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<!-- Generated by pkgdown: do not edit by hand -->
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<title>melting — melting • rmelting</title>
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<meta property="og:description" content="R interface to the
MELTING 5 software (Le
Novère, 2001; Dumousseau et al., 2012) for computation of enthalpy and entropy
of the helix-coil transition, and then the melting temperature of a nucleic
acid duplex." />
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<h1>melting</h1>
<small class="dont-index">Source: <a href='https://github.com/aravind-j/rmelting/blob/master/R/melting.R'><code>R/melting.R</code></a></small>
<div class="hidden name"><code>melting.Rd</code></div>
</div>
<div class="ref-description">
<p>R interface to the
<a href='https://www.ebi.ac.uk/biomodels/tools/melting/'>MELTING 5 software</a> (Le
Novère, 2001; Dumousseau et al., 2012) for computation of enthalpy and entropy
of the helix-coil transition, and then the melting temperature of a nucleic
acid duplex.</p>
</div>
<pre class="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, self = FALSE, correction.factor,
method.approx = c("ahs01", "che93", "che93corr",
"marschdot", "owe69", "san98",
"wetdna91", "wetrna91", "wetdnarna91"),
method.nn = c("all97", "bre86", "san04", "san96", "sug96",
"tan04", "fre86", "xia98", "sug95", "tur06"),
method.GU = c("tur99"),
method.singleMM = c("allsanpey", "tur06", "zno07", "zno08"),
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("mct04"),
correction.Na = c("ahs01", "kam71", "marschdot",
"owc1904", "owc2004", "owc2104", "owc2204",
"san96", "san04", "schlif",
"tanna06", "tanna07", "wet91"),
correction.Mg = c("oxcmg08", "tanmg06", "tanmg07"),
correction.NaMg = c("oxcmix08", "tanmix07"),
method.Naeq = c("ahs01", "mit96", "pey00"),
correction.DMSO = c("ahs01", "cul76", "esc80", "mus80"),</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>sequence</th>
<td><p>Sequence (5' to 3') of one strand of the nucleic acid duplex
as a character string.</p></td>
</tr>
<tr>
<th>comp.sequence</th>
<td><p>Complementary sequence (3' to 5') of the nucleic acid
duplex as a character string.</p></td>
</tr>
<tr>
<th>nucleic.acid.conc</th>
<td><p>Concentration of the nucleic acid strand
(mol L<sup>-1</sup>) in excess as
a numeric value.</p></td>
</tr>
<tr>
<th>hybridisation.type</th>
<td><p>The hybridisation type. Either <code>"dnadna"</code>,
<code>"rnarna"</code>, <code>"dnarna"</code>, <code>"rnadna"</code>, <code>"mrnarna"</code> or
<code>"rnamrna"</code> (see <strong>Hybridisation type options</strong>).</p></td>
</tr>
<tr>
<th>Na.conc</th>
<td><p>Concentration of Na ions (M) as a numeric value (see
<strong>Ion and agent concentrations</strong>).</p></td>
</tr>
<tr>
<th>Mg.conc</th>
<td><p>Concentration of Mg ions (M) as a numeric value (see
<strong>Ion and agent concentrations</strong>).</p></td>
</tr>
<tr>
<th>Tris.conc</th>
<td><p>Concentration of Tris ions (M) as a numeric value (see
<strong>Ion and agent concentrations</strong>).</p></td>
</tr>
<tr>
<th>K.conc</th>
<td><p>Concentration of K ions (M) as a numeric value (see <strong>Ion
and agent concentrations</strong>).</p></td>
</tr>
<tr>
<th>dNTP.conc</th>
<td><p>Concentration of dNTP (M) as a numeric value (see <strong>Ion
and agent concentrations</strong>).</p></td>
</tr>
<tr>
<th>DMSO.conc</th>
<td><p>Concentration of DMSO (%) as a numeric value (see
<strong>Ion and agent concentrations</strong>).</p></td>
</tr>
<tr>
<th>formamide.conc</th>
<td><p>Concentration of formamide (M or % depending on
correction method) as a numeric value (see <strong>Ion and agent
concentrations</strong>).</p></td>
</tr>
<tr>
<th>size.threshold</th>
<td><p>Sequence length threshold to decide approximative or
nearest-neighbour approach for computation. Default is 60.</p></td>
</tr>
<tr>
<th>self</th>
<td><p>logical. Specifies that <code>sequence</code> is self complementary and
<code>complementary sequence</code> is not required (seed <strong>Self
complementary sequences</strong>). Default is <code>FALSE</code>.</p></td>
</tr>
<tr>
<th>correction.factor</th>
<td><p>Correction factor to be used to modulate the effect
of the nucleic acid concentration (<code>nucleic.acid.conc</code>) in the
computation of melting temperature (see <strong>Correction factor for
nucleic acid concentration</strong>).</p></td>
</tr>
<tr>
<th>method.approx</th>
<td><p>Specify the approximative formula to be used for melting
temperature calculation for sequences of length greater than
<code>size.threshold</code>. Either <code>"ahs01"</code>, <code>"che93"</code>,
<code>"che93corr"</code>, <code>"schdot"</code>, <code>"owe69"</code>, <code>"san98"</code>,
<code>"wetdna91"</code>, <code>"wetrna91"</code> or <code>"wetdnarna91"</code> (see
<strong>Approximative formulas</strong>).</p></td>
</tr>
<tr>
<th>method.nn</th>
<td><p>Specify the nearest neighbor model to be used for melting
temperature calculation for sequences of length lesser than
<code>size.threshold</code>. Either <code>"all97"</code>, <code>"bre86"</code>,
<code>"san04"</code>, <code>"san96"</code>, <code>"sug96"</code>, <code>"tan04"</code>,
<code>"fre86"</code>, <code>"xia98"</code>, <code>"sug95"</code> or <code>"tur06"</code> (see
<strong>Nearest neighbor models</strong>).</p></td>
</tr>
<tr>
<th>method.GU</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of GU base pairs to the thermodynamic of helix-coil transition.
