Provided by: melting_5.2.0-1_all 
NAME
melting - nearest-neighbor computation of nucleic acid hybridation
SYNOPSIS
melting [options]
DESCRIPTION
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.
OPTIONS
The options are treated sequentially. If there is a conflict between the value of two
options, the latter normally erases the former.
Information about
Melting
-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.
Mandatory options
-Ssequence
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.
-Csequence
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 programm 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 IMPORTANT: Uridine and thymidine are not considered as
identical. The bases can be upper or lowercase.
-Eion1_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 percent)
and the formamide concentrations (in percent 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.
-Px.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 M.
-Hhybridization_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.
General options
-Txxx 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).
-nnpathfolder_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.
-Ooutput_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:
###beginning###
- The sequence ATCGCGAT is self complementary. The option -self
is not necessary because the programm can automatically detect it.
- The sequence -TCGCGAT is self complementary but with a single dangling end. The
option -self
is not necessary because the programm can automatically detect it.
- 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 programm can't
automatically detect it.
###end###
-Fxxx This is the correction factor used to modulate the effect of the nucleic acid
concentration in the computation of the melting temperature. 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.
Set of thermodynamic parameters and methods (models)
By default, the approximative mode is used for oligonucleotides longer than 60 bases (the
default threshold value), otherwise the nearest neighbor model is used.
-ammethod_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 et al. 1993)
che93corr (from von Ahsen et al. 2001, Marmur 1962, Chester et al. 1993)
schdot (Marmur-Schildkraut-Doty formula)
owe69 (from Owen et al. 1969)
san98 (from Santalucia et al. 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 :
###beginning###
- "-am" if you want to force the approximative approach with the default formula.
- "-am ahs01" if you want to use the approximative formula from Ahsen et al. 2001.
###end###
-nnmethod_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 Kierzeck 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:
###beginning###
- "-nn" if you want to force the nearest neighbor computation with the default
model.
- "-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.
- "-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.
- "-nn :fileName" if you want to use the default nearest neighbor model with the
thermodynamic parameters in the file fileName.
###end###
-sinMMmethod_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)
RNA duplexes
tur06 (from Lu et al. 2006)
zno07 (from Davis et al. 2007) (by default)
zno08 (from Davis et al. 2008)
DNA/RNA duplexes
wat10 (from Watkins et al. 2011) (by default)
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.
-GUMmethod_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.
-tanMMmethod_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.
-intLPmethod_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 Badhwarr 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.
-sinDEmethod_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.
-secDEmethod_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.
-lonDEmethod_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.
-sinBUmethod_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 Hicks and 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.
-lonBUmethod_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 Lu et al. 1999 and 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.
-CNGmethod_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.
-inomethod_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 et al. 2005) (by default)
RNA duplexes
zno07 (from Wright et al. 2007) (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.
-hamethod_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)
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.
-azomethod_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.
-lckmethod_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.) (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. -tanLckmethod_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. -sinMMLckmethod_name Forces to use a specific
nearest neighbor model to compute the contribution of consecutive locked nucleic
acids with a single mismatch (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 with single mismatch, 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.
-ionmethod_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 et al 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^0.5
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. examples :
###beginning###
- "-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.
###end###
-naeqmethod_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. examples :
###beginning###
- "-naeq ahs01" if you want to force the use of the magnesium correction 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. - "-naeq ahs01 -ion san04" 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)
###end###
-DMSOmethod_name
Forces to use a specific DMSO correction (DMSO is always in percent). 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 :
###beginning###
- "-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.
###end###
-formethod_name
Forces to use a specific formamide correction. You can use one of the following :
DNA duplexes}]
bla96 (from Blake et al 1996) with formamide concentration in M (by default)
lincorr (linear correction) with a percent 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 :
###beginning###
- "-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.
###end###
REFERENCES
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.
Amanda S. O'toole, Stacy Miller and Martin J Serra (2005) Stability of 3' double
nucleotide overhangs that model the 3'ends of siRNA. RNA 11: 512-516
Amanda S. O'toole, Stacy Miller, Nathan Haines, M. Coleen Zink and Martin J Serra (2006).
Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-
Crick terminal base pairs. Nucleic Acids research 34: 3338-3344
Amber R. Davis, and Brent M. Znosko (2007) Thermodynamic Characterization of Single
Mismatches Found in Naturally Occurring RNA. Biochemistry 46: 13425-13436
Amber R. Davis, and Brent M. Znosko (2008) Thermodynamic Characterization of Naturally
Occurring RNA Single Mismatches with G-U Nearest Neighbors. Biochemistry 47: 10178-10187
Blake, R. D., and Delcourt, S. G. (1998) Thermal stability of DNA. Nucleic Acids Res 26:
3323-3332 and corrigendum.
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., Bl�ker H., Marky L.A. (1986). Predicting DNA duplex stability
from the base sequence. Proc Natl Acad Sci USA 83: 3746-3750
Broda Magdalena, Elbieta Kierzek, Zofia Gdaniec, Tadeusz Kulinski and Ryszard Kierzek
(2005) Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats.
Implication for prediction of RNA structure. Biochemistry 44: 10873-10882.
Casey J., and Davidson N. (1977) Nucleic acids research 4: 1539-1532.
Cullen Br, Bick Md (1976) Thermal denaturation of DNA from bromodeoxyuridine substitued
cells. Nucleic acids research 3: 49-62.
David H. Mathews, Jeffrey Sabina, Michael Zucker and Douglas H Turner (1999) Expanded
sequence dependence of thermodynamic parameters improves prediction of RNA secondary
structure. J. Mol. Biol 288 : 911-940
Elzbieta Kierzek, David H. Mathews, Anna Ciesielska, Douglas H. Turner and Ryszard Kierzek
(2006) Nearest neighbor parameters for Watson Crick complementary heteroduplexes formed
between 2-O-methyl RNA and RNA oligonucleotides. Nucleic acids research 34: 3609-3614
Escara JF, Hutton Jr (1980) Thermal stability and renaturation of DNA in dimethyl
sulfoxide solutions: acceleration of the renaturation rate. Biopolymers 19: 1315-1327.
Frank-Kamenetskii, M. D. (1971) Simplification of the empirical relationship between
melting temperature of DNA, its GC content and concentration of sodium ions in solution
Biopolymers 10: 2623-2624.
Freier S.M., Kierzek R., Jaeger J.A., Sugimoto N., Caruthers M.H., Neilson T., Turner D.H.
(1986). Improved free-energy parameters for predictions of RNA duplex stability.
Biochemistry 83: 9373-9377
Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto and Azuma Ohuchi (2004). Thermodynamic
Parameters based on a nearest neighbor model for DNA sequences with a single bulge loop.
Biochemistry 43 : 7143-7150
Hiroyuki Asanuma, Daijiro Matsunaga and Makoto Komiyama (2005) 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
Hutton Jr (1977) Nucleic acids research 4: 3537-3555.
Jaya Badhwar, Saradasri Karri, Cody K. Cass, Erica L. Wunderlich and Brent M. Znosco
(2007). Thermodynamic characterization of RNA duplexes containing naturally occuring 1x2
nucleotide internal loops. Biochemistry 46: 14715-14724.
Joshua M. Blose, Michelle L. Manni, Kelly A. Klapec, Yukiko Stranger-Jones, Allison C.
Zyra, Vasiliy Sim, Chad A. Griffith, Jason D. Long, and Martin J. Serra (2007) 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
Junji Kawakami1,2, Hiroyuki Kamiya3, Kyohko Yasuda2, Hiroyoshi Fujiki1, Hiroshi Kasai3 and
Naoki Sugimoto (2001) 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
Marmur, J., and Doty, P. (1962) Determination of the base composition of deoxyribonucleic
acid from its thermal denaturation temperature J. Mol. Biol. 5: 109-118.
McConaughy, B.L., Laird, C.D. and McCarthy, B.I. (1969) Biochemistry
8: 3289-3295.
