MELTING - nearest-neighbor computation of nucleic acid hybridation
melting [options ]
MELTING computes, for a nucleic acid duplex, the enthalpy and the
entropy of the helix-coil transition, and then its melting temperature. Three
types of hybridisation are possible: DNA/DNA, DNA/RNA, and 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 ISO C and can be compiled on any
operating system. Some perl scripts are provided to show how melting can be used
as a block to construct more ambitious programs.
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.
The options are treated sequentially. If there is a conflict between the value
of two options, the latter normally erases the former.
- -Afile.nn
-
Informs the program to use file.nn as an alternative set of
nearest-neighbor parameters, rather than the default for the specified
hybridisation type (option -H). The standard distribution of melting
provides some files ready-to-use: all97a.nn (Allawi et al 1997),
bre86a.nn (Breslauer et al 1986), san96a.nn (SantaLucia et
al 1996), sug96a.nn (Sugimoto et al 1996), san04a.nn (Santalucia
et al 2004) (DNA/DNA),
fre86a.nn (Freier et al 1986), xia98a.nn (Xia et al 1998)
(RNA/RNA) and sug95a.nn (Sugimoto et al 1995) (DNA/RNA). 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. Be careful, the option -A changes the default
parameter set defined by the option -H.
- -Ccomplementary_sequence
-
Enters the complementary sequence, from 3' to 5'. This option is mandatory if
there are mismatches 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
- -Ddnadnade.nn
-
Informs the program to use the file dnadnade.nn to compute the
contribution of dangling ends to the thermodynamic of helix-coil transition.
The dangling ends are not taken into account by the approximative mode.
- -Ffactor
-
This is the a correction factor used to modulate the effect of the nucleic
acid concentration in the computation of the melting temperature. See section
ALGORITHM for details.
- -Gx.xxe-xx
-
Magnesium concentration (No maximum concentration for the moment). The effect
of ions on thermodynamic stability of nucleic acid duplexes is complex,
and the correcting functions are at best rough approximations.The published
Tm correction formula for divalent Mg2+ ions of Owczarzy et al.(2008) can
take in account the competitive binding of monovalent and divalent ions on DNA.
However this formula is only for DNA duplexes.
- -h
-
Displays a short help and quit with EXIT_SUCCESS.
- -Hhybridisation_type
-
Specifies the hybridisation type. This will set the nearest-neighbor set to
use if no alternative set is provided by the option -A (remember the
options are read sequentially). Moreover this parameter determines the
equation to use if the sequence length exceeds the limit of application of the
nearest-neighbor approach (arbitrarily set up by the author). Possible values
are dnadna, dnarna and rnadna (synonymous), and
rnarna. For reasons of compatibility the values of the previous
versions of melting A,B,C,F,R,S,T,U,W are still available although
strongly deprecated. Use the option -A to require an
alternative set of thermodynamic parameters. Important: If the duplex
is a DNA/RNA heteroduplex, the sequence of the DNA strand has to be entered
with the option -S
- -Iinput_file
-
Provides the name of an input file containing the parameters of the
run. The input has to contain one parameter per line, formatted as in
the command line. The order is not important, as well as blank lines.
example:
-Hdnadna
-Asug96a.nn
-SAGCTCGACTC
-CTCGAGGTGAG
-N0.2
-P0.0001
-v
-Ksan96a
- -ifile.nn
-
Informs the program to use file.nn as an alternative set of inosine pair
parameters, rather than the default for the specified hybridisation type.
The standard distribution of melting provides some files ready-to-use: san05a.nn
(Santalucia et al 2005) for deoxyinosine in DNA duplexes, bre07a.nn (Brent M Znosko
et al 2007)for inosine in RNA duplexes. Note that not all the inosine mismatched
wobble's pairs have been investigated. Therefore it could be impossible to compute
the Tm of a duplex with inosine pairs. Moreover, those inosine pairs are not taken
into account by the approximative mode.
- -Ksalt_correction
-
Permits to chose another correction for the concentration in sodium. Currently,
one can chose between wet91a, san96a, san98a. See section ALGORITHM
- -kx.xxe-xx
-
Potassium concentration (No maximum concentration for the moment). The effect of ions
on thermodynamic stability of nucleic acid duplexes is complex, and the correcting
functions are at best rough approximations.The published Tm correction formula for
sodium ions of Owczarzy et al.(2008) is therefore also applicable to buffers containing Tris or
KCl. Monovalent K+, Na+, Tris+ ions stabilize DNA duplexes
with similar potency, and their effects on duplex stability are additive. However this formula
is only for DNA duplexes.
- -L
-
Prints the legal informations and quit
with EXIT_SUCCESS.