Available method is <code>"tur99"</code> (see <strong>GU wobble base pairs
effect</strong>).</p></td>
</tr>
<tr>
<th>method.singleMM</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of single mismatch to the thermodynamic of helix-coil
transition. Either <code>"allsanpey"</code>, <code>"tur06"</code>, <code>"zno07"</code> or
<code>"zno08"</code> (see <strong>Single mismatch effect</strong>).</p></td>
</tr>
<tr>
<th>method.tandemMM</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of tandem mismatches to the thermodynamic of helix-coil
transition. Either <code>"allsanpey"</code> or <code>"tur99"</code> (see <strong>Tandem
mismatches effect</strong>).</p></td>
</tr>
<tr>
<th>method.single.dangle</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of single dangling end to the thermodynamic of helix-coil
transition. Either <code>"bom00"</code>, <code>"sugdna02"</code>, <code>"sugrna02"</code> or
<code>"ser08"</code> (see <strong>Single dangling end effect</strong>).</p></td>
</tr>
<tr>
<th>method.double.dangle</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of double dangling end to the thermodynamic of helix-coil
transition. Either <code>"sugdna02"</code>, <code>"sugrna02"</code>, <code>"ser05"</code> or
<code>"ser06"</code> (see <strong>Double dangling end effect</strong>).</p></td>
</tr>
<tr>
<th>method.long.dangle</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of long dangling end to the thermodynamic of helix-coil
transition. Either <code>"sugdna02"</code> or <code>"sugrna02"</code> (see <strong>Long
dangling end effect</strong>).</p></td>
</tr>
<tr>
<th>method.internal.loop</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of internal loop to the thermodynamic of helix-coil transition.
Either <code>"san04"</code>, <code>"tur06"</code> or <code>"zno07"</code> (see
<strong>Internal loop effect</strong>).</p></td>
</tr>
<tr>
<th>method.single.bulge.loop</th>
<td><p>Specify the nearest neighbor model to compute
the contribution of single bulge loop to the thermodynamic of helix-coil
transition. Either <code>"san04"</code>, <code>"tan04"</code>, <code>"ser07"</code> or
<code>"tur06"</code> (see <strong>Single bulge loop effect</strong>).</p></td>
</tr>
<tr>
<th>method.long.bulge.loop</th>
<td><p>Specify the nearest neighbor model to compute
the contribution of long bulge loop to the thermodynamic of helix-coil
transition. Either <code>"san04"</code> or <code>"tur06"</code> (see <strong>Long bulge
loop effect</strong>).</p></td>
</tr>
<tr>
<th>method.CNG</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of CNG repeats to the thermodynamic of helix-coil transition.
Available method is <code>"bro05"</code> (see <strong>CNG repeats effect</strong>).</p></td>
</tr>
<tr>
<th>method.inosine</th>
<td><p>Specify the pecific nearest neighbor model to compute
the contribution of inosine bases (I) to the thermodynamic of helix-coil
transition. Either <code>"san05"</code> or <code>"zno07"</code> (see <strong>Inosine
bases effect</strong>).</p></td>
</tr>
<tr>
<th>method.hydroxyadenine</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of hydroxyadenine bases (A*) to the thermodynamic of helix-coil
transition. Available method is <code>"sug01"</code> (see <strong>Hydroxyadenine
bases effect</strong>).</p></td>
</tr>
<tr>
<th>method.azobenzenes</th>
<td><p>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 <code>"asa05"</code> (see <strong>Azobenzenes effect</strong>).</p></td>
</tr>
<tr>
<th>method.locked</th>
<td><p>Specify the nearest neighbor model to compute the
contribution of locked nucleic acids (AL, GL, TL and CL) to the
thermodynamic of helix-coil transition. Available method is <code>"mct04"</code>
(see <strong>Locked nucleic acids effect</strong>).</p></td>
</tr>
<tr>
<th>correction.Na</th>
<td><p>Specify the correction method for Na ions. Either
<code>"ahs01"</code>, <code>"kam71"</code>, <code>"owc1904"</code>, <code>"owc2004"</code>,
<code>"owc2104"</code>, <code>"owc2204"</code>, <code>"san96"</code>, <code>"san04"</code>,
<code>"schlif"</code>, <code>"tanna06"</code>, <code>"wetdna91"</code>, <code>"tanna07"</code>,
<code>"wetrna91"</code> or <code>"wetdnarna91"</code> (see <strong>Sodium corrections</strong>).</p></td>
</tr>
<tr>
<th>correction.Mg</th>
<td><p>Specify the correction method for Mg ions. Either
<code>"owcmg08"</code>, <code>"tanmg06"</code> or <code>"tanmg07"</code> (see
<strong>Magnesium corrections</strong>).</p></td>
</tr>
<tr>
<th>correction.NaMg</th>
<td><p>Specify the correction method for mixed Na and Mg ions.
Either <code>"owcmix08"</code>, <code>"tanmix07"</code> or <code>"tanmix07"</code> (see
<strong>Mixed Sodium and Magnesium corrections</strong>).</p></td>
</tr>
<tr>
<th>method.Naeq</th>
<td><p>Specify the ion correction which gives a sodium equivalent
concentration if other cations are present. Either <code>"ahs01"</code>,
<code>"mit96"</code> or <code>"pey00"</code> (see <strong>Sodium equivalent
concentration methods</strong>).</p></td>
</tr>
<tr>
<th>correction.DMSO</th>
<td><p>Specify the correction method for DMSO. Specify the
correction method for DMSO. Either <code>"ahs01"</code>, <code>"mus81"</code>,
<code>"cul76"</code> or <code>"esc80"</code> (see <strong>DMSO corrections</strong>).</p></td>
</tr>
<tr>
<th>correction.formamide</th>
<td><p>Specify the correction method for formamide.
