthalpy of a symmetric tandem mismatch composed of
the second closing base pair and the second mismatch nucleotides.
accounts for a GG pair adjacent to a AA pair or any non canonical pair containing a pyrimidine.
accounts for an AG or GA pairs adjacent to a UC, CC or CU pair and a UU pair adjacent to an AA pair .
Example :
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
allsanpey |
DNA |
Allawi and SantaLucia (1997) |
|
only GT |
Biochemistry 36: 10581-10594 |
|
mismatches |
Allawi and SantaLucia (1998) |
|
and TA/TG |
Biochemistry 37: 2170-2179 |
|
mismatches |
Allawi and SantaLucia (1998) |
|
|
Nuc Acids Res 26: 2694-2701 |
|
|
Allawi and SantaLucia (1998) |
|
|
Biochemistry 37: 9435-9444 |
|
|
Peyret et al. (1999) |
|
|
Biochemistry 38: 3468-3477 |
tur99 |
RNA |
Mathiews et al (1999) |
|
no adjacent |
J.Mol.Biol. 288: 911-940 |
|
GU or UG base |
|
|
pairs |
|
Figure:
Comparison of experimental and computed Tm for various sets of
RNA sequences containing one tandem mismatch.
Na
M,
nucleic acid
M
 |
The internal loops (more than two adjacent mismatches) are taken into account but the two first and positions cannot
be mismatched. Moreover the thermodynamic parameters are still not available for every possible cases.
In such a case, the program, unable to compute any relevant result, will quit with a warning.
Moreover, the thermodynamics of the nucleic acids within the internal loop are salt
independent and no salt correction will be applied to it. However, the thermodynamics
of the terminal mismatches are salt dependent and a salt correction will be applied
to them.
The thermodynamic model for DNA and RNA duplexes are similar.
Where :
accounts for the internal loop of n nucleotides.
accounts for the internal loop asymmetry (when the number of
nucleic acid within the internal loop is higher in one of the strand).
accounts for the identity of the first mismatch
nucleotides of the loop.
accounts for the identity of the last mismatch
nucleotides of the loop.
Example : Symmetric internal loop
Where :
accounts for the internal loop of n nucleotides.
accounts for the internal loop asymmetry (when the number of
there is an unequal numbers of nucleotides on each side) with n1 and n2 the
number of nucleotides on each strand..
accounts for each AU or GU base pair adjacent
to the internal loop.
accounts for each sequence
specific first mismatch (bonus). It is not applied to loops of the form 1 x (n-1) with
n > 2.
Example : asymmetric internal loop
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
san04 |
DNA |
Santalucia and Hicks (2004) |
|
missing asymmetry |
Annu. Rev. Biophys. Biomol. Struct 33 : 415-440 |
|
penalty, |
|
|
not tested |
|
|
with experimental |
|
|
results |
|
tur06 |
RNA |
Lu et al (2006) |
|
not tested |
Nucleic Acids Research 34: 4912-4924 |
|
with experimental |
|
|
results |
|
Figure:
Comparison of experimental and computed Tm for various sets of
RNA sequences containing one 1x2 internal loop.
Na
M,
nucleic acid
M
 |
The wobble GU base pairs are taken into account. This pairing is a non-Watson-Crick base pairing between two nucleotides
in RNA molecules, but the thermodynamic stability of a wobble base pair is comparable to that of a Watson-Crick base pair.
Melting can also compute the thermodynamic of patterns with several adjacent GU base pairs.
This program computes the hybridisation enthalpy and entropy from the elementary
parameters of each Crick's pair containing the GU base pairs.
Examples : One GU base pair
Examples : Two adjacent GU base pairs
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
tur99 |
RNA |
Mathiews et al (1999) |
|
|
J.Mol.Biol. 288: 911-940 |
model |
limits |
Article |
ser12 |
RNA |
Serra et al (2012) |
|
|
Biochemistry 51: 3508-3522 |
Figure:
Comparison of experimental and computed Tm for various sets of
RNA sequences containing GU base pairs.
Na
M,
nucleic acid
M
 |
The single dangling ends, that is the unmatched terminal nucleotides, can be taken into
account, but all the thermodynamic parameters are not available. In such a case,
the result is unpredictable, and all cases are possible.
For DNA and RNA duplexes, this program computes the hybridisation enthalpy and entropy from the elementary
parameters of the Crick's pair containing the single dangling end.
Example :
If the duplex is :
GCTAG-
CGATCA
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
bom00 |
DNA |
Bommarito et al. (2000) |
|
|
Nuc Acids Res 28: 1929-1934 |
sugdna02 |
DNA |
Ohmichi et al. (2002) |
|
only terminal |
J. Am. Chem. Soc. 124: 10367-10372 |
|
poly A |
|
|
self complementary |
|
|
sequences |
|
sugrna02 |
RNA |
Ohmichi et al. (2002) |
|
only terminal poly A |
J. Am. Chem. Soc. 124: 10367-10372 |
|
self complementary |
|
|
sequences |
|
ser08 |
RNA |
O'tool et al. (2006) |
|
only 3' UA, |
Nucleic Acids research 34: 3338-3344 |
|
GU and UG terminal |
Miller et al. (2008) |
|
base pairs |
Nucleic Acids research 36: 5652-5659 |
|
only 5' UG and GU |
|
|
terminal base pairs |
|
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing single dangling ends.
Na
M,
nucleic acid
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of
RNA sequences containing single dangling ends.
Na
M,
nucleic acid
M
 |
The double dangling ends, that is the two adjacent unmatched terminal nucleotides, can be taken into
account (mostly for RNA sequences). This program computes the hybridisation enthalpy and entropy in two times :
First, it computes the energy from the single dangling end as if the duplex contained
only a single danging end and then, it adds a bonus for the second dangling end if it is necessary.
