Package 'rmelting'

Compute melting temperature of a nucleic acid duplex

Description

Compute the enthalpy and entropy of helix-coil transition, and then the melting temperature of a nucleic acid duplex with the MELTING 5 software (Le Novère, 2001; Dumousseau et al., 2012).

Usage

melting(sequence, comp.sequence = NULL,
        nucleic.acid.conc,
        hybridisation.type = c("dnadna", "rnarna", "dnarna",
                               "rnadna", "mrnarna", "rnamrna"),
        Na.conc, Mg.conc, Tris.conc, K.conc,
        dNTP.conc, DMSO.conc, formamide.conc,
        size.threshold = 60, force.self = FALSE, correction.factor,
        method.approx = c("ahs01", "che93", "che93corr",
                          "schdot", "owe69", "san98",
                          "wetdna91", "wetrna91", "wetdnarna91"),
        method.nn = c("all97", "bre86", "san04", "san96", "sug96",
                      "tan04", "fre86", "xia98", "sug95", "tur06"),
        method.GU = c("tur99", "ser12"),
        method.singleMM = c("allsanpey", "tur06", "zno07", "zno08", "wat11"),
        method.tandemMM = c("allsanpey", "tur99"),
        method.single.dangle = c("bom00", "sugdna02", "sugrna02", "ser08"),
        method.double.dangle = c("sugdna02", "sugrna02", "ser05", "ser06"),
        method.long.dangle = c("sugdna02", "sugrna02"),
        method.internal.loop = c("san04", "tur06", "zno07"),
        method.single.bulge.loop = c("tan04", "san04", "ser07" ,"tur06"),
        method.long.bulge.loop = c("san04", "tur06"),
        method.CNG = c("bro05"),
        method.inosine = c("san05", "zno07"),
        method.hydroxyadenine = c("sug01"),
        method.azobenzenes = c("asa05"),
        method.locked = c("owc11", "mct04"),
        method.consecutive.locked = c("owc11"),
        method.consecutive.locked.singleMM = c("owc11"),
        correction.ion = c("ahs01", "kam71", "marschdot",
                           "owc1904", "owc2004", "owc2104",
                           "owc2204", "san96", "san04", "schlif",
                           "tanna06", "tanna07", "wet91",
                           "owcmg08", "tanmg06", "tanmg07",
                           "owcmix08", "tanmix07"),
        method.Naeq = c("ahs01", "mit96", "pey00"),
        correction.DMSO = c("ahs01", "cul76", "esc80", "mus81"),
        correction.formamide = c("bla96", "lincorr"))