Specify the correction method for formamide Either <code>"bla96"</code> or
<code>"lincorr"</code> (see <strong>Formamide corrections</strong>).</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="mandatory-arguments"><a class="anchor" href="#mandatory-arguments"></a>Mandatory arguments</h2>
<p>The following are the arguments which are
mandatory for computation.</p><ul>
<li><p><code>sequence</code></p></li>
<li><p><code>comp.sequence</code>: Mandatory if there are mismatches, inosine(s) or
hydroxyadenine(s) between the two strands. If not specified, it is computed
as the complement of <code>sequence</code>. Self-complementarity in
<code>sequence</code> is detected even though there may be (are) dangling end(s)
and <code>comp.sequence</code> is computed (see <strong>Self complementary
sequences</strong>).</p></li>
<li><p><code>nucleic.acid.conc</code></p></li>
<li><p><code>Na.conc, Mg.conc,
Tris.conc, K.conc</code>: At least one cation (Na, Mg, Tris, K) concentration is
mandatory, the other agents(dNTP, DMSO, formamide) are optional.</p></li>
<li><p><code>hybridisation.type</code></p></li>
</ul>
<h2 class="hasAnchor" id="hybridisation-type-options"><a class="anchor" href="#hybridisation-type-options"></a>Hybridisation type options</h2>
<p>The details of the possible options for
hybridisation type specified in the argument <code>hybridisation.type</code> are
as follows:</p>
<p></p><table class='table'>
<tr><td><strong>Option</strong></td><td><strong><code>Sequence</code></strong></td><td><strong><code>Complementary sequence</code></strong></td></tr>
<tr><td><code>dnadna</code></td><td>DNA</td><td>DNA</td></tr>
<tr><td><code>rnarna</code></td><td>RNA</td><td>RNA</td></tr>
<tr><td><code>dnarna</code></td><td>DNA</td><td>RNA</td></tr>
<tr><td><code>rnadna</code></td><td>RNA</td><td>DNA</td></tr>
<tr><td><code>mrnarna</code></td><td>2-o-methyl RNA</td><td>RNA</td></tr>
</table>
<p>This parameter determines the nature of the sequences in the arguments
<code>sequence</code> and <code>comp.sequence</code>.</p>
<h2 class="hasAnchor" id="ion-and-agent-concentrations"><a class="anchor" href="#ion-and-agent-concentrations"></a>Ion and agent concentrations</h2>
<p>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+ concentration is about half of the total tris
buffer concentration.</p>
<h2 class="hasAnchor" id="self-complementary-sequences"><a class="anchor" href="#self-complementary-sequences"></a>Self complementary sequences</h2>
<p>Self complementarity for perfect
matching sequences or sequences with dangling ends is detected
automatically. However it can be specified by the argument <code>self</code>.</p>
<h2 class="hasAnchor" id="correction-factor-for-nucleic-acid-concentration"><a class="anchor" href="#correction-factor-for-nucleic-acid-concentration"></a>Correction factor for nucleic acid concentration</h2>
<p>For self
complementary sequences (Auto detected or specified in <code>self</code>) it is 1.
Otherwise it is 4 if the both strands are present in equivalent amount and 1
if one strand is in excess.</p>
<h2 class="hasAnchor" id="approximative-estimation-formulas"><a class="anchor" href="#approximative-estimation-formulas"></a>Approximative estimation formulas</h2>
<p>The calculation is increasingly
incorrect when the length of the duplex decreases. Moreover, it does not
take into account nucleic acid concentration.</p><table class='table'>
<tr><td><strong>Formula</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>ahs01</code></td><td>DNA</td><td>No mismatch</td><td>von Ahsen et
al., 2001</td></tr>
<tr><td><code>che93</code></td><td>DNA</td><td>No mismatch; Na=0, Mg=0.0015,</td><td>Marmur and Doty, 1962</td></tr>
<tr><td></td><td>Tris=0.01, K=0.05</td><td><code>che93corr</code></td><td>DNA</td></tr>
<tr><td>No mismatch; Na=0, Mg=0.0015,</td><td>Marmur and
Doty, 1962</td><td></td><td>Tris=0.01, K=0.05</td></tr>
<tr><td><code>marschdot</code></td><td>DNA</td><td>No mismatch</td><td>Wetmur, 1991; Marmur and</td></tr>
<tr><td></td><td></td><td>Doty,
1962; Chester and</td><td></td></tr>
<tr><td></td><td>Marshak, 1993; Schildkraut</td><td></td><td></td></tr>
<tr><td>and Lifson, 1965; Wahl et</td><td></td><td></td><td>al., 1987; Britten et al.,</td></tr>
<tr><td></td><td></td><td>1974; Hall et al., 1980</td><td><code>owe69</code></td></tr>
<tr><td>DNA</td><td>No
mismatch</td><td>Owen et al., 1969;</td><td></td></tr>
<tr><td></td><td>Frank-Kamenetskii, 1971;</td><td></td><td></td></tr>
<tr><td>Blake, 1996; Blake and</td><td></td><td></td><td>Delcourt, 1998</td></tr>
<tr><td><code>san98</code></td><td>DNA</td><td>No mismatch</td><td>SantaLucia, 1998; von Ahsen</td></tr>
<tr><td></td><td></td><td>et al., 2001</td><td><code>wetdna91</code>*</td></tr>
<tr><td>DNA</td><td></td><td>Wetmur,
1991</td><td><code>wetrna91</code>*</td></tr>
<tr><td>RNA</td><td></td><td>Wetmur, 1991</td><td><strong>Formula</strong></td></tr>
</table>
<h2 class="hasAnchor" id="nearest-neighbor-models"><a class="anchor" href="#nearest-neighbor-models"></a>Nearest neighbor models</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>all97</code>*</td><td>DNA</td><td>Allawi and SantaLucia, 1997</td><td><code>tur06</code>*</td></tr>
<tr><td>2'-O-MeRNA/</td><td>A sodium correction</td><td>Kierzek et al.,
2006</td><td></td></tr>
<tr><td>RNA</td><td>(<code>san04</code>) is</td><td></td><td>automatically
applied to</td></tr>
<tr><td></td><td>convert the entropy (Na =</td><td></td><td>0.1M)