Example :
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
sugdna02 |
DNA |
Ohmichi et al. (2002) |
|
only terminal |
J. Am. Chem. Soc. 124: 10367-10372 |
|
poly A |
|
|
self complementary |
|
|
sequences |
|
sugrna02 |
RNA |
Ohmichi et al. (2002) |
|
only terminal |
J. Am. Chem. Soc. 124: 10367-10372 |
|
poly A |
|
|
self complementary |
|
|
sequences |
|
ser05 |
RNA |
O'toole et al. (2005) |
|
depends on |
RNA 11: 512-516 |
|
the available |
|
|
thermodynamic |
|
|
parameters for |
|
|
single dangling |
|
|
ends |
|
ser06 |
RNA |
O'toole et al. (2006) |
|
|
Nucleic Acids research 34: 3338-3344 |
Figure:
Comparison of experimental and computed Tm for various sets of
RNA sequences containing double dangling ends.
Na
M,
nucleic acid
M
 |
The long dangling ends, that is all the adjacent unmatched terminal nucleotides, can be taken into
account (only for polyA dangling ends for the moment). It is possible to compute the thermodynamic
form one to four poly A dangling end. This program computes the hybridisation enthalpy
and entropy from the parameters of the long dangling end with the adjacent terminal base pair.
Example :
If the duplex is :
GCTAG--
CGATCAAA
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
sugdna02 |
DNA |
Ohmichi et al. (2002) |
|
only terminal |
J. Am. Chem. Soc. 124: 10367-10372 |
|
poly A |
|
|
self complementary |
|
|
sequences |
|
sugrna02 |
RNA |
Ohmichi et al. (2002) |
|
only terminal |
J. Am. Chem. Soc. 124: 10367-10372 |
|
poly A |
|
|
self complementary |
|
|
sequences |
|
Figure:
Comparison of experimental and computed Tm for various sets of DNA sequences containing long polyA dangling ends.
Na
M,
nucleic acid
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of RNA sequences containing long polyA dangling ends.
Na
M,
nucleic acid
M
 |
The single bulge loops, that is the single unmatched internal nucleotides, can be taken into
account. , but all the thermodynamic parameters are not available. In such a case,
the result is unpredictable, and all cases are possible.
There are several different models to compute the thermodynamic of single bulge loop:
Example :
If the duplex is :
GCTTAGGC
CGA-TCCG
(The same computation is performed for
)
However, some types of single bulge loop can't be only modelled with a NNN nearest
neighbor model and the following models can give more reliable and accurate results (mostly
for RNA single bulge loops.)
Where :
accounts for the bulge loop of 1 nucleotide.
accounts for the intervening base pair stack.
accounts for each AT base pair adjacent
to the single bulge loop.
Example :
(The same computation is performed for
)
Where :
accounts for the initiation of bulge loop of 1 nucleotide.
accounts for the intervening base pair stack.
Example :
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
tan04 |
DNA |
Tanaka et al (2004) |
|
|
Biochemistry 43 : 7143-7150 |
san04 |
DNA |
Santalucia and Hicks (2004) |
|
missing |
Annu. Rev. Biophys. Biomol. Struct 33 : 415-440 |
|
closing AT |
|
|
penalty |
|
ser07 |
RNA |
Blose et al (2007) |
|
les reliable |
Biochemistry 46 : 15123-15135 |
|
results |
|
|
some missing |
|
|
parameters |
|
tur06 |
RNA |
Lu et al (2006) |
|
|
Nucleic Acids Research 34: 4912-4924 |
Figure:
Comparison of experimental and computed Tm for various sets of DNA sequences containing one single bulge loop.
Na
M,
nucleic acid
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of RNA sequences containing one single bulge loop.
Na
M,
nucleic acid
M
 |
The long bulge loops, that is all the adjacent unmatched internal nucleotides, can be taken into
account. , but all the thermodynamic parameters are not available. In such a case,
the result is unpredictable, and all cases are possible.
The RNA and DNA thermodynamic models are similar :
Where :
accounts for the bulge loop of n nucleotides.
accounts for each AT base pair adjacent
to the long bulge loop.
Example :
Where :
accounts for the initiation of the bulge loop of n nucleotides.
accounts for each AU or GU base pair adjacent
to the long bulge loop.
Example :
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
san04 |
DNA |
Santalucia and Hicks (2004) |
|
missing closing |
Annu. Rev. Biophys. Biomol. Struct 33 : 415-440 |
|
AT penalty |
|
|
not tested |
|
|
with experimental |
|
|
results |
|
tur06 |
RNA |
Lu et al (2006) |
|
not tested |
Nucleic Acids Research 34: 4912-4924 |
|
with experimental |
|
|
results |
|
The inosine bases (I) are taken into account, but all the thermodynamic parameters are not available.
In such a case, the result is unpredictable, and all cases are possible, so the
program quit with a warning. For the RNA duplexes, only the thermodynamic parameters
for IU base pairs are available for the moment.
This program computes the hybridisation enthalpy and entropy from the elementary
parameters of each Crick's pair containing the inosine base.
Examples : One inosine base
Examples : Two adjacent base pairs containing inosine
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
san05 |
DNA |
Watkins and Santalucia (2005) |
|
missing parameters |
Nucleic acids research 33 : 6258-6267 |
|
for tandem |
|
|
base pairs |
|
|
containing |
|
|
inosine bases |
|
zno07 |
RNA |
Wright et al. (2007) |
|
only IU base |
Biochemistry 46 : 4625-4634 |
|
pairs |
|
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing inosine.
Na
M,
nucleic acid
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of
RNA sequences containing inosine.
Na
M,
nucleic acid
M
 |
The trans azobenzenes (X_T) and cis azobenzenes (X_C) in DNA duplexes are taken
into account. Be aware : when the number of cis azobenzenes increases in the sequence,
the predictions are less accurate and less reliable.