Arguments

sequence	Sequence (5' to 3') of one strand of the nucleic acid duplex as a character string (Note: Uridine and thymidine are not considered as identical).
comp.sequence	Complementary sequence (3' to 5') of the nucleic acid duplex as a character string.
nucleic.acid.conc	Concentration of the nucleic acid strand (M or mol L-1) in excess as a numeric value.
hybridisation.type	The hybridisation type. Either "dnadna", "rnarna", "dnarna", "rnadna", "mrnarna" or "rnamrna" (see Hybridisation type options).
Na.conc	Concentration of Na ions (M) as a positive numeric value (see Ion and agent concentrations).
Mg.conc	Concentration of Mg ions (M) as a positive numeric value (see Ion and agent concentrations).
Tris.conc	Concentration of Tris ions (M) as a positive numeric value (see Ion and agent concentrations).
K.conc	Concentration of K ions (M) as a positive numeric value (see Ion and agent concentrations).
dNTP.conc	Concentration of dNTP (M) as a positive numeric value (see Ion and agent concentrations).
DMSO.conc	Concentration of DMSO (%) as a positive numeric value (see Ion and agent concentrations).
formamide.conc	Concentration of formamide (M or % depending on correction method) as a positive numeric value (see Ion and agent concentrations).
size.threshold	Sequence length threshold to decide approximative or nearest-neighbour approach for computation. Default is 60.
force.self	logical. Enforces that sequence is self complementary and complementary sequence is not required (seed Self complementary sequences). Default is FALSE.
correction.factor	Correction factor to be used to modulate the effect of the nucleic acid concentration (nucleic.acid.conc) in the computation of melting temperature (see Correction factor for nucleic acid concentration).
method.approx	Specify the approximative formula to be used for melting temperature calculation for sequences of length greater than size.threshold. Either "ahs01", "che93", "che93corr", "schdot", "owe69", "san98", "wetdna91", "wetrna91" or "wetdnarna91" (see Approximative formulas).
method.nn	Specify the nearest neighbor model to be used for melting temperature calculation for perfectly matching sequences of length lesser than size.threshold. Either "all97", "bre86", "san04", "san96", "sug96", "tan04", "fre86", "xia98", "sug95" or "tur06" (see Perfectly matching sequences).
method.GU	Specify the nearest neighbor model to compute the contribution of GU base pairs to the thermodynamic of helix-coil transition. Either "tur99" or "ser12" (see GU wobble base pairs effect).
method.singleMM	Specify the nearest neighbor model to compute the contribution of single mismatch to the thermodynamic of helix-coil transition. Either "allsanpey", "tur06", "zno07" "zno08" or "wat11" (see Single mismatch effect).
method.tandemMM	Specify the nearest neighbor model to compute the contribution of tandem mismatches to the thermodynamic of helix-coil transition. Either "allsanpey" or "tur99" (see Tandem mismatches effect).
method.single.dangle	Specify the nearest neighbor model to compute the contribution of single dangling end to the thermodynamic of helix-coil transition. Either "bom00", "sugdna02", "sugrna02" or "ser08" (see Single dangling end effect).
method.double.dangle	Specify the nearest neighbor model to compute the contribution of double dangling end to the thermodynamic of helix-coil transition. Either "sugdna02", "sugrna02", "ser05" or "ser06" (see Double dangling end effect).
method.long.dangle	Specify the nearest neighbor model to compute the contribution of long dangling end to the thermodynamic of helix-coil transition. Either "sugdna02" or "sugrna02" (see Long dangling end effect).
method.internal.loop	Specify the nearest neighbor model to compute the contribution of internal loop to the thermodynamic of helix-coil transition. Either "san04", "tur06" or "zno07" (see Internal loop effect).
method.single.bulge.loop	Specify the nearest neighbor model to compute the contribution of single bulge loop to the thermodynamic of helix-coil transition. Either "san04", "tan04", "ser07" or "tur06" (see Single bulge loop effect).
method.long.bulge.loop	Specify the nearest neighbor model to compute the contribution of long bulge loop to the thermodynamic of helix-coil transition. Either "san04" or "tur06" (see Long bulge loop effect).
method.CNG	Specify the nearest neighbor model to compute the contribution of CNG repeats to the thermodynamic of helix-coil transition. Available method is "bro05" (see CNG repeats effect).
method.inosine	Specify the specific nearest neighbor model to compute the contribution of inosine bases (I) to the thermodynamic of helix-coil transition. Either "san05" or "zno07" (see Inosine bases effect).
method.hydroxyadenine	Specify the nearest neighbor model to compute the contribution of hydroxyadenine bases (A*) to the thermodynamic of helix-coil transition. Available method is "sug01" (see Hydroxyadenine bases effect).
method.azobenzenes	Specify the 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. Available method is "asa05" (see Azobenzenes effect).
method.locked	Specify the nearest neighbor model to compute the contribution of single locked nucleic acids (AL, GL, TL and CL) to the thermodynamic of helix-coil transition. Either "owc11" or "mct04" (see Single locked nucleic acids effect).
method.consecutive.locked	Specify the nearest neighbor model to compute the contribution of consecutive locked nucleic acids (AL, GL, TL and CL) to the thermodynamic of helix-coil transition. Available method is "owc11" (see Consecutive locked nucleic acids effect).
method.consecutive.locked.singleMM	Specify the nearest neighbor model to compute the contribution of consecutive locked nucleic acids (AL, GL, TL and CL) with a single mismatch to the thermodynamic of helix-coil transition. Available method is "owc11" (see Consecutive locked nucleic acids with single mismatch effect).
correction.ion	Specify the correction method for ions. Either one of the following: Na corrections"ahs01", "kam71", "owc1904", "owc2004", "owc2104", "owc2204", "san96", "san04", "schlif", "tanna06", "wetdna91", "tanna07", "wetrna91" or "wetdnarna91" (see Sodium corrections) Mg corrections"owcmg08", "tanmg06" or "tanmg07" (see Magnesium corrections) Mixed Na Mg corrections"owcmix08", "tanmix07" or "tanmix07" (see Mixed Sodium and Magnesium corrections) .
method.Naeq	Specify the ion correction which gives a sodium equivalent concentration if other cations are present. Either "ahs01", "mit96" or "pey00" (see Sodium equivalent concentration methods).
correction.DMSO	Specify the correction method for DMSO. Specify the correction method for DMSO. Either "ahs01", "mus81", "cul76" or "esc80" (see DMSO corrections).
correction.formamide	Specify the correction method for formamide. Specify the correction method for formamide Either "bla96" or "lincorr" (see Formamide corrections).