into the entropy (Na =</td></tr>
<tr><td></td><td>1M).</td><td><code>bre86</code></td><td>DNA</td></tr>
<tr><td>Breslauer et al., 1986</td><td><code>san04</code></td><td>DNA</td><td>SantaLucia and Hicks, 2004</td></tr>
<tr><td><code>san96</code></td><td>DNA</td><td>SantaLucia et
al., 1996</td><td><code>sug96</code></td></tr>
<tr><td>DNA</td><td>Sugimoto et al., 1996</td><td><code>tan04</code></td><td>DNA</td></tr>
<tr><td>Tanaka et al., 2004</td><td><code>fre86</code></td><td>RNA</td><td>Freier et al., 1986</td></tr>
<tr><td><code>xia98</code>*</td><td>RNA</td><td>Xia et al.,
1998</td><td><code>sug95</code>*</td></tr>
<tr><td>DNA/</td><td>SantaLucia et al., 1996</td><td><strong>Model</strong></td><td><strong>Type</strong></td></tr>
</table>
<h2 class="hasAnchor" id="gu-wobble-base-pairs-effect"><a class="anchor" href="#gu-wobble-base-pairs-effect"></a>GU wobble base pairs effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
</table>
<h2 class="hasAnchor" id="single-mismatch-effect"><a class="anchor" href="#single-mismatch-effect"></a>Single mismatch effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>allsanpey</code>*</td><td>DNA</td><td></td><td>Allawi and SantaLucia, 1997;</td></tr>
<tr><td></td><td></td><td>Allawi and SantaLucia, 1998;</td><td></td></tr>
<tr><td></td><td>Allawi and SantaLucia,
1998;</td><td></td><td></td></tr>
<tr><td>Allawi and SantaLucia,</td><td></td><td></td><td>1998; Peyret
et al., 1999</td></tr>
<tr><td><code>tur06</code></td><td>RNA</td><td></td><td>Lu et al., 2006</td></tr>
<tr><td><code>zno07</code>*</td><td>RNA</td><td></td><td>Davis and Znosko, 2007</td></tr>
<tr><td><code>zno08</code></td><td>RNA</td><td>At least one adjacent GU base</td><td>Davis and Znosko, 2008</td></tr>
</table>
<h2 class="hasAnchor" id="tandem-mismatches-effect"><a class="anchor" href="#tandem-mismatches-effect"></a>Tandem mismatches effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>allsanpey</code>*</td><td>DNA</td><td>Only GT mismatches and TA/TG</td><td>Allawi and
SantaLucia, 1997;</td></tr>
<tr><td></td><td>mismatches.</td><td>Allawi and SantaLucia,
1998;</td><td></td></tr>
<tr><td>Allawi and SantaLucia, 1998;</td><td></td><td>Allawi
and SantaLucia,</td><td></td></tr>
<tr><td>1998; Peyret et al., 1999</td><td><code>tur99</code>*</td><td>RNA</td><td>No adjacent GU or UG base</td></tr>
<tr><td>Mathews et al., 1999</td><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td></tr>
</table>
<p>Tandem mismatches are not taken into account by the
approximative mode. Note that not all the mismatched Crick's pairs have been
investigated.</p>
<h2 class="hasAnchor" id="single-dangling-end-effect"><a class="anchor" href="#single-dangling-end-effect"></a>Single dangling end effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>bom00</code>*</td><td>DNA</td><td></td><td>Bommarito et al., 2000</td></tr>
<tr><td><code>sugdna02</code></td><td>DNA</td><td>Only terminal poly A self</td><td>Ohmichi et al., 2002</td></tr>
<tr><td></td><td>complementary sequences.</td><td></td><td><code>sugrna02</code></td></tr>
<tr><td>RNA</td><td>Only terminal
poly A self</td><td>Ohmichi et al., 2002</td><td></td></tr>
<tr><td>complementary
sequences.</td><td></td><td><code>ser08</code>*</td><td>RNA</td></tr>
<tr><td>Only 3' UA, GU and UG</td><td>Miller et al., 2008</td><td></td><td>terminal base pairs only 5'</td></tr>
<tr><td></td><td></td><td>UG and GU terminal base</td><td></td></tr>
</table>
<p>Single
dangling ends are not taken into account by the approximative mode.</p>
<h2 class="hasAnchor" id="double-dangling-end-effect"><a class="anchor" href="#double-dangling-end-effect"></a>Double dangling end effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>sugdna02</code>*</td><td>DNA</td><td>Only terminal poly A self</td><td>Ohmichi et al.,
2002</td></tr>
<tr><td></td><td>complementary sequences.</td><td></td><td><code>sugrna02</code></td></tr>
<tr><td>RNA</td><td>Only terminal poly A self</td><td>Ohmichi et al., 2002</td><td></td></tr>
<tr><td>complementary sequences.</td><td></td><td><code>ser05</code></td><td>RNA</td></tr>
<tr><td>Depends on the
available</td><td>O'Toole et al., 2005</td><td></td><td>thermodynamic parameters for</td></tr>
<tr><td></td><td></td><td>single dangling end.</td><td></td></tr>
</table>
<p>Double dangling ends are not taken into
account by the approximative mode.</p>
<h2 class="hasAnchor" id="long-dangling-end-effect"><a class="anchor" href="#long-dangling-end-effect"></a>Long dangling end effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>sugdna02</code>*</td><td>DNA</td><td>Only terminal poly A self</td><td>Ohmichi et al.,
2002</td></tr>
<tr><td></td><td>complementary sequences.</td><td></td><td><code>sugrna02</code>*</td></tr>
<tr><td>RNA</td><td>Only terminal poly A self</td><td>Ohmichi et al., 2002</td><td><strong>Model</strong></td></tr>
</table>
<p>Long dangling ends are not taken into account
by the approximative mode.</p>
<h2 class="hasAnchor" id="internal-loop-effect"><a class="anchor" href="#internal-loop-effect"></a>Internal loop effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>san04</code>*</td><td>DNA</td><td>Missing asymmetry penalty.</td><td>SantaLucia and
Hicks, 2004</td></tr>
<tr><td></td><td>Not tested with experimental</td><td></td><td></td></tr>
<tr><td>results.</td><td></td><td><code>tur06</code></td><td>RNA</td></tr>
<tr><td>Not tested with experimental</td><td>Lu et al., 2006</td><td></td><td>results.</td></tr>