Example :
If the duplex is :
GCTX_CAGGC
CGATCCG
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
asa05 |
DNA |
Asanuma et al. (2005) |
|
less reliable |
Nucleic acids Symposium Series 49 : 35-36 |
|
results when |
|
|
the number |
|
|
of cis azobenzene |
|
|
increases |
|
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing azobenzene.
Na
M,
nucleic acid
M
 |
The 2-hydroxyadenine bases (A*) in DNA duplexes are taken into account, but only in this two different
sequence contexts : 5' GA*C 3' and 5' TA*A 3'. The program computes the enthalpy and the entropy in two
times : first it computes the enthalpy and entropy of the two Crick's pairs containing the hydroxyadenine
as if the base pair containing the hydroxyadenine was a simple AT base pair, and then it computes the hydroxyadenine
increments.
Examples
(The same computation is performed for
)
For further information, see the referenced articles.
model |
limits |
Article |
sug01 |
DNA |
Kawakami et al.(2001) |
|
only in 5' |
Nucleic acids research 29 : 3289-3296 |
|
GA*C 3' |
|
|
and 5' TA*A |
|
|
contexts |
|
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing hydroxyadenine.
Na
M,
nucleic acid
M
 |
The locked nucleic acids (AL, GL, CL, TL) in DNA duplexes are taken into account.
The program computes the enthalpy and the entropy in two times : first it computes the enthalpy and entropy of
the two Crick's pairs containing the locked nucleic acid as if the locked nucleic acid was a simple nucleic acid,
and then it computes the locked nucleic acid increments for each Crick's base pair containing the locked nucleic acid.
Examples
(The same computation is performed for
)
The program computes the enthalpy and the entropy following the same nearest-neighbor formula as for perfectly matching Crick's pairs.
Examples
For further information, see the referenced articles.
model |
limits |
Article |
mct04 |
DNA |
McTigue et al.(2004) |
|
|
Biochemistry 43 : 5388-5405 |
owc11 |
DNA |
Owczarzy et al.(2011) |
|
|
Biochemistry 50 : 9352-9367 |
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing single Locked Nucleic Acid.
Na
M,
nucleic acid
M
 |
The consecutive locked nucleic acids (AL, GL, CL, TL) in DNA duplexes are taken into account.
The program computes the enthalpy and the entropy following the same nearest-neighbor formula as for perfectly matching Crick's pairs.
Examples
For further information, see the referenced articles.
model |
limits |
Article |
owc11 |
DNA |
Owczarzy et al.(2011) |
|
|
Biochemistry 50 : 9352-9367 |
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing consecutive Locked Nucleic Acids.
Na
M,
nucleic acid
M
 |
The consecutive locked nucleic acids with a single mismatch (AL, GL, CL, TL) in DNA duplexes are taken into account.
The program computes the enthalpy and the entropy following the same nearest-neighbor formula as for perfectly matching Crick's pairs.
Examples
For further information, see the referenced articles.
model |
limits |
Article |
owc11 |
DNA |
Owczarzy et al.(2011) |
|
|
Biochemistry 50 : 9352-9367 |
Figure:
Comparison of experimental and computed Tm for various sets of
DNA sequences containing consecutive Locked Nucleic Acids and a single mismatch.
Na
M,
nucleic acid
M
 |
Then the melting temperature is computed by the following formula:
Tm |
= |
 |
|
|
|
|
|
|
|
|
|
In case of self complementary sequences, if the sequence (5' 3') is a sequence of type G(CNG)xC
and x > 4, the sequence mainly turns into hairpin loops and this program will compute the melting
temperature with this formula :
Tm |
= |
 |
|
|
|
|
|
|
|
|
|
Moreover, no ion correction will be applied to this formula.
F is 1 in the case of self-complementarity oligonucleotides. If the
ODNs are not self-complementary, F is 4 if both strands are present in
equivalent amount and F is 1 if one strand is in excess (for instance
in PCR experiments). As a matter of facts, when the oligonucleotides are not self-complementary,
the formula in the denominator is
where
is the concentration of the strand in excess
and
the concentration of the other strand. If the excess is sufficient, the total concentration is equivalent to the concentration of the strand in excess. Therefore, if one strand is in excess, the actual formula is effectively
but if
,
is equivalent to the total concentration
. If
is close
to
,
is equivalent to
, which is the default
correction.
F is 4 by default but note that MELTING can detect self complementary sequences
for perfectly matching sequences even though there is(are) dangling end(s). In this case, the program will
automatically change F to 1. In addition to that, the computation takes an entropic term to correct
for self-complementarity.
In case of other self complementary sequences which doesn't match perfetcly, the option -self must be
used to inform the program of the self complementarity.
Figure:
Comparison of experimental and computed Tm for various sets of
DNA self complementary sequences.
Na
M,
nucleic acid
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of
RNA self complementary sequences.
Na
M,
nucleic acid
M
 |
After the program computed the melting temperature for
Na
=1, an ion correction wille be applied
either directly on the computed melting temperature or on the computed entropy. In the last case, the melting
temperature is computed using the first formula of the Melting temperature section.
We must enter at least one of the following ion concentrations :
Na
,
K
,
Tris
or
Mg
and several ion corrections are proposed (see the reference table to have more information):
- ahs01
Where N is the length of the duplex.
- kam71
Where
is the frequence of GC base pairs in the duplex.
- marschdot
Where
is the frequence of GC base pairs in the duplex.
- owc1904
Where
is the frequence of GC base pairs in the duplex.
- owc2004
Where
is the frequence of GC base pairs in the duplex.
- owc2104

Na
Where
is the frequence of GC base pairs in the duplex.
- owc2204
Where
is the frequence of GC base pairs in the duplex.
- san96

Na
- san04
Where N is the length of the duplex.