- -Mdnadnamm.nn
-
Informs the program to use the file dnadnamm.nn to compute
the contribution of mismatches to the thermodynamic of helix-coil
transition. Note that not all the mismatched Crick's pairs have been
investigated. Therefore it could be impossible to compute the Tm of a
mismatched duplex. Moreover, those mismatches are not taken into
account by the approximative mode.
- -Nx.xxe-xx
-
Sodium concentration (between 0 and 10 M). The effect of ions on thermodynamic
stability of nucleic acid duplexes is complex, and the correcting functions
are at best rough approximations. Moreover, they are generally reliable only
for [Na+] belonging to [0.1,1 M]. If there are no other ions in
solution, we can use only the sodium correction. In the other case, we use the Owczarzy's
algorithm.
- -Ooutput_file
-
The output is directed to this file instead of the standard
output. The name of the file can be omitted. An automatic name is then
generated, of the form meltingYYYYMMMDD_HHhMMm.out (of course,
on POSIX compliant systems, you can emulate this with the redirection
of stdout to a file constructed with the program date).
- -Px.xxe-xx
-
Concentration of the nucleic acid strand in excess (between 0 and 0.1 M).
- -p
-
Return the directory supposed to contain the sets of calorimetric parameters and quit with
EXIT_SUCCESS. If the environment variable NN_PATH is set, it is returned. Otherwise, the value
defined by default during the compilation is returned.
- -q
-
Turn off the interactive correction of wrongly entered
parameter. Useful for run through a server, or a batch script. Default
is OFF (i.e. interactive on). The switch works in both sens.
Therefore if -q has been set in an input file, another
-q on the command line will switch the quiet mode OFF (same
thing if two -q are set on the same command line).
- -Ssequence
-
Sequence of one strand of the nucleic
acid duplex, entered 5' to 3'. Important: If it is a DNA/RNA heteroduplex,
the sequence of the DNA strand has to be entered.
Uridine and thymidine are
considered as identical. The bases can be upper or lowercase.
- -Txxx
-
Size threshold before approximative computation. The nearest-neighbour approach
will be used only if the length of the sequence is inferior to this threshold.
- -tx.xxe-xx
-
Tris buffer concentration (No maximum concentration for the moment).
The effect of ions on thermodynamic stability of nucleic acid
duplexes is complex, and the correcting functions are at best
rough approximations.The published Tm correction formula for sodium ions of
Owczarzy et al (2008)is therefore also applicable to buffers containing Tris or
KCl. Monovalent K+, Na+, Tris+ ions stabilize DNA duplexes with similar potency, and
their effects on duplex stability are additive. However this formula is only for DNA
duplexes. Be aware, the Tris+ ion concentration is about half of the total tris buffer
concentration.
- -v
-
Control the verbose
mode, issuing a lot more information about the current run (try it once
to see if you can get something interesting). Default is OFF. The switch
works in both sens. Therefore if -v has been set in an input file, another
-v on the command line will switch the verbose mode OFF (same thing if
two -v are set on the same command line).
- -V
-
Displays the version number
and quit with EXIT_SUCCESS
- -x
-
Force the program to compute an approximative
tm, based on G+C content. 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.
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. Therefore, the 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). This program first
computes the hybridisation enthalpy and entropy from the elementary parameters
of each Crick's pair.
See Wetmur J.G. (1991) and SantaLucia (1998)
for deep reviews on the nucleic acid hybridisation and on the different
set of nearest-neighbor parameters.
Figure 1:
Comparison of experimental and computed Tm for various sets of
nearest-neighbor parameters. [Na+] = 1 M, [nucleic acid] = 4.10-4 M
 |
Figure 2:
Comparison of experimental and computed Tm for various sets of
nearest-neighbor parameters. [Na+] = 0.11 M, [nucleic acid] = 8.10-6 M
 |
The mismatching (inosine mismatches included) pairs are also taken into account. However the thermodynamic
parameters are still not available for every possible cases (notably when both
positions are mismatched). In such a case, the program, unable to compute any
relevant result, will quit with a warning. 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
The dangling ends, that is the unmatched terminal nucleotides, can be taken into
account.
(The same computation is performed for ΔG)
Then the melting temperature is computed by the following formula:
Tm |
= |
 |
![$ \mathcal{F}([\mathrm{Na}^+]) - 273.15 $](melting/img5.png) |
|
|
|
|
|
|
Tm in K (for [Na+] = 1 M) |
correction for the
salt concentration (if there are only Na+ cations in the solution) and to get the temperature in degree Celsius. (In fact
some corrections are directly included in the ΔS. See that of SanLucia
1998)
|
Many thanks to Ivano Zara (zarivan@cribi.unipd.it), who gave me most of
the following explanation.
In a reaction
, where A is the strand in
excess, B the other strand, and D the duplex, and where the
oligonucleotides are not self-complementary,
and
If ξ is the fraction of molecules B that forms the duplex,
Therefore,
and, at melting temperature, when
,
If both strands are present in equivalent amount,
and
, then
(
). If
, then
and
(
).