Value

A list with the following components:

Environment	A list with details about the melting temperature computation environment.
Options	A list with details about the options (default or user specified) used for melting temperature computation.
Results	A list with the results of the melting temperature computation including the enthalpy and entropy in case of nearest neighbour methods.
Message	Error and/or Warning messages, if any.

Mandatory arguments

The following are the arguments which are mandatory for computation.

sequence

5' to 3' sequence of one strand of the nucleic acid duplex as a character string. Recognises A, C, G, T, U, I, X_C, X_T, A*, AL, TL, GL and CL. U and T are not considered identical (see Recognized nucleotides).

comp.sequence

Mandatory if there are mismatches, inosine(s) or hydroxyadenine(s) between the two strands. If not specified, it is computed as the complement of sequence. Self-complementarity in sequence is detected even though there may be (are) dangling end(s) and comp.sequence is computed (see Self complementary sequences).

nucleic.acid.conc

See Correction factor for nucleic acid concentration.

Na.conc, Mg.conc, Tris.conc, K.conc

At least one cation (Na, Mg, Tris, K) concentration is mandatory, the other agents(dNTP, DMSO, formamide) are optional (see Ion and agent concentrations).

hybridisation.type

See Hybridisation type options.

Recognized nucleotides

Code	Type
A	Adenine
C	Cytosine
G	Guanine
T	Thymine
U	Uracil
I	Inosine
X_C	Trans azobenzenes
X_T	Cis azobenzenes
A*	Hydroxyadenine
AL	Locked nucleic acid
TL	"
GL	"
CL	"

U and T are not considered identical.

Hybridisation type options

The details of the possible options for hybridisation type specified in the argument hybridisation.type are as follows:

Option	Sequence	Complementary sequence
dnadna	DNA	DNA
rnarna	RNA	RNA
dnarna	DNA	RNA
rnadna	RNA	DNA
mrnarna	2-o-methyl RNA	RNA
rnamrna	RNA	2-o-methyl RNA

This parameter determines the nature of the sequences in the arguments sequence and comp.sequence.

Ion and agent concentrations

Ion concentrations are specified by the arguments Na.conc, Mg.conc, Tris.conc and K.conc, while agent concentrations are specified by the arguments dNTP.conc, DMSO.conc and formamide.conc.

These values are used for different correction functions which approximately adjusts for effects of these ions (Na, Mg, Tris, K) and/or agents (dNTP, DMSO, formamide) on on thermodynamic stability of nucleic acid duplexes. Their concentration limits depends on the correction method used. All the concentrations must be in M, except for the DMSO (%) and formamide (% or M depending on the correction method). Note that [Tris⁺] is about half of the total tris buffer concentration.