- schlif
- tanna06
Where N is the length of the duplex.

Mg
item tanna07
Where N is the length of the duplex.

Mg
- wet91
correction |
contexts |
Article |
ahs01 |
DNA |
von Ahsen et al ,2001 |
|
Na>0 |
Clinical Chemistry, 47, 1956-1961. |
kam71 |
DNA |
Frank-Kamenetskii et al. 1971 |
|
Na>=0.069 |
Biopolymers 10, 2623-2624. |
|
Na<=1.02 |
|
marschdot |
DNA |
Marmur, J., and Doty, P. (1962) |
|
Na>=0.069 |
J. Mol. Biol. 5, 109-118. |
|
Na<=1.02 |
Blake and Delcourt. (1998) Nucleic Acids Res. 26, 3323-3332 |
|
|
and corrigendum. |
owc1904 |
DNA |
Owczarzy et al.,2004 |
|
Na>0 |
Biochemistry,43, 3537-3554. |
owc2004 |
DNA |
Owczarzy et al., 2004 |
|
Na>0 |
Biochemistry, 43, 3537-3554. |
owc2104 |
DNA |
Owczarzy et al., 2004 |
|
Na>0 |
Biochemistry, 43, 3537-3554. |
owc2204 |
DNA |
Owczarzy et al., 2004 |
|
Na>0 |
Biochemistry, 43, 3537-3554. |
owc2204 |
DNA |
Owczarzy et al., 2004 |
|
Na>0 |
Biochemistry,43, 3537-3554. |
san96 |
DNA |
SantaLucia et al.(1996) |
|
Na>=0.1 |
Biochemistry 35 : 3555-3562 |
san04 |
DNA |
Santalucia and Hicks (2004) |
|
Na>=0.05 |
Annu. Rev. Biophys. Biomol. Struct 33 : 415-440 |
|
Na<=1.1 |
John Santalucia, Jr., 1998 |
|
|
Proc. Natl. Acad. Sci. USA, 95, 1460-1465 |
|
oligonucleotides |
|
|
inferior to 16 bases |
|
schlif |
DNA |
Schildkraut, C., and Lifson, S. (1965) |
|
Na>=0.07 |
Biopolymers 3, 195-208. |
|
Na<=0.12 |
|
tanna06 |
DNA |
Tan et al. 2006, |
|
Na>=0.001 |
Biophysical Journal, 90, 1175-1190. |
|
Na<=1 |
|
tanna07 |
RNA |
Tan et al, 2007 |
|
Na>=0.003 |
Biophysical Journal, 92, 3615-3632. |
|
Na<=1 |
|
wet91 |
RNA, DNA |
Wetmur 1991 |
|
and RNA/DNA |
Critical reviews in biochemistry and molecular |
|
Na>0 |
biology, 26, 227-259 |
correction |
limits |
Article |
oxcmg08 |
DNA |
Owczarzy et al.,2008 |
|
Mg>=0.0005 |
Biochemistry, 47, 5336-5353. |
|
Mg<=0.6 |
|
tanmg06 |
DNA |
Tan et al. 2006 |
|
Mg>=0.0001 |
Biophysical Journal, 90, 1175-1190. |
|
Mg<=1 |
|
|
oligomer |
|
|
length |
|
|
superior to |
|
|
6 base pairs |
|
tanmg07 |
RNA |
Tan et al, 2007 |
|
Mg>=0.1 |
Biophysical Journal, 92, 3615-3632. |
|
Mg<=0.3 |
|
- owcmix08
Where
is the frequence of GC base pairs in the duplex.
Nbp is the number of base pairs.
b, c, e, f are fixed as in the magnesium correction owcmg08.
- tanmix07
Where N is the length of the duplex.

Na
See what is g1 and g2 in the sodium corrections tanna06 and tanna07 (g1) and
magnesium corrections tanmg06 and tanmg07 (g2).
Formula representing the fractional contribution of Na+ ions.
Formula representing the fractional contribution of Mg2+ ions.
correction |
limits |
Article |
oxcmix08 |
DNA |
Owczarzy et al.,2008 |
|
Mg>=0.0005 |
Biochemistry, 47, 5336-5353. |
|
Mg<=0.6 |
|
|
Na+K+Tris/2>0 |
|
tanmix07 |
DNA |
Tan et al, 2007 |
|
and RNA |
Biophysical Journal, 92, 3615-3632. |
|
Mg>=0.1 |
|
|
Mg<=0.3 |
|
|
Na+K+Tris/2>=0.1 |
|
|
Na+K+Tris/2<=0.3 |
|
If the user doesn't enter any ion correction, the algorithm from Owczarzy et al. (2008) will
be used by default :
Where
Tris
is equal to half of total tris buffer concentration. (in the option -t, it is the Tris buffer concentration
which is entered).
- if
Mon
= 0, a default sodium correction will be used.
- if
Mg
/
Mon
< 0.22, a default sodium correction is used.
Monovalent ion influence is dominant, divalent cations can be
disregarded.
- if
Mg
/
Mon
>= 0.22 and
Mg
/
Mon
< 6,
a default mixed Na Mg correction is used.
We can have a competitive DNA or RNA binding between monovalent and divalent
cations.
- if
Mg
/
Mon
>= 6, a default magnesium correction is used.
Divalent cation influence is dominant, monovalent cations can be
disregarded.
Moreover, if the user wants to use a sodium correction but also enters a potassium, Tris buffer
and/or a magnesium concentration, a sodium equivalent concentration which takes into account the other
ion concentrations is computed before applying the sodium correction.