<tr><td></td><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td></tr>
</table>
<p>Internal loops are not taken into
account by the approximative mode.</p>
<h2 class="hasAnchor" id="single-bulge-loop-effect"><a class="anchor" href="#single-bulge-loop-effect"></a>Single bulge loop effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>tan04</code>*</td><td>DNA</td><td></td><td>Tan and Chen, 2007</td></tr>
<tr><td><code>san04</code></td><td>DNA</td><td>Missing closing AT penalty.</td><td>SantaLucia and Hicks, 2004</td></tr>
<tr><td><code>ser07</code></td><td>RNA</td><td>Less reliable results. Some</td><td>Blose et al.,
2007</td></tr>
<tr><td></td><td>missing parameters.</td><td></td><td><strong>Model</strong></td></tr>
</table>
<p>Internal loops are not taken into account by the
approximative mode.</p>
<h2 class="hasAnchor" id="long-bulge-loop-effect"><a class="anchor" href="#long-bulge-loop-effect"></a>Long bulge loop effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>san04</code>*</td><td>DNA</td><td>Missing closing AT penalty.</td><td>SantaLucia and
Hicks, 2004</td></tr>
<tr><td><code>tur06</code>*</td><td>RNA</td><td>Not tested with experimental</td><td>Lu et al., 2006</td></tr>
</table>
<p>Long bulge loops are not taken
into account by the approximative mode.</p>
<h2 class="hasAnchor" id="cng-repeats-effect"><a class="anchor" href="#cng-repeats-effect"></a>CNG repeats effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>bro05</code>*</td><td>RNA</td><td>Self complementary sequences.</td><td>Broda et al., 2005</td></tr>
</table>
<p>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.</p>
<h2 class="hasAnchor" id="inosine-bases-effect"><a class="anchor" href="#inosine-bases-effect"></a>Inosine bases effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>san05</code>*</td><td>DNA</td><td>Missing parameters for tandem</td><td>Watkins and
SantaLucia, 2005</td></tr>
<tr><td></td><td>base pairs containing inosine</td><td></td><td></td></tr>
<tr><td>bases.</td><td></td><td><strong>Model</strong></td><td><strong>Type</strong></td></tr>
</table>
<h2 class="hasAnchor" id="hydroxyadenine-bases-effect"><a class="anchor" href="#hydroxyadenine-bases-effect"></a>Hydroxyadenine bases effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>sug01</code>*</td><td>DNA</td><td>Only 5' GA*C 3'and 5' TA*A 3'</td><td>Kawakami et
al., 2001</td></tr>
</table>
<p>Hydroxyadenine bases (A*) are not
taken into account by the approximative mode.</p>
<h2 class="hasAnchor" id="azobenzenes-effect-effect"><a class="anchor" href="#azobenzenes-effect-effect"></a>Azobenzenes effect effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>asa05</code>*</td><td>DNA</td><td>Less reliable results when</td><td>Asanuma et al.,
2005</td></tr>
<tr><td></td><td>the number of cis azobenzene</td><td></td><td><strong>Model</strong></td></tr>
</table>
<p>Azobenzenes (X_T for trans azobenzenes and X_C for cis azobenzenes)
are not taken into account by the approximative mode.</p>
<h2 class="hasAnchor" id="locked-nucleic-acids-effect"><a class="anchor" href="#locked-nucleic-acids-effect"></a>Locked nucleic acids effect</h2>
<p></p><table class='table'>
<tr><td><strong>Model</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
</table>
<p>Locked nucleic acids
(AL, GL, TL and CL) are not taken into account by the approximative mode.</p>
<h2 class="hasAnchor" id="sodium-corrections"><a class="anchor" href="#sodium-corrections"></a>Sodium corrections</h2>
<p></p><table class='table'>
<tr><td><strong>Correcion</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>ahs01</code></td><td>DNA</td><td>Na>0.</td><td>von Ahsen et al., 2001</td></tr>
<tr><td><code>schlif</code></td><td>DNA</td><td>Na>=0.07; Na<=0.12.</td><td>Schildkraut and Lifson,
1965</td></tr>
<tr><td><code>tanna06</code></td><td>DNA</td><td>Na>=0.001; Na<=1.</td><td>Tan and Chen,
2006</td></tr>
<tr><td><code>tanna07</code>*</td><td>RNA</td><td>Na>=0.003; Na<=1.</td><td>Tan and Chen,
2007</td></tr>
<tr><td></td><td>or</td><td></td><td></td></tr>
<tr><td>2'-O-MeRNA/RNA</td><td></td><td><code>wet91</code></td><td>RNA,</td></tr>
<tr><td>Na>0.</td><td>Wetmur, 1991</td><td></td><td>DNA</td></tr>
<tr><td></td><td></td><td>and</td><td></td></tr>
<tr><td></td><td>RNA/DNA</td><td></td><td><code>kam71</code></td></tr>
<tr><td>DNA</td><td>Na>0;
Na>=0.069; Na<=1.02.</td><td>Frank-Kamenetskii, 1971</td><td><code>marschdot</code></td></tr>
<tr><td>DNA</td><td>Na>=0.069; Na<=1.02.</td><td>Marmur and Doty, 1962; Blake</td><td></td></tr>
<tr><td>and Delcourt, 1998</td><td><code>owc1904</code></td><td>DNA</td><td>Na>0.</td></tr>
<tr><td>Owczarzy et al., 2004</td><td><code>owc2004</code></td><td>DNA</td><td>Na>0.</td></tr>
<tr><td>Owczarzy et
al., 2004</td><td><code>owc2104</code></td><td>DNA</td><td>Na>0.</td></tr>
<tr><td>Owczarzy et al., 2004</td><td><code>owc2204</code>*</td><td>DNA</td><td>Na>0.</td></tr>
<tr><td>Owczarzy et al., 2004</td><td><code>san96</code></td><td>DNA</td><td>Na>=0.1.</td></tr>
<tr><td>SantaLucia et al., 1996</td><td><code>san04</code></td><td>DNA</td><td>Na>=0.05; Na<=1.1;</td></tr>
<tr><td>SantaLucia and Hicks,
2004;</td><td></td><td>Oligonucleotides inferior to</td><td>SantaLucia, 1998</td></tr>
</table>
<h2 class="hasAnchor" id="magnesium-corrections"><a class="anchor" href="#magnesium-corrections"></a>Magnesium corrections</h2>
<p></p><table class='table'>