Mitsuhashi M. (1996) Technical report: Part 1. Basic requirements for designing optimal
oligonucleotide probe sequences. J. Clin. Lab. Anal 10: 277-284.
Musielski H., Mann W, Laue R, Michel S (1981) Influence of dimethylsulfoxide on
transcription by bacteriophage T3-induced RNA polymerase. Z allg Microbiol 21: 447-456.
Nicolas Von Ahsen, Carl T Wittwer and Ekkehard Schutz (2001) Oligonucleotide melting
temperatures under PCR conditions : deoxynucleotide Triphosphate and Dimethyl sulfoxide
concentrations with comparison to alternative empirical formulas Clinical Chemistry 47:
1956-1961.
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.
Patricia M. McTigue, Raymond J. Peterson, and Jason D. Kahn (2004) Sequence-Dependent
Thermodynamic Parameters for Locked Nucleic Acid (LNA) DNA Duplex Formation. Biochemistry
43 : 5388-5405
Peyret N. (2000) Prediction of nucleic acid hybridization : parameters and algorithms.
Ph.D Thesis Section .5.4.2, 128, Wayne State University, Detroit, MI.
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
R. D. Blake and Scott G. Delcourt (1996) Thermodynamic effects of formamide on DNA
stability. Nucleic Acids Research 24, No. 11 : 2095-2103
Record, M.T., Jr (1967) Biopolymers 5: 975-992.
Richard Owczarzy, Yong You, Bernardo G. Moreira, Jeffrey A.Manthey, Lingyan Huang, Mark A.
Behlke and Joseph A.Walder (2004) Effects of sodium ions on DNA duplex oligomers: Improved
predictions of melting temperatures. Biochemistry 43: 3537-3554.
SantaLucia J. Jr, Allawi H.T., Seneviratne P.A. (1996). Improved nearest-neighbor
parameters for predicting DNA duplex stability. Biochemistry 35: 3555-3562
Schildkraut, C., and Lifson, S. (1965) Dependence of the melting temperature of DNA on
salt concentration. Biopolymers 3: 195-208.
Stacy Miller, Laura E. Jones, Karen Giovannitti, Dan Piper and Martin J. Serra (2008)
Thermodynamic analysis of 5 and 3 single- and 3 double-nucleotide overhangs neighboring
wobble terminal base pairs. Nucleic Acids research 36: 5652-5659
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
Tatsuo Ohmichi, Shu-ichi Nakano, Daisuke Miyoshi and Naoki Sugimoto (2002) Long RNA
dangling end has large energetic contribution to duplex stability. J. Am. Chem. Soc.
124: 10367-10372
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
Zhi-Jie Tan and Shi-Jie Chen, (2006). Nucleic acid helix stability: effects of Salt
concentration, cation valence and size, and chain length. Biophysical Journal 90:
1175-1190.
Zhi-Jie Tan and Shi-Jie Chen (2007). RNA helix stability in Mixed Na+/Mg2+ solutions"
Biophysical Journal 92: 3615-3632.
Zhi John Lu, Douglas H. Turner and David H. Mathews (2006). A set of nearest neighbor
parameters for predicting the enthalpy change of RNA secondary structure formation.
Nucleic Acids Research 34: 4912-4924.
Jonathan L. Chen,† Abigael L. Dishler, Scott D. Kennedy, Ilyas Yildirim, Biao Liu, Douglas
H. Turner and Martin J. Serra (2012). Testing the Nearest Neighbor Model for Canonical
RNA Base Pairs: Revision of GU Parameters. Biochemistry 51: 3508–3522.
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
SEE ALSO
New versions and related material can be found at
http://www.pasteur.fr/recherche/unites/neubiomol/meltinghome.html
htpps://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.html http://www.ebi.ac.uk/compneur-
srv/melting/melt.php
COPYRIGHT
Melting is copyright (C) 1997, 2009 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
AUTHORS
Nicolas Le Novère, Marine Dumousseau and William John Gowers
EMBL-EBI
Wellcome-Trust Genome Campus
Hinxton Cambridge
CB10 1SD United-Kingdom
e-mail: n.lenovere@gmail.com