Self complementary sequences

Self complementarity for perfect matching sequences or sequences with dangling ends is detected automatically. However it can be enforced by the argument force.self = TRUE.

Correction factor for nucleic acid concentration

For self complementary sequences (Auto detected or specified by force.self) it is 1. Otherwise it is 4 if the both strands are present in equivalent amount and 1 if one strand is in excess.

Approximative estimation formulas

Formula	Type	Limits/Remarks	Reference
ahs01	DNA	No mismatch	von Ahsen et al., 2001
che93	DNA	No mismatch; Na=0, Mg=0.0015,	Marmur and Doty, 1962
		Tris=0.01, K=0.05
che93corr	DNA	No mismatch; Na=0, Mg=0.0015,	Marmur and Doty, 1962
		Tris=0.01, K=0.05
schdot	DNA	No mismatch	Wetmur, 1991; Marmur and
			Doty, 1962; Chester and
			Marshak, 1993; Schildkraut
			and Lifson, 1965; Wahl et
			al., 1987; Britten et al.,
			1974; Hall et al., 1980
owe69	DNA	No mismatch	Owen et al., 1969;
			Frank-Kamenetskii, 1971;
			Blake, 1996; Blake and
			Delcourt, 1998
san98	DNA	No mismatch	SantaLucia, 1998; von Ahsen
			et al., 2001
wetdna91*	DNA		Wetmur, 1991
wetrna91*	RNA		Wetmur, 1991
wetdnarna91*	DNA/RNA		Wetmur, 1991

* Default formula for computation.

Note that calculation is increasingly incorrect when the length of the duplex decreases. Further, it does not take into account nucleic acid concentration.

Nearest neighbor models

Perfectly matching sequences

Model	Type	Limits/Remarks	Reference
all97*	DNA		Allawi and SantaLucia, 1997
tur06*	2'-O-MeRNA/	A sodium correction	Kierzek et al., 2006
	RNA	(san04) is
		automatically applied to
		convert the entropy (Na =
		0.1M) into the entropy (Na =
		1M).
bre86	DNA		Breslauer et al., 1986
san04	DNA		SantaLucia and Hicks, 2004
san96	DNA		SantaLucia et al., 1996
sug96	DNA		Sugimoto et al., 1996
tan04	DNA		Tanaka et al., 2004
fre86	RNA		Freier et al., 1986
xia98*	RNA		Xia et al., 1998
sug95*	DNA/		SantaLucia et al., 1996
	RNA

* Default model for computation.

GU wobble base pairs effect

Model	Type	Limits/Remarks	Reference
tur99	RNA		Mathews et al., 1999
ser12*	RNA		Chen et al., 2012

* Default model for computation.

GU base pairs are not taken into account by the approximative mode.

Single mismatch effect

Model	Type	Limits.Remarks	Reference
allsanpey*	DNA		Allawi and SantaLucia, 1997;
			Allawi and SantaLucia, 1998;
			Allawi and SantaLucia, 1998;
			Allawi and SantaLucia, 1998;
			Peyret et al., 1999
wat11*	DNA/RNA		Watkins et al., 2011
tur06	RNA		Lu et al., 2006
zno07*	RNA		Davis and Znosko, 2007
zno08	RNA	At least one adjacent GU base	Davis and Znosko, 2008
		pair.

* Default model for computation.

Single mismatches are not taken into account by the approximative mode.

Tandem mismatches effect

Model	Type	Limits.Remarks	Reference
allsanpey*	DNA	Only GT mismatches and TA/TG	Allawi and SantaLucia, 1997;
		mismatches.	Allawi and SantaLucia, 1998;
			Allawi and SantaLucia, 1998;
			Allawi and SantaLucia, 1998;
			Peyret et al., 1999
tur99*	RNA	No adjacent GU or UG base	Mathews et al., 1999; Lu et
		pairs.	al., 2006

* Default model for computation.