If the oligonucleotides are self-complementary,
and (
).
Note however that MELTING makes the assumption of no self-assembly,
i.e. the computation does not take any entropic term to correct for
self-complementarity.
If there are only sodium ions in the solution, we can use the following
corrections. the correction can be chosen between wet91a, presented in
Wetmur 1991 i.e.
san96a presented in SantaLucia et al. 1996
i.e.

Na
and san98a presented in SantaLucia 1998 i.e. a correction
of the entropic term without modification of enthalpy
Where N is the length of the duplex (SantaLucia 1998 actually used 'N' the number of non-terminal phosphates, that is effectively equal to our N-1).
Figure 3:
Comparison of experimental and computed Tm for various correction
of salt concentration.
![\includegraphics[]{salt.eps}](melting/salt.png) |
If there are only Na+ ions, we can use the correction for the concentration of salt
(see above). In the opposite case, we will use the magnesium and monovalent ions correction
from Owczarzy et al (2008). (only for DNA duplexes)
[Mon+] = [Na+] + [K+] + [Tris+]
Where [Tris+] is equal to half of total tris buffer concentration. (in the option -t, it is the Tris buffer concentration
which is entered).
When the divalent ions are the only ions present, the melting temperature is :
where :
a = 3.92 x 10-5
b = 9.11 x 10-6
c = 6.26 x 10-5
d = 1.42 x 10-5
e = 4.82 x 10-4
f = 5.25 x 10-4
g = 8.31 x 10-5.
Fgc is the fraction of GC base pairs in the sequence and
Nbp is the length of the sequence (Number of base pairs).
When there are both monovalent and divalent ions, there are several cases because we can have
a competitive DNA binding between monovalent and divalent
cations :
If the following ratio :
is inferior to 0.22, monovalent ion influence is dominant, divalent cations can be
disregarded and the melting temperature is :
Figure 4:
Comparison of experimental and computed Tm with the algorithm published in Owczarzy et al.(2008). [Mon+] = 0.055 M,[Mg2+] = 0 M, [nucleic acid] = 2.10-6 M
 |
If the ratio is included in [0.22, 6[,
we must take in account both Mg2+ and monovalent cations
concentrations. The melting temperature is calculated with the first equation but with monovalent ions concentration dependent parameters a, d and g :
a = 3.92 x 10
-5 x (0.843 - 0.352 x [Mon
+]0.5 x ln([Mon
+]))
d = 1.42 x 10
-5 x (1.279 - 4.03 x 10
-3 x ln([mon
+]) - 8.03 x 10
-3 x ln([mon
+] x ln([mon
+])
g = 8.31 x 10
-5 x (0.486 - 0.258 x ln([mon
+]) + 5.25 x 10
+ x ln([mon
+] x ln([mon
+] x ln([mon
+])
.
and b, c, e, f are constant.
Figure 5:
Comparison of experimental and computed Tm with the algorithm published in Owczarzy et al.(2008). [Mon+] = 0.055 M,[Mg2+] = 0.0015 M, [nucleic acid] = 2.10-6 M
 |
Finally, if the ratio is superior to 6,
divalent ion influence is dominant, monovalent cations can be disregarded and the melting temperature is calculated with the first equation and the constant parameters a, b, c, d,
e, f, g.
Figure 6:
Comparison of experimental and computed Tm with the algorithm published in Owczarzy et al.(2008). [Mon+] = 0.001 M,[Mg2+] = 0.0015 M, [nucleic acid] = 2.10-6 M
 |
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 is computed by the following formulas:
ADN/ADN:
ADN/ARN:
ARN/ARN:
The usage of this mode is nevertheless strongly disencouraged.
MELTING is currently accurate only when the hybridisation is performed
at pH 71. The computation is valid only for the hybridisations performed
in aqueous medium. Therefore the use of denaturing agents such as formamide
completely invalidates the results.
Allawi
H.T., SantaLucia J. (1997). Thermodynamics and NMR of internal G-T mismatches
in DNA. Biochemistry 36: 10581-10594
Allawi H.T., SantaLucia J. (1998).
Nearest Neighbor thermodynamics parameters for internal G.A mismatches in DNA.
Biochemistry
37: 2170-2179
Allawi H.T., SantaLucia J. (1998).
Thermodynamics of internal C.T mismatches in DNA.
Nucleic Acids Res
26: 2694-2701
Allawi H.T., SantaLucia J. (1998).
Nearest Neighbor thermodynamics of internal A.C mismatches in DNA: sequence
dependence and pH effects.
Biochemistry
37: 9435-9444.