<tr><td><strong>Correcion</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>owcmg08</code>*</td><td>DNA</td><td>Mg>=0.0005; Mg<=0.6.</td><td>Owczarzy et al.,
2008</td></tr>
<tr><td><code>tanmg06</code></td><td>DNA</td><td>Mg>=0.0001; Mg<=1; Oligomer</td><td>Tan and
Chen, 2006</td></tr>
<tr><td></td><td>length superior to 6 base</td><td></td><td>pairs.</td></tr>
</table>
<h2 class="hasAnchor" id="mixed-sodium-and-magnesium-corrections"><a class="anchor" href="#mixed-sodium-and-magnesium-corrections"></a>Mixed Sodium and Magnesium corrections</h2>
<p></p><table class='table'>
<tr><td><strong>Correcion</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>owcmix08</code>*</td><td>DNA</td><td>Mg>=0.0005; Mg<=0.6;</td><td>Owczarzy et al., 2008</td></tr>
<tr><td></td><td>Na+K+Tris/2>0.</td><td><code>tanmix07</code></td><td>DNA</td></tr>
<tr><td>Mg>=0.1; Mg<=0.3;</td><td>Tan and Chen, 2007</td><td></td><td>and</td></tr>
<tr><td>Na+K+Tris/2>=0.1;</td><td><strong>Correcion</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td></tr>
</table>
<h2 class="hasAnchor" id="sodium-equivalent-concentration-methods"><a class="anchor" href="#sodium-equivalent-concentration-methods"></a>Sodium equivalent concentration methods</h2>
<p></p><table class='table'>
<tr><td><strong>Correcion</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>ahs01</code>*</td><td>DNA</td><td>von Ahsen et al.,
2001</td><td><code>mit96</code></td></tr>
<tr><td>DNA</td><td>Mitsuhashi, 1996</td><td><strong>Correcion</strong></td><td><strong>Type</strong></td></tr>
</table>
<h2 class="hasAnchor" id="dmso-corrections"><a class="anchor" href="#dmso-corrections"></a>DMSO corrections</h2>
<p></p><table class='table'>
<tr><td><strong>Correcion</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>ahs01</code></td><td>DNA</td><td>Not tested with experimental</td><td>von Ahsen et
al., 2001</td></tr>
<tr><td></td><td>results.</td><td><code>cul76</code></td><td>DNA</td></tr>
<tr><td>Not tested
with experimental</td><td>Cullen and Bick, 1976</td><td></td><td>results.</td></tr>
<tr><td><code>esc80</code></td><td>DNA</td><td>Not tested with experimental</td><td>Escara and
Hutton, 1980</td></tr>
<tr><td></td><td>results.</td><td><code>mus80</code></td><td>DNA</td></tr>
<tr><td>Not
tested with experimental</td><td>Musielski et al., 1981</td><td><strong>Correcion</strong></td><td><strong>Type</strong></td></tr>
</table>
<h2 class="hasAnchor" id="formamide-corrections"><a class="anchor" href="#formamide-corrections"></a>Formamide corrections</h2>
<p></p><table class='table'>
<tr><td><strong>Correcion</strong></td><td><strong>Type</strong></td><td><strong>Limits.Remarks</strong></td><td><strong>Reference</strong></td></tr>
<tr><td><code>bla96</code></td><td>DNA</td><td>With formamide concentration</td><td>Blake, 1996</td></tr>
<tr><td></td><td>in mol/L.</td><td></td><td><code>lincorr</code></td></tr>
<tr><td>DNA</td><td>With a <!-- % of -->
formamide volume.</td><td>McConaughy et al., 1969;</td><td></td></tr>
<tr><td></td><td>Record,
1967; Casey and</td><td><strong>Correcion</strong></td><td><strong>Type</strong></td></tr>
</table>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Marmur J and Doty P (1962).
“Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature.”
<em>Journal of Molecular Biology</em>, <b>5</b>(1), pp. 109--118.
doi: <a href='http://doi.org/10.1016/S0022-2836(62)80066-7'>10.1016/S0022-2836(62)80066-7</a>
.</p>
<p>Schildkraut C and Lifson S (1965).
“Dependence of the melting temperature of DNA on salt concentration.”
<em>Biopolymers</em>, <b>3</b>(2), pp. 195--208.
doi: <a href='http://doi.org/10.1002/bip.360030207'>10.1002/bip.360030207</a>
.</p>
<p>Record MT (1967).
“Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH.”
<em>Biopolymers</em>, <b>5</b>(10), pp. 975--992.
doi: <a href='http://doi.org/10.1002/bip.1967.360051010'>10.1002/bip.1967.360051010</a>
.</p>
<p>McConaughy BL, Laird C and McCarthy BJ (1969).
“Nucleic acid reassociation in formamide.”
<em>Biochemistry</em>, <b>8</b>(8), pp. 3289--3295.
doi: <a href='http://doi.org/10.1021/bi00836a024'>10.1021/bi00836a024</a>
.</p>
<p>Owen R, Hill L and Lapage S (1969).
“Determination of DNA base compositions from melting profiles in dilute buffers.”
<em>Biopolymers</em>, <b>7</b>(4), pp. 503--516.
doi: <a href='http://doi.org/10.1002/bip.1969.360070408'>10.1002/bip.1969.360070408</a>
.</p>
<p>Frank-Kamenetskii MD (1971).
“Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution.”
<em>Biopolymers</em>, <b>10</b>(12), pp. 2623--2624.
doi: <a href='http://doi.org/10.1002/bip.360101223'>10.1002/bip.360101223</a>
.</p>
<p>Britten RJ, Graham DE and Neufeld BR (1974).
“Analysis of repeating DNA sequences by reassociation.”
<em>Methods in Enzymology</em>, <b>29</b>, pp. 363--418.
doi: <a href='http://doi.org/10.1016/0076-6879(74)29033-5'>10.1016/0076-6879(74)29033-5</a>
.</p>
<p>Cullen BR and Bick MD (1976).
“Thermal denaturation of DNA from bromodeoxyuridine substituted cells.”
<em>Nucleic Acids Research</em>, <b>3</b>(1), pp. 49--62.
doi: <a href='http://doi.org/10.1093/nar/3.1.49'>10.1093/nar/3.1.49</a>
.</p>
<p>Hutton JR (1977).
“Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea.”
<em>Nucleic Acids Research</em>, <b>4</b>(10), pp. 3537--3555.
doi: <a href='http://doi.org/10.1093/nar/4.10.3537'>10.1093/nar/4.10.3537</a>
.</p>
<p>Casey J and Davidson N (1977).
“Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide.”