Several sodium equivalence ready to use are proposed by this program :
For further information, see the referenced articles :
correction |
limits |
Article |
ahs01 |
DNA |
von Ahsen et al. 2001 |
|
|
Clinical Chemistry, 47, 1956-1961. |
mit96 |
DNA |
Mitsuhashi. et al, 1996 |
|
|
J. Clin. Lab. Anal, 10, 277-284. |
pey00 |
DNA |
Peyret, 2000 |
|
|
Ph.D Thesis, Section .5.4.2, 128, Wayne State |
|
|
University, Detroit, MI |
MELTING is currently accurate when the hybridisation is performed at pH
,
but some temperature corrections for the formamide and DMSO concentrations exists and can be
applied. However, these corrections are rough approximations and results accuracy may be lost.
For further information, see the referenced articles :
correction |
limits |
Article |
ahs01 |
DNA |
von Ahsen et al. 2001 |
|
not tested |
Clinical Chemistry, 47, 1956-1961. |
|
with experimental |
|
|
values |
|
cul76 |
DNA |
Cullen et al., 1976 |
|
not tested |
3, 49-62. |
|
with experimental |
|
|
values |
|
esc80 |
DNA |
Escara et al., 1980 |
|
not tested |
19, 1315-1327. |
|
with experimental |
|
|
values |
|
mus80 |
DNA |
Musielski et al., 1981 |
|
not tested |
Z allg Microbiol 1981; 21, 447-456. |
|
with experimental |
|
|
values |
|
- bla96
Where
is the frequence of GC base pairs in the sequence.
formamide is in mol/L
- lincorr
Where formamide is in %.
For further information, see the referenced articles :
correction |
limits |
Article |
bla96 |
DNA |
Blake and Delcourt, 1996 |
|
not tested |
Vol. 24, No. 11 2095-2103 |
|
with experimental |
|
|
values |
|
|
formamide in mol/L |
|
lincorr |
DNA |
McConaughy et al., 1969 |
|
not tested |
Biochemistry 8, 3289-3295. |
|
with experimental |
Record, M.T., Jr, 1967 |
|
in % |
Biopolymers, 5, 975-992. |
|
values |
Casey et al, 1977 |
|
Formamide in |
Nucleic acids research, 4, 1539-1532. |
|
% |
Hutton, 1977 |
|
|
Nucleic acids research, 4, 3537-3555. |
It is important to realise that the nearest-neighbor approach has been established
on small oligonucleotides. Therefore the use of MELTING in the non-approximative
mode is really accurate only for relatively short sequences (Although if the sequences are
two short, let's say
6 bp, the influence of extremities becomes too important and the
reliability decreases a lot). For long sequences an approximative mode has been designed.
This mode is launched if the sequence length is higher than the value given by the option -T
(the default threshold is 60 bp).
The melting temperature can be computed by one of the following formulas:
- ahs01

Na
- che93
- che93corr
- marschdot

Na
- owe69

Na
- san98

Na
- wetdna91
- wetrna91
- wetdnarna91
For further information, see the referenced articles :
formula |
limits |
Article |
ahs01 |
DNA |
von Ahsen et al. 2001 |
|
no mismatch |
Clinical Chemistry, 47, 1956-1961. |
che93 |
DNA |
Marmur et al., 1962 |
|
no mismatch |
Journal of molecular biology, 5, 109-118. |
|
Na=0 |
Chester N et al. 1993 |
|
Mg=0.0015 |
Analytical Biochemistry, 209, 284-290. |
|
Tris=0.01 |
|
|
K=0.05 |
|
che93corr |
DNA |
Marmur et al., 1962 |
|
no mismatch |
Journal of molecular biology, 5, 109-118. |
|
Na=0 |
Chester N et al. 1993 |
|
Mg=0.0015 |
Analytical Biochemistry, 209, 284-290. |
|
Tris=0.01 |
Nicolas Von Ahsen et al. 2001 |
|
K=0.05 |
Clinical Chemistry, 47, 1956-1961. |
marschdot |
DNA |
Wetmur,1991 |
|
no mismatch |
Critical reviews in biochemistry |
|
|
and molecular biology, 26, 227-259 |
|
|
Marmur et al., 1962 |
|
|
Journal of molecular biology, 5, 109-118. |
|
|
Chester et al., 1993 |
|
|
Analytical Biochemistry, 209, 284-290. |
|
|
Schildkraut et al., 1965 |
|
|
Biopolymers, 3, 95-110. |
|
|
Wahl et al., 1987 |
|
|
Methods Enzymol;152:399 - 407. |
|
|
Britten et al.,1974 |
|
|
Methods Enzymol ;29:363-418. |
|
|
Hall et al., 1980 |
|
|
J Mol Evol ;16:95-110. |
owe69 |
DNA |
Owen et al., 1969 |
|
no mismatch |
Biopolymers, 7:503-16. |
|
|
Frank-Kamenetskii,1971 |
|
|
Biopolymers;10:2623- 4. |
|
|
Blake, 1996 |
|
|
Encyclopedia of molecular biology and |
|
|
molecular medicine, Vol. 2., :1-19. |
|
|
Blake et al.,1998 |
|
|
Nucleic Acids Res;26:3323-32. |
san98 |
DNA |
Santalucia, 1998 |
|
no mismatch |
Proc Nacl Acad Sci USA |
|
|
95, 1460-1465. |
|
|
von Ahsen et al. 2001, |
|
|
Clinical Chemistry, 47, 1956-1961. |
wetdna91 |
DNA |
Wetmur,1991, |
|
|
Critical reviews in biochemistry |
|
|
and molecular biology, 26, 227-259 |
wetrna91 |
RNA |
Wetmur,1991, |
|
|
Critical reviews in biochemistry |
|
|
and molecular biology, 26, 227-259 |
wetdnarna91 |
DNA/RNA |
Wetmur,1991, |
|
|
Critical reviews in biochemistry |
|
|
and molecular biology, 26, 227-259 |
Figure:
Comparison of experimental and computed Tm for various sets of
DNA approximative formulas.
