melting: Compute melting temperature of a nucleic acid duplex

View source: R/melting.R

meltingR Documentation

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

\insertRef

marmur_determination_1962rmelting

\insertRef

schildkraut_dependence_1965rmelting

\insertRef

record_electrostatic_1967rmelting

\insertRef

mcconaughy_nucleic_1969rmelting

\insertRef

owen_determination_1969rmelting

\insertRef

frank-kamenetskii_simplification_1971rmelting

\insertRef

britten_analysis_1974rmelting

\insertRef

cullen_thermal_1976rmelting

\insertRef

hutton_renaturation_1977rmelting

\insertRef

casey_rates_1977rmelting

\insertRef

hall_evolution_1980rmelting

\insertRef

escara_thermal_1980rmelting

\insertRef

musielski_influence_1981rmelting

\insertRef

freier_improved_1986rmelting

\insertRef

breslauer_predicting_1986rmelting

\insertRef

wahl_molecular_1987rmelting

\insertRef

wetmur_dna_1991rmelting

\insertRef

chester_dimethyl_1993rmelting

\insertRef

sugimoto_rna/dna_1994rmelting

\insertRef

sugimoto_thermodynamic_1995rmelting

\insertRef

santalucia_improved_1996rmelting

\insertRef

sugimoto_improved_1996rmelting

\insertRef

blake_thermodynamic_1996rmelting

\insertRef

blake_denaturation_1996rmelting

\insertRef

mitsuhashi_technical_1996rmelting

\insertRef

allawi_thermodynamics_1997rmelting

\insertRef

santalucia_unified_1998rmelting

\insertRef

xia_thermodynamic_1998rmelting

\insertRef

allawi_thermodynamics_1998rmelting

\insertRef

blake_thermal_1998rmelting

\insertRef

allawi_nearest_1998rmelting

\insertRef

allawi_nearest-neighbor_1998rmelting

\insertRef

mathews_expanded_1999rmelting

\insertRef

peyret_nearest-neighbor_1999rmelting

\insertRef

peyret_prediction_2000rmelting

\insertRef

bommarito_thermodynamic_2000rmelting

\insertRef

kawakami_thermodynamic_2001rmelting

\insertRef

von_ahsen_oligonucleotide_2001rmelting

\insertRef

le_novere_melting_2001rmelting

\insertRef

ohmichi_long_2002rmelting

\insertRef

santalucia_thermodynamics_2004rmelting

\insertRef

tanaka_thermodynamic_2004rmelting

\insertRef

mctigue_sequence-dependent_2004rmelting

\insertRef

owczarzy_stability_2011rmelting

\insertRef

owczarzy_effects_2004rmelting

\insertRef

broda_thermodynamic_2005rmelting

\insertRef

watkins_nearest-neighbor_2005rmelting

\insertRef

asanuma_clear-cut_2005rmelting

\insertRef

otoole_stability_2005rmelting

\insertRef

lu_set_2006rmelting

\insertRef

kierzek_nearest_2006rmelting

\insertRef

tan_nucleic_2006rmelting

\insertRef

otoole_comprehensive_2006rmelting

\insertRef

tan_rna_2007rmelting

\insertRef

wright_nearest_2007rmelting

\insertRef

davis_thermodynamic_2007rmelting

\insertRef

blose_non-nearest-neighbor_2007rmelting

\insertRef

badhwar_thermodynamic_2007rmelting

\insertRef

davis_thermodynamic_2008rmelting

\insertRef

miller_thermodynamic_2008rmelting

\insertRef

owczarzy_predicting_2008rmelting

\insertRef

watkins_thermodynamic_2011rmelting

\insertRef

chen_testing_2012rmelting

\insertRef

dumousseau_melting_2012rmelting

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)


aravind-j/rmelting documentation built on May 16, 2023, 10:47 p.m.