Tandem mismatches are not taken into account by the approximative mode. Note that not all the mismatched Crick's pairs have been investigated.

Single dangling end effect

Model	Type	Limits.Remarks	Reference
bom00*	DNA		Bommarito et al., 2000
sugdna02	DNA	Only terminal poly A self	Ohmichi et al., 2002
		complementary sequences.
sugrna02	RNA	Only terminal poly A self	Ohmichi et al., 2002
		complementary sequences.
ser08*	RNA	Only 3' UA, GU and UG	O'Toole et al., 2006; Miller
		terminal base pairs only 5'	et al., 2008
		UG and GU terminal base
		pairs.

* Default model for computation.

Single dangling ends are not taken into account by the approximative mode.

Double dangling end effect

Model	Type	Limits/Remarks	Reference
sugdna02*	DNA	Only terminal poly A self	Ohmichi et al., 2002
		complementary sequences.
sugrna02	RNA	Only terminal poly A self	Ohmichi et al., 2002
		complementary sequences.
ser05	RNA	Depends on the available	O'Toole et al., 2005
		thermodynamic parameters for
		single dangling end.
ser06*	RNA		O'Toole et al., 2006

* Default model for computation.

Double dangling ends are not taken into account by the approximative mode.

Long dangling end effect

Model	Type	Limits/Remarks	Reference
sugdna02*	DNA	Only terminal poly A self	Ohmichi et al., 2002
		complementary sequences.
sugrna02*	RNA	Only terminal poly A self	Ohmichi et al., 2002
		complementary sequences.

* Default model for computation.

Long dangling ends are not taken into account by the approximative mode.

Internal loop effect

Model	Type	Limits.Remarks	Reference
san04*	DNA	Missing asymmetry penalty.	SantaLucia and Hicks, 2004
		Not tested with experimental
		results.
tur06	RNA	Not tested with experimental	Lu et al., 2006
		results.
zno07*	RNA	Only for 1x2 loop.	Badhwar et al., 2007

* Default model for computation.

Internal loops are not taken into account by the approximative mode.

Single bulge loop effect

Model	Type	Limits/Remarks	Reference
tan04*	DNA		Tan and Chen, 2007
san04	DNA	Missing closing AT penalty.	SantaLucia and Hicks, 2004
ser07	RNA	Less reliable results. Some	Blose et al., 2007
		missing parameters.
tur06*	RNA		Lu et al., 2006

* Default model for computation.

Single bulge loops are not taken into account by the approximative mode.

Long bulge loop effect

Model	Type	Limits.Remarks	Reference
san04*	DNA	Missing closing AT penalty.	SantaLucia and Hicks, 2004
tur06*	RNA	Not tested with experimental	Mathews et al., 1999; Lu et
		results.	al., 2006

* Default model for computation.

Long bulge loops are not taken into account by the approximative mode.

CNG repeats effect

Model	Type	Limits/Remarks	Reference
bro05*	RNA	Self complementary sequences.	Broda et al., 2005
		2 to 7 CNG repeats.

* Default model for computation.

CNG repeats are not taken into account by the approximative mode. The contribution of CNG repeats to the thermodynamic of helix-coil transition can be computed only for 2 to 7 CNG repeats. N represents a single mismatch of type N/N.

Inosine bases effect

Model	Type	Limits/Remarks	Reference
san05*	DNA	Missing parameters for tandem	Watkins and SantaLucia, 2005
		base pairs containing inosine
		bases.
zno07*	RNA	Only IU base pairs.	Wright et al., 2007

* Default model for computation.

Inosine bases (I) are not taken into account by the approximative mode.

Hydroxyadenine bases effect

Model	Type	Limits/Remarks	Reference
sug01*	DNA	Only 5' GA*C 3'and 5' TA*A 3'	Kawakami et al., 2001
		contexts.

* Default model for computation.

Hydroxyadenine bases (A*) are not taken into account by the approximative mode.