Bommarito S., Peyret N., SantaLucia J. (2000). Thermodynamic parameters for DNA
sequences with dangling ends. Nucleic Acids Res 28: 1929-1934
Breslauer K.J., Frank R., Blöcker
H., Marky L.A. (1986). Predicting DNA duplex stability from the base sequence.
Proc Natl Acad Sci USA 83: 3746-3750
Freier S.M., Kierzek R., Jaeger
J.A., Sugimoto N., Caruthers M.H., Neilson T., Turner D.H. (1986). Biochemistry
83:9373-9377
Owczarzy R., Moreira B.G., You Y., Behlke M.B., Walder J.A.(2008) Predicting stability of DNA duplexes
in solutions containing Magnesium and Monovalent Cations. Biochemistry 47: 5336-5353.
Peyret N., Seneviratne P.A., Allawi H.T., SantaLucia J. (1999).
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
SantaLucia J. Jr, Allawi H.T., Seneviratne P.A. (1996). Improved
nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry
35: 3555-3562
Sugimoto N., Katoh M., Nakano S., Ohmichi T., Sasaki M. (1994).
RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs hve identical
stability. FEBS Letters 354: 74-78
Sugimoto N., Nakano S., Katoh M., Matsumura
A., Nakamuta H., Ohmichi T., Yoneyama M., Sasaki M. (1995). Thermodynamic parameters
to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34: 11211-11216
Sugimoto N., Nakano S., Yoneyama M., Honda K. (1996). Improved thermodynamic
parameters and helix initiation factor to predict stability of DNA duplexes.
Nuc Acids Res 24: 4501-4505
Watkins N.E., Santalucia J. Jr. (2005). Nearest-neighbor thermodynamics of deoxyinosine
pairs in DNA duplexes. Nucleic Acids Research 33: 6258-6267
Wright D.J., Rice J.L., Yanker D.M., Znosko B.M. (2007). Nearest neighbor parameters for
inosine-uridine pairs in RNA duplexes. Biochemistry 46: 4625-4634
Xia T., SantaLucia J., Burkard M.E., Kierzek
R., Schroeder S.J., Jiao X., Cox C., Turner D.H. (1998). Thermodynamics parameters
for an expanded nearest-neighbor model for formation of RNA duplexes with
Watson-Crick base pairs. Biochemistry 37: 14719-14735
For review see:
SantaLucia J. (1998) A unified view of polymer, dumbbell, and oligonucleotide
DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95: 1460-1465
SantaLucia J., Hicks Donald (2004) The Thermodynamics of DNA structural motifs.
Annu. Rev. Biophys. Struct. 33: 415-440
Wetmur J.G. (1991) DNA probes: applications of the principles of nucleic
acid hybridization. Crit Rev Biochem Mol Biol 26: 227-259
- *.nn
- Files containing the nearest-neighbor parameters, enthalpy and entropy,
for each Crick's pair. They have to be placed in a directory defined during
the compilation or targeted by the environment variable NN_PATH.
- tkmelting.pl
- A Graphical User Interface written in perl/tk is available for users
who prefer the 'button and menu' approach.
- *.pl
- Scripts are available to
use MELTING iteratively. For instance, the script multi.pl permits to predict
the Tm of several duplexes in one shot. The script profil.pl allow
an interactive computation along a sequence, by sliding a window of specified width.
New versions and
related material can be found at http://www.ebi.ac.uk/~lenov/meltinghome.html
and at https://sourceforge.net/projects/melting/
You can use MELTING through a web server at http://bioweb.pasteur.fr/seqana
l/interfaces/melting.html
The infiles have to be ended by a blank line because otherwise the last line is not decoded.
If an infile is called, containing the
address of another input file, it does not care of this latter. If it
is its own address, the program quit (is it a bug or a feature?).
In interactive mode, a sequence can be entered on several lines with a backslash
AGCGACGAGCTAGCCTA\
AGGACCTATACGAC
If by mistake it is entered as
AGCGACGAGCTAGCCTA\AGGACCTATACGAC
The backslash will be considered
as an illegal character. Here again, I do not think it is actually a bug
(even if it is unlikely, there is a small probability that the backslash
could actually be a mistyped base).
Melting is copyright
©1997, 2013 by Nicolas Le Novère and Marine Dumousseau
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
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. Markus Piotrowski
updated TkMELTING to cover version 4.3. Finally thanks to the usenet helpers, particularly Olivier Dehon and Nicolas Chuche.
Nicolas Le Novère
Babraham Institute
Babraham Research Campus
Babraham CB22 3AT Cambridge UK
n.lenovere@gmail.com
Marine Dumousseau,
EMBL-EBI,
Wellcome-Trust Genome Campus
Hinxton Cambridge, CB10 1SD, UK
marine@ebi.ac.uk
See the file ChangeLog for the changes of the versions 4 and more recent.