<em>Nucleic Acids Research</em>, <b>4</b>(5), pp. 1539--1552.
doi: <a href='http://doi.org/10.1093/nar/4.5.1539'>10.1093/nar/4.5.1539</a>
.</p>
<p>Hall TJ, Grula JW, Davidson EH and Britten RJ (1980).
“Evolution of sea urchin non-repetitive DNA.”
<em>Journal of Molecular Evolution</em>, <b>16</b>(2), pp. 95--110.
doi: <a href='http://doi.org/10.1007/BF01731580'>10.1007/BF01731580</a>
.</p>
<p>Escara JF and Hutton JR (1980).
“Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: Acceleration of the renaturation rate.”
<em>Biopolymers</em>, <b>19</b>(7), pp. 1315--1327.
doi: <a href='http://doi.org/10.1002/bip.1980.360190708'>10.1002/bip.1980.360190708</a>
.</p>
<p>Musielski H, Mann W, Laue R and Michel S (1981).
“Influence of dimethylsulfoxide on transcription by bacteriophage T3-induced RNA polymerase.”
<em>Zeitschrift fur allgemeine Mikrobiologie</em>, <b>21</b>(6), pp. 447--456.
doi: <a href='http://doi.org/10.1002/jobm.19810210606'>10.1002/jobm.19810210606</a>
.</p>
<p>Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T and Turner DH (1986).
“Improved free-energy parameters for predictions of RNA duplex stability.”
<em>Proceedings of the National Academy of Sciences</em>, <b>83</b>(24), pp. 9373.
<a href='http://www.pnas.org/content/83/24/9373.abstract'>http://www.pnas.org/content/83/24/9373.abstract</a>.</p>
<p>Breslauer KJ, Frank R, Blocker H and Marky LA (1986).
“Predicting DNA duplex stability from the base sequence.”
<em>Proceedings of the National Academy of Sciences</em>, <b>83</b>(11), pp. 3746.
<a href='http://www.pnas.org/content/83/11/3746.abstract'>http://www.pnas.org/content/83/11/3746.abstract</a>.</p>
<p>Wahl GM, Barger SL and Kimmel AR (1987).
“Molecular hybridization of immobilized nucleic acids: Theoretical concepts and practical considerations.”
<em>Methods in Enzymology</em>, <b>152</b>, pp. 399--407.
doi: <a href='http://doi.org/10.1016/0076-6879(87)52046-8'>10.1016/0076-6879(87)52046-8</a>
.</p>
<p>Wetmur JG (1991).
“DNA probes: Applications of the principles of nucleic acid hybridization.”
<em>Critical Reviews in Biochemistry and Molecular Biology</em>, <b>26</b>(3-4), pp. 227--259.
doi: <a href='http://doi.org/10.3109/10409239109114069'>10.3109/10409239109114069</a>
.</p>
<p>Chester N and Marshak D (1993).
“Dimethyl sulfoxide-mediated primer Tm reduction: A method for analyzing the role of renaturation temperature in the polymerase chain reaction.”
<em>Analytical Biochemistry</em>, <b>209</b>(2), pp. 284--290.
doi: <a href='http://doi.org/10.1006/abio.1993.1121'>10.1006/abio.1993.1121</a>
.</p>
<p>Sugimoto N, Katoh M, Nakano S, Ohmichi T and Sasaki M (1994).
“RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs have identical stability.”
<em>FEBS Letters</em>, <b>354</b>(1), pp. 74--78.
doi: <a href='http://doi.org/10.1016/0014-5793(94)01098-6'>10.1016/0014-5793(94)01098-6</a>
.</p>
<p>Sugimoto N, Nakano S, Katoh M, Matsumura A, Nakamuta H, Ohmichi T, Yoneyama M and Sasaki M (1995).
“Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes.”
<em>Biochemistry</em>, <b>34</b>(35), pp. 11211--11216.
doi: <a href='http://doi.org/10.1021/bi00035a029'>10.1021/bi00035a029</a>
.</p>
<p>SantaLucia J, Allawi HT and Seneviratne PA (1996).
“Improved nearest-neighbor parameters for predicting DNA duplex stability.”
<em>Biochemistry</em>, <b>35</b>(11), pp. 3555--3562.
doi: <a href='http://doi.org/10.1021/bi951907q'>10.1021/bi951907q</a>
.</p>
<p>Sugimoto N, Nakano S, Yoneyama M and Honda K (1996).
“Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes.”
<em>Nucleic Acids Research</em>, <b>24</b>(22), pp. 4501--4505.
doi: <a href='http://doi.org/10.1093/nar/24.22.4501'>10.1093/nar/24.22.4501</a>
.</p>
<p>Blake RD and Delcourt SG (1996).
“Thermodynamic effects of formamide on DNA stability.”
<em>Nucleic Acids Research</em>, <b>24</b>(11), pp. 2095--2103.
doi: <a href='http://doi.org/10.1093/nar/24.11.2095'>10.1093/nar/24.11.2095</a>
.</p>
<p>Blake RD (1996).
“Denaturation of DNA.”
In Meyers RA (ed.), <em>Encyclopedia of molecular biology and molecular medicine</em>, volume 2, pp. 1--19.
VCH Verlagsgesellschaft, Weinheim, Germany.</p>
<p>Mitsuhashi M (1996).
“Technical report: Part 1. Basic requirements for designing optimal oligonucleotide probe sequences.”
<em>Journal of Clinical Laboratory Analysis</em>, <b>10</b>(5), pp. 277--284.
doi: <a href='http://doi.org/10.1002/(sici)1098-2825(1996)10:5<277::aid-jcla8>3.0.co;2-5'>10.1002/(sici)1098-2825(1996)10:5<277::aid-jcla8>3.0.co;2-5</a>
.</p>
<p>Allawi HT and SantaLucia J (1997).
“Thermodynamics and NMR of internal G-T mismatches in dna.”
<em>Biochemistry</em>, <b>36</b>(34), pp. 10581--10594.
doi: <a href='http://doi.org/10.1021/bi962590c'>10.1021/bi962590c</a>
.</p>
<p>SantaLucia J (1998).
“A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.”
<em>Proceedings of the National Academy of Sciences</em>, <b>95</b>(4), pp. 1460.
<a href='http://www.pnas.org/content/95/4/1460.abstract'>http://www.pnas.org/content/95/4/1460.abstract</a>.</p>
<p>Xia T, SantaLucia J, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C and Turner DH (1998).
“Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.”
<em>Biochemistry</em>, <b>37</b>(42), pp. 14719--14735.
doi: <a href='http://doi.org/10.1021/bi9809425'>10.1021/bi9809425</a>
.</p>
<p>Allawi HT and SantaLucia J (1998).
“Thermodynamics of internal C-T mismatches in DNA.”
<em>Nucleic Acids Research</em>, <b>26</b>(11), pp. 2694--2701.
doi: <a href='http://doi.org/10.1093/nar/26.11.2694'>10.1093/nar/26.11.2694</a>
.</p>
<p>Blake RD and Delcourt SG (1998).
“Thermal stability of DNA.”
<em>Nucleic Acids Research</em>, <b>26</b>(14), pp. 3323--3332.
doi: <a href='http://doi.org/10.1093/nar/26.14.3323'>10.1093/nar/26.14.3323</a>
.</p>
<p>Allawi HT and SantaLucia J (1998).
“Nearest neighbor thermodynamic parameters for internal G-A mismatches in DNA.”
<em>Biochemistry</em>, <b>37</b>(8), pp. 2170--2179.
doi: <a href='http://doi.org/10.1021/bi9724873'>10.1021/bi9724873</a>
.</p>
<p>Allawi HT and SantaLucia J (1998).
“Nearest-neighbor thermodynamics of internal A-C mismatches in dna: sequence dependence and pH effects.”
<em>Biochemistry</em>, <b>37</b>(26), pp. 9435--9444.
doi: <a href='http://doi.org/10.1021/bi9803729'>10.1021/bi9803729</a>
.</p>
<p>Mathews DH, Sabina J, Zuker M and Turner DH (1999).
“Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.”
<em>Journal of Molecular Biology</em>, <b>288</b>(5), pp. 911--940.
doi: <a href='http://doi.org/10.1006/jmbi.1999.2700'>10.1006/jmbi.1999.2700</a>
.</p>
<p>Peyret N, Seneviratne PA, Allawi HT and SantaLucia J (1999).
“Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A-A, C-C, G-G, and T-T Mismatches.”
<em>Biochemistry</em>, <b>38</b>(12), pp. 3468--3477.
doi: <a href='http://doi.org/10.1021/bi9825091'>10.1021/bi9825091</a>
.</p>
<p>Peyret N (2000).
<em>Prediction of nucleic acid hybridization: Parameters and algorithms.</em>.
PhD thesis, Wayne State University, Detroit, MI.</p>
<p>Bommarito S, Peyret N and SantaLucia J (2000).
“Thermodynamic parameters for DNA sequences with dangling ends.”
<em>Nucleic Acids Research</em>, <b>28</b>(9), pp. 1929--1934.
doi: <a href='http://doi.org/10.1093/nar/28.9.1929'>10.1093/nar/28.9.1929</a>
.</p>
<p>Kawakami J, Kamiya H, Yasuda K, Fujiki H, Kasai H and Sugimoto N (2001).
“Thermodynamic stability of base pairs between 2-hydroxyadenine and incoming nucleotides as a determinant of nucleotide incorporation specificity during replication.”
<em>Nucleic Acids Research</em>, <b>29</b>(16), pp. 3289--3296.
doi: <a href='http://doi.org/10.1093/nar/29.16.3289'>10.1093/nar/29.16.3289</a>
.</p>
<p>von
Ahsen N, Wittwer CT and Schutz E (2001).
“Oligonucleotide melting temperatures under PCR conditions: Nearest-neighbor corrections for Mg2+, deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas.”
<em>Clinical Chemistry</em>, <b>47</b>(11), pp. 1956--1961.
<a href='http://clinchem.aaccjnls.org/content/47/11/1956'>http://clinchem.aaccjnls.org/content/47/11/1956</a>.</p>
<p>Le Novere N (2001).
“MELTING, computing the melting temperature of nucleic acid duplex.”
<em>Bioinformatics</em>, <b>17</b>(12), pp. 1226--1227.
doi: <a href='http://doi.org/10.1093/bioinformatics/17.12.1226'>10.1093/bioinformatics/17.12.1226</a>
.</p>
<p>Ohmichi T, Nakano S, Miyoshi D and Sugimoto N (2002).
“Long RNA dangling end has large energetic contribution to duplex stability.”
<em>Journal of the American Chemical Society</em>, <b>124</b>(35), pp. 10367--10372.
doi: <a href='http://doi.org/10.1021/ja0255406'>10.1021/ja0255406</a>
.</p>
<p>SantaLucia J and Hicks D (2004).
“The thermodynamics of DNA structural motifs.”
<em>Annual Review of Biophysics and Biomolecular Structure</em>, <b>33</b>(1), pp. 415--440.
doi: <a href='http://doi.org/10.1146/annurev.biophys.32.110601.141800'>10.1146/annurev.biophys.32.110601.141800</a>
.</p>
<p>Tanaka F, Kameda A, Yamamoto M and Ohuchi A (2004).
“Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop.”
<em>Biochemistry</em>, <b>43</b>(22), pp. 7143--7150.
doi: <a href='http://doi.org/10.1021/bi036188r'>10.1021/bi036188r</a>
.</p>
<p>McTigue PM, Peterson RJ and Kahn JD (2004).
“Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation.”
<em>Biochemistry</em>, <b>43</b>(18), pp. 5388--5405.
doi: <a href='http://doi.org/10.1021/bi035976d'>10.1021/bi035976d</a>
.</p>
<p>Owczarzy R, You Y, Moreira BG, Manthey JA, Huang L, Behlke MA and Walder JA (2004).
“Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures.”
<em>Biochemistry</em>, <b>43</b>(12), pp. 3537--3554.
doi: <a href='http://doi.org/10.1021/bi034621r'>10.1021/bi034621r</a>
.</p>
<p>Broda M, Kierzek E, Gdaniec Z, Kulinski T and Kierzek R (2005).
“Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure.”
<em>Biochemistry</em>, <b>44</b>(32), pp. 10873--10882.
doi: <a href='http://doi.org/10.1021/bi0502339'>10.1021/bi0502339</a>
.</p>
<p>Watkins NE and SantaLucia J (2005).
“Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes.”