Azobenzenes effect effect

Model	Type	Limits/Remarks	Reference
asa05*	DNA	Less reliable results when	Asanuma et al., 2005
		the number of cis azobenzene
		increases.

* Default model for computation.

Azobenzenes (X_T for trans azobenzenes and X_C for cis azobenzenes) are not taken into account by the approximative mode.

Single locked nucleic acids effect

Model	Type	Limits.Remarks	Reference
mct04	DNA		McTigue, Peterson, and Kahn,
			2004
owc11*	DNA		Owczarzy, You, Groth, and
			Tataurov, 2011

* Default model for computation.

Locked nucleic acids (AL, GL, TL and CL) are not taken into account by the approximative mode.

Consecutive locked nucleic acids effect

Model	Type	Limits.Remarks	Reference
owc11*	DNA		Owczarzy et al., 2011

* Default model for computation.

Locked nucleic acids (AL, GL, TL and CL) are not taken into account by the approximative mode.

Consecutive locked nucleic acids with single mismatch effect

Model	Type	Limits.Remarks	Reference
owc11*	DNA		Owczarzy et al., 2011

* Default model for computation.

Locked nucleic acids (AL, GL, TL and CL) are not taken into account by the approximative mode.

Ion corrections

Sodium corrections

Correction	Type	Limits.Remarks	Reference
ahs01	DNA	Na>0.	von Ahsen et al., 2001
schlif	DNA	Na>=0.07; Na<=0.12.	Schildkraut and Lifson, 1965
tanna06	DNA	Na>=0.001; Na<=1.	Tan and Chen, 2006
tanna07*	RNA	Na>=0.003; Na<=1.	Tan and Chen, 2007
	or
	2'-O-MeRNA/RNA
wet91	RNA,	Na>0.	Wetmur, 1991
	DNA
	and
	RNA/DNA
kam71	DNA	Na>0; Na>=0.069; Na<=1.02.	Frank-Kamenetskii, 1971
marschdot	DNA	Na>=0.069; Na<=1.02.	Marmur and Doty, 1962; Blake
			and Delcourt, 1998
owc1904	DNA	Na>0. (equation 19)	Owczarzy et al., 2004
owc2004	DNA	Na>0. (equation 20)	Owczarzy et al., 2004
owc2104	DNA	Na>0. (equation 21)	Owczarzy et al., 2004
owc2204*	DNA	Na>0. (equation 22)	Owczarzy et al., 2004
san96	DNA	Na>=0.1.	SantaLucia et al., 1996
san04	DNA	Na>=0.05; Na<=1.1;	SantaLucia and Hicks, 2004;
		Oligonucleotides inferior to	SantaLucia, 1998
		16 bases.

* Default correction method for computation.

Magnesium corrections

Correction	Type	Limits/Remarks	Reference
owcmg08*	DNA	Mg>=0.0005; Mg<=0.6.	Owczarzy et al., 2008
tanmg06	DNA	Mg>=0.0001; Mg<=1; Oligomer	Tan and Chen, 2006
		length superior to 6 base
		pairs.
tanmg07*	RNA	Mg>=0.1; Mg<=0.3.	Tan and Chen, 2007

* Default correction method for computation.

Mixed Sodium and Magnesium corrections

Correction	Type	Limits.Remarks	Reference
owcmix08*	DNA	Mg>=0.0005; Mg<=0.6;	Owczarzy et al., 2008
		Na+K+Tris/2>0.
tanmix07	DNA,	Mg>=0.1; Mg<=0.3;	Tan and Chen, 2007
	RNA	Na+K+Tris/2>=0.1;
	or	Na+K+Tris/2<=0.3.
	2'-O-MeRNA/RNA

* Default correction method for computation.

The ion correction by Owczarzy et al. (2008) is used by default according to the [Mg²⁺]^0.5 ⁄ [Mon⁺] ratio, where [Mon⁺] = [Na⁺] + [Tris⁺] + [K⁺] .

If,

[Mon⁺] = 0

Default sodium correction is used.