Na
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of
RNA approximative formulas.
Na
M
 |
Figure:
Comparison of experimental and computed Tm for various sets of
DNARNA approximative formulas.
Na
M,
nucleic acid
M
 |
- 1
-
H.T. Allawi and J. SantaLucia.
Thermodynamics and NMR of internal G-T mismatches in DNA.
Biochemistry, 36:10581-10594, 1997.
- 2
-
H.T. Allawi and J. SantaLucia.
Nearest neighbor thermodynamics of internal A.C mismatches in
DNA: sequence dependence and pH effects.
Biochemistry, 37:9435-9444, 1998.
- 3
-
H.T. Allawi and J. SantaLucia.
Nearest neighbor thermodynamics parameters for internal G.A
mismatches in DNA.
Biochemistry, 37:2170-2179, 1998.
- 4
-
H.T. Allawi and J. SantaLucia.
Thermodynamics of internal C.T mismatches in DNA.
Biochemistry, 26:2694-2701, 1998.
- 5
-
Hiroyuki Asanuma, Daijiro Matsunaga, and Makoto Komiyama.
Clear-cut photo-regulation of the formation and dissociation of the
DNA duplex by modified oligonucleotide involving multiple azobenzenes.
Nucleic acids Symposium Series, 49:35-36, 2005.
- 6
-
Jaya Badhwar, Saradasri Karri, Cody K. Cass, Erica L. Wunderlich, and Brent M.
Znosco.
Thermodynamic characterization of RNA duplexes containing naturally
occuring 1x2 nucleotide internal loops.
Biochemistry, 46:14715-14724, 2007.
- 7
-
R. D. Blake and S. G. Delcourt.
Thermal stability of DNA.
Nucleic Acids Res, 26:3323-3332 and corrigendum, 1998.
- 8
-
R. D. Blake and Scott G. Delcourt.
Thermodynamic effects of formamide on DNA stability.
Nucleic Acids Research, 24, 11:2095-2103, 1996.
- 9
-
RD. Blake.
Denaturation of DNA.
In: Meyers RA, ed. Encyclopediaof molecular biology and
molecular medicine, 2:1-19, 1996.
- 10
-
Joshua Blose, M. Michelle L. Manni, Kelly A. Klapec, Yukiko Stranger-Jones,
Allison C. Zyra, Vasiliy Sim, Chad A. Griffith, Jason D. Long, and Martin J.
Serra.
Non-nearest-neighbor dependence of stability for RNA bulge loops
based on the complete set of Group I single nucleotide bulge loops.
Biochemistry, 46:15123-15135, 2007.
- 11
-
S. Bommarito, N. Peyret, and J. SantaLucia.
Thermodynamic parameters for DNA sequences with dangling ends.
Nucleic Acids Res, 28:1929-1934, 2000.
- 12
-
K.J. Breslauer, R. Frank, H. Blöcker, and Marky L.A.
Predicting DNA duplex stability from the base sequence.
Proc Natl Acad Sci USA, 83:3746-3750, 1986.
- 13
-
RJ Britten, DE Graham, and BR Neufeld.
Analysis of repeating DNA sequences by reassociation.
Methods Enzymol, 29:363-418, 1974.
- 14
-
N. Casey, J.and Davidson.
Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA
duplexes at high concentrations of formamide.
Nucleic acids research, 4:1539-1532, 1977.
- 15
-
Jonathan L. Chen, Abigael L. Dishler, Scott D. Kennedy, Ilyas Yildirim, Biao
Liu, Douglas H. Turner, and Martin J. Serra.
Testing the nearest neighbor model for canonical RNA base pairs:
Revision of GU parameters.
Biochemistry, 51:3508-3522, 2012.
- 16
-
N Chester and DR Marshak.
dimethyl sulfoxide-mediated primer tm reduction : a method for
analyzing the role of renaturation temperature in the polymerase chain
reaction.
Analytical Biochemistry, 209:284-290, 1993.
- 17
-
Br Cullen and Md Bick.
Thermal denaturation of DNA from bromodeoxyuridine substitued
cells.
Nucleic acids research, 3:49-62, 1976.
- 18
-
Amber R. Davis and Brent M. Znosko.
Thermodynamic characterization of single mismatches found in
naturally occurring RNA.
Biochemistry, 46:13425-13436, 2007.
- 19
-
Amber R. Davis and Brent M. Znosko.
Thermodynamic characterization of naturally occurring RNA single
mismatches with G-U nearest neighbors.
Biochemistry, 47:10178-10187, 2008.
- 20
-
JF Escara and Jr Hutton.
Thermal stability and renaturation of DNA in dimethyl
sulfoxidesolutions: acceleration of the renaturation rate.
Biopolymers, 19:1315-1327, 1980.
- 21
-
M. D. Frank-Kamenetskii.
Simplification of the empirical relationship between melting
temperature of DNA, its GC content and concentration of sodium ions in
solution.
Biopolymers, 10:2623-2624, 1971.
- 22
-
S.M. Freier, R. Kierzek, J.A. Jaeger, N. Sugimoto, M.H. Caruthers, T. Neilson,
and D.H. Turner.
Biochemistry, 83:9373-9377, 1986.
- 23
-
TJ Hall, JW Grula, EH Davidson, and RJ Britten.
Evolution of sea urchin non-repetitive DNA.
J Mol Evol, 16:95-110, 1980.
- 24
-
JR Hutton.
Renaturation kinetics and thermal stability of DNA in aqueous
solutions of formamide and urea.
Nucleic acids research, 4:3537-3555, 1977.
- 25
-
Junji Kawakami, Hiroyuki Kamiya, Kyohko Yasuda, Hiroyoshi Fujiki, Hiroshi
Kasai, and Naoki Sugimoto.
Thermodynamic stability of base pairs between 2-hydroxyadenine and
incoming nucleotides as a determinant of nucleotide incorporation specificity
during replication.