Ratio < 0.22,

Default sodium correction is used.

0.22 <= Ratio < 6

Default mixed Na and Mg correction is used.

Ratio >= 6

Default magnesium correction is used.

Note that [Tris⁺] is about half of the total tris buffer concentration.

Sodium equivalent concentration methods

Correction	Type	Limits/Remarks	Reference
ahs01*	DNA		von Ahsen et al., 2001
mit96	DNA		Mitsuhashi, 1996
pey00	DNA		Peyret, 2000

* Default correction method for computation.

For the other types of hybridization, the DNA default correction is used. If there are other cations when an approximative approach is used, a sodium equivalence is automatically computed. In case of nearest neighbor approach, the sodium equivalence will be used only if a sodium correction is specified by the argument correction.ion.

Denaturing agent corrections

DMSO corrections

Correction	Type	Limits/Remarks	Reference
ahs01*	DNA	Not tested with experimental	von Ahsen et al., 2001
		results.
cul76	DNA	Not tested with experimental	Cullen and Bick, 1976
		results.
esc80	DNA	Not tested with experimental	Escara and Hutton, 1980
		results.
mus81	DNA	Not tested with experimental	Musielski et al., 1981
		results.

* Default correction method for computation.

For the other types of hybridization, the DNA default correction is used. If there is DMSO when an approximative approach is used, a DMSO correction is automatically computed. In case of nearest neighbor approach and approximative approach, the DMSO correction will be used only if a sodium correction is specified by the argument correction.ion.

Formamide corrections

Correction	Type	Limits/Remarks	Reference
bla96*	DNA	With formamide concentration	Blake, 1996
		in mol/L.
lincorr	DNA	With a formamide volume.	McConaughy et al., 1969;
			Record, 1967; Casey and
			Davidson, 1977; Hutton, 1977

* Default correction method for computation.

For the other types of hybridization, the DNA default correction is used. If there is formamide when an approximative approach is used, a formamide correction is automatically computed. In case of nearest neighbor approach and approximative approach, the formamide correction will be used only if a sodium correction is specified by the argument correction.ion.

References

Marmur J, Doty P (1962). “Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature.” Journal of Molecular Biology, 5(1), 109–118.

Schildkraut C, Lifson S (1965). “Dependence of the melting temperature of DNA on salt concentration.” Biopolymers, 3(2), 195–208.

Record MT (1967). “Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH.” Biopolymers, 5(10), 975–992.

McConaughy BL, Laird C, McCarthy BJ (1969). “Nucleic acid reassociation in formamide.” Biochemistry, 8(8), 3289–3295.

Owen RJ, Hill LR, Lapage SP (1969). “Determination of DNA base compositions from melting profiles in dilute buffers.” Biopolymers, 7(4), 503–516.

Frank-Kamenetskii MD (1971). “Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution.” Biopolymers, 10(12), 2623–2624.

Britten RJ, Graham DE, Neufeld BR (1974). “Analysis of repeating DNA sequences by reassociation.” Methods in Enzymology, 29, 363–418.

Cullen BR, Bick MD (1976). “Thermal denaturation of DNA from bromodeoxyuridine substituted cells.” Nucleic Acids Research, 3(1), 49–62.

Hutton JR (1977). “Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea.” Nucleic Acids Research, 4(10), 3537–3555.

Casey J, Davidson N (1977). “Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide.” Nucleic Acids Research, 4(5), 1539–1552.

Hall TJ, Grula JW, Davidson EH, Britten RJ (1980). “Evolution of sea urchin non-repetitive DNA.” Journal of Molecular Evolution, 16(2), 95–110.

Escara JF, Hutton JR (1980). “Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: Acceleration of the renaturation rate.” Biopolymers, 19(7), 1315–1327.

Musielski H, Mann W, Laue R, Michel S (1981). “Influence of dimethylsulfoxide on transcription by bacteriophage T3-induced RNA polymerase.” Zeitschrift fur allgemeine Mikrobiologie, 21(6), 447–456.