Nucleic acids research, 29:3289-3296, 2001.
- 26
-
Elzbieta Kierzek, David H. Mathews, Anna Ciesielska, Douglas H. Turner, and
Ryszard Kierzek.
Nearest neighbor parameters for Watson Crick complementary
heteroduplexesformed between 2-O-methyl RNA and RNA oligonucleotides.
Nucleic acids research, 34:3609-3614, 2006.
- 27
-
Zhi John Lu, Douglas H. Turner, and David H. Mathews.
A set of nearest neighbor parameters for predicting the enthalpy
change of RNA secondary structure formation.
Nucleic Acids Research, 34:4912-4924, 2006.
- 28
-
Broda Magdalena, Elbieta Kierzek, Zofia Gdaniec, Tadeusz Kulinski, and Ryszard
Kierzek.
Thermodynamic stability of RNA structures formed by CNG
trinucleotide repeats. implication for prediction of RNA structure.
Biochemistry, 44:10873-10882, 2005.
- 29
-
J. Marmur and P. Doty.
Determination of the base composition of deoxyribonucleic acid from
its thermal denaturation temperature.
J. Mol. Biol., 5:109-118, 1962.
- 30
-
David H. Mathews, Jeffrey Sabina, Michael Zucker, and Douglas H Turner.
Expanded sequence dependence of thermodynamic parameters improves
predictionof RNA secondary structure.
J. Mol. Biol, 288:911-940, 1999.
- 31
-
B.L. McConaughy, C.D. Laird, and B.I. McCarthy.
Nucleic acid reassociation in formamide.
Biochemistry, 8:3289-3295, 1969.
- 32
-
Patricia M. McTigue, Raymond J. Peterson, and Jason D. Kahn.
Sequence-dependent thermodynamic parameters for locked nucleic acid
(LNA)DNA duplexformation.
Biochemistry, 43:5388-5405, 2004.
- 33
-
Stacy Miller, Laura E. Jones, Karen Giovannitti, Dan Piper, and Martin J.
Serra.
Thermodynamic analysis of 5 and 3 single- and 3 double-nucleotide
overhangs neighboring wobble terminal base pairs.
Nucleic Acids research, 36:5652-5659, 2008.
- 34
-
M. Mitsuhashi.
Technical report: Part 1. basic requirements for designing optimal
oligonucleotide probe sequences.
J. Clin. Lab. Anal, 10:277-284, 1996.
- 35
-
H. Musielski, W Mann, R Laue, and S Michel.
Influence of dimethylsulfoxide on transcription by bacteriophage
T3-induced RNA polymerase.
Z allg Microbiol, 21:447-456, 1981.
- 36
-
Tatsuo Ohmichi, Shu-ichi Nakano, Daisuke Miyoshi, and Naoki Sugimoto.
Long RNA danglingend has large energetic contribution to duplex
stability.
J. Am. Chem. Soc., 124:10367-10372, 2002.
- 37
-
Amanda S. O'toole, Stacy Miller, Nathan Haines, M. Coleen Zink, and Martin J
Serra.
Comprehensive thermodynamic analysis of 3' double-nucleotide
overhangs neighboring Watson-Crick terminal base pairs.
Nucleic Acids research, 34:3338-3344, 2006.
- 38
-
Amanda S. O'toole, Stacy Miller, and Martin J Serra.
Stability of 3' double nucleotide overhangs that model the 3'
ends of siRNA.
RNA, 11:512-516, 2005.
- 39
-
R. Owczarzy, B.G. Moreira, Y. You, M.B. Behlke, and J.A. Walder.
Predicting stability of DNA duplexes in solutions containing
magnesium and monovalent cations.
Biochemistry, 47:5336-5353, 2008.
- 40
-
Richard Owczarzy, Yong You, Christopher L. Groth, and Andrey V. Tataurov.
Stability and mismatch discrimination of locked nucleic acid DNA
duplexes.
Biochemistry, 50:9352-9367, 2011.
- 41
-
Richard Owczarzy, Yong You, Bernardo G. Moreira, Jeffrey A. Manthey, Lingyan
Huang, Mark A. Behlke, and Joseph A. Walder.
Effects of sodium ions on dna duplex oligomers: Improved predictions
of melting temperatures.
Biochemistry, 43:3537-3554, 2004.
- 42
-
RJ Owen, LR Hill, and SP. Lapage.
Determination of DNA base compositions from melting profiles in
dilute buffers.
Biopolymers, 7:503-516, 1969.
- 43
-
N. Peyret.
Prediction of nucleic acid hybridization : parameters and algorithms.
Ph.D Thesis 4.2, 128, Wayne State University, Detroit, MI., 5,
2000.
- 44
-
N. Peyret, P.A. Seneviratne, H.T. Allawi, and J. SantaLucia.
Nearest neighbor thermodynamics and NMR of DNA sequences with
internal A.A, C.C, G.G and T.T mismatches. dependence and pH effects.
Biochemistry, 38:3468-3477, 1999.
- 45
-
M.T. Record, Jr.
Electrostatic effects on polynucleotide transitions. I. Behavior at
neutral pH.
Biopolymers, 5:975-992, 1967.
- 46
-
J. SantaLucia.
A unified view of polymer, dumbbell, and oligonucleotide DNA
nearest-neighbor thermodynamics.
Proc Natl Acad Sci USA, 95:1460-1465, 1998.
- 47
-
J. SantaLucia and Donald Hicks.
The thermodynamics of DNA structural motifs.
Annu. Rev. Biophys. Struct, 33:415-440, 2004.
- 48
-
J. SantaLucia, Jr, H.T. Allawi, and P.A. Seneviratne.
Improved nearest-neighbor parameters for predicting DNA duplex
stability.
Biochemistry, 35:3555-3562, 1996.
- 49
-
C. Schildkraut and S. Lifson.
Dependence of the melting temperature of DNA on salt concentration.
Biopolymers, 3:195-208, 1965.
- 50
-
N. Sugimoto, M. Katoh, S. Nakano, T. Ohmichi, and M. Sasaki.
RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs
have identical stability.
FEBS Letters, 354:74-78, 1994.
- 51
-
N. Sugimoto, S. Nakano, M. Katoh, A. Matsumura, H. Nakamuta, T. Ohmichi,
M. Yoneyama, and M. Sasaki.
Thermodynamic parameters to predict stability of RNA/DNA hybrid
duplexes.
Biochemistry, 34:11211-11216, 1995.
- 52
-
N. Sugimoto, S. Nakano, M. Yoneyama, and K. Honda.
Improved thermodynamic parameters and helix initiation factor to
predict stability of DNA duplexes.
Nuc Acids Res, 24:4501-4505, 1996.
- 53
-
Zhi-Jie Tan and Shi-Jie Chen.
Nucleic acid helix stability: effects of salt concentration, cation
valence and size, and chain length.
Biophysical Journal, 90:1175-1190, 2006.
- 54
-
Zhi-Jie Tan and Shi-Jie Chen.
Rna helix stability in mixed Na+/Mg2+ solutions.
Biophysical Journal, 92:3615-3632, 2007.
- 55
-
Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, and Azuma Ohuchi.
Thermodynamic parameters based on a nearest neighbor model for DNA
sequences with a single bulge loop.
Biochemistry, 43:7143-7150, 2004.
- 56
-
Nicolas von Ahsen, Carl T Wittwer, and Ekkehard Schutz.
Oligonucleotide melting temperatures under PCR conditions :
deoxynucleotide triphosphate and dimethyl sulfoxide concentrations with
comparison to alternative empirical formulas.
Clinical Chemistry, 47:1956-1961, 2001.
- 57
-
GM Wahl, SL Berger, and AR. Kimmel.
Molecular hybridization of immobilized nucleic acids: theoretical
concepts and practical considerations.
Methods Enzymol, 152:399-407, 1987.
- 58
-
N.E. Watkins and J. Santalucia, Jr.
Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA
duplexes.
Nuc Acids Res, 33:6258-6267, 2005.
- 59
-
Norman E. Watkins, Jr, William J. Kennely, Mike J. Tsay, Astrid Tuin, Lara
Swenson, Hyung-Ran Lee, Svetlana Morosyuk, Donald A. Hicks, and John
Santalucia, Jr.
Thermodynamic contributions of single internal rA.dA, rC.dC,
rG.dG and rU.dT mismatches in RNA/DNA duplexes.
Nucleic Acids Research, 39:1894-1902, 2011.
- 60
-
J.G. Wetmur.
DNA probes: applications of the principles of nucleic acid
hybridization.
Crit Rev Biochem Mol Biol, 26:227-259, 1991.
- 61
-
D.J. Wright, J.L. Rice, D.M. Yanker, and B.M. Znosko.
Nearest neighbor parameters for inosine-uridine pairs in RNA
duplexes.
Biochemistry, 46:4625-4634, 2007.
- 62
-
T. Xia, J. SantaLucia, M.E. Burkard, R. Kierzek, S.J. Schroeder, X. Jiao,
C. Cox, and D.H. Turner.
Thermodynamics parameters for an expanded nearest-neighbor model for
formation of RNA duplexes with Watson-Crick base pairs.
Biochemistry, 37:14719-14735, 1998.
New versions and
related material can be found at
http://www.pasteur.fr/recherche/unites/neubiomol/meltinghome.html
https://sourceforge.net/projects/melting/
http://www.ebi.ac.uk/compneur-srv/melting/
You can use MELTING through a web server at
http://bioweb.pasteur.fr/seqanal/interfaces/melting.htmlhttp://www.ebi.ac.uk/compneur-srv/melting/melt.php
Melting is copyright
©1997, 2014 by Nicolas Le Novère, Marine Dumousseau and William John Gowers.
This program is free software;
you can redistribute it and/or modify it under the terms of the GNU General
Public License as published by the Free Software Foundation; either version
2 of the License, or (at your option) any later version.
This program
is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Thanks to Richard Owczarzy for reporting typos in several thermodynamic parameters and reporting new public parameters.
Nicolas Joly is an efficient and kind debugger and advisor. Catherine
Letondal wrote the HTML interface to melting. Thanks to Nirav Merchant,
Taejoon Kwon, Leo Schalkwyk, Mauro Petrillo, Andrew Thompson, Wong Chee Hong, Ivano
Zara for their bug fixes and comments. Thanks to Richard Owczarzy for his magnesium
correction. Thanks to Charles Plessy for the graphical interface files. Thanks to Daniel McGreal for the SOAP interface of MELTING at the EMBL-EBI. Thanks to Nicolas Rodriguez for the current web interface and finally thanks
to the usenet helpers, particularly Olivier Dehon and Nicolas Chuche.
Nicolas Le Novère, Marine Dumousseau and William John Gowers,
EMBL-EBI,
Wellcome-Trust Genome Campus
Hinxton Cambridge, CB10 1SD, UK
n.lenovere@gmail.com
The Java version has been rewriten from the beginning.
See the file ChangeLog for the changes of the versions 4 and more recent.
MELTING - nearest-neighbor computation of nucleic acid hybridation
This document was generated using the
LaTeX2HTML translator Version 2008 (1.71)
Copyright © 1993, 1994, 1995, 1996,
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Computer Based Learning Unit, University of Leeds.
Copyright © 1997, 1998, 1999,
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The command line arguments were:
latex2html -split 1 -dir html/ -local_icons melting.tex
The translation was initiated by Marine on 2014-08-08
Marine
2014-08-08