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See Also

For more details about algorithm, formulae and methods, see the documentation for MELTING 5.

Examples

# Basic usage
melting(sequence = "CAGTGAGACAGCAATGGTCG", nucleic.acid.conc = 2e-06,
        hybridisation.type = "dnadna", Na.conc = 1)

# For more detailed examples refer the vignette.
## Not run: 

browseVignettes(package = 'rmelting')

## End(Not run)

---

Compute melting temperature of multiple nucleic acid duplexes in batch

Description

Compute the enthalpy and entropy of helix-coil transition, and then the melting temperature of multiple nucleic acid duplexes in batch.

Usage

meltingBatch(
  sequence,
  comp.sequence = NULL,
  environment.out = TRUE,
  options.out = TRUE,
  message.out = TRUE,
  ...
)

Arguments

sequence	A character vector of 5' to 3' sequences of one strand of the nucleic acid duplex (Note: Uridine and thymidine are not considered as identical).
comp.sequence	A character vector of 3' to 5' complementary sequences of the nucleic acid duplex. Complementary sequences are computed by default, but need to be specified in case of mismatches, inosine(s) or hydroxyadenine(s) between the two strands.
environment.out	logical. If TRUE, gives the melting temperature computation environment details in the output. Default is TRUE.
options.out	logical. If TRUE, gives the details about the options (default or user specified) used for melting temperature computation in the output. Default is TRUE.
message.out	logical. If TRUE, gives the error and/or warning messages, if any in the output. Default is TRUE.
...	Arguments for melting temperature computation (See melting).

Value

A data frame of the melting temperature computation results along with the details of environment, options and messages if specified by the arguments environment.out, options.out and message.out respectively.

See Also

melting

Examples

sequence <- c("CAAAAAG", "CAAAAAAG", "TTTTATAATAAA", "CCATCGCTACC",
              "CAAACAAAG", "CCATTGCTACC", "CAAAAAAAG", "GTGAAC", "AAAAAAAA",
              "CAACTTGATATTATTA", "CAAATAAAG", "GCGAGC", "GGGACC",
              "CAAAGAAAG", "CTGACAAGTGTC", "GCGAAAAGCG")

meltingBatch(sequence, nucleic.acid.conc = 0.0004,
             hybridisation.type = "dnadna", Na.conc = 1)

seq <- c("GCAUACG", "CAGUAGGUC", "CGCUCGC", "GAGUGGAG", "GACAGGCUG",
         "CAGUACGUC", "GACAUCCUG", "GACCACCUG", "CAGAAUGUC", "GCGUCGC",
         "CGUCCGG", "GACUCUCUG", "CAGCUGGUC", "GACUAGCUG", "CUCUGCUC",
         "GCGUCCG", "GUCCGCG", "CGAUCAC", "GACUACCUG", "GACGAUCUG")

comp.seq <- c("CGUUUGC", "GUCGGCCAG", "GCGUGCG", "CUCUUCUC", "CUGUGCGAC",
              "GUCGGGCAG", "CUGUUGGAC", "CUGGGGGAC", "GUCUGGCAG", "CGCUGCG",
              "GCUGGCC", "CUGAUAGAC", "GUCGUUCAG", "CUGAGCGAC", "GAGUUGAG",
              "CGCUGGC", "CUGGCGC", "GCUUGUG", "CUGAGGGAC", "CUGCCAGAC")

meltingBatch(sequence = seq, comp.seq = comp.seq, nucleic.acid.conc = 0.0004,
             hybridisation.type = "rnarna", Na.conc = 1,
             method.singleMM = "tur06")

---

Prints melting temperature from a melting object

Description

print.melting prints to console the melting temperature value from an object of class melting.

Usage

## S3 method for class 'melting'
print(x, ...)

Arguments

x	An object of class melting.
...	Unused

Value

The melting temperature value (degree Celsius) in the console.

See Also

melting

---