SherbyNet - /page/wikibook/entry.mu

Micron Document

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<caption>DAPI

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<th colspan="2" style="background: #f8eaba;color:inherit; text-align: center;">Names

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<td colspan="2" style="text-align:left;"><a href="Chemical_nomenclature" title="Chemical nomenclature">IUPAC name</a>

<div style="max-width:22em; word-wrap:break-word; padding-left:1.7em;">2-(4-Amidinophenyl)-1<i>H</i>-indole-6-carboxamidine</div>

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<td colspan="2" style="text-align:left;">Other names

<div style="max-width:22em; word-wrap:break-word; padding-left:1.7em;">4′,6-Diamidino-2-phenylindole</div>

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<th colspan="2" style="background: #f8eaba;color:inherit; text-align: center;">Identifiers

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<td><div style="display: inline-block; line-height: 1.2em; padding: .1em 0;"><a href="CAS_Registry_Number" title="CAS Registry Number">CAS Number</a></div>

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</style><div class="plainlist"><ul><li><span title="commonchemistry.cas.org"><a rel="nofollow" class="external text" href="https://commonchemistry.cas.org/detail?cas_rn=28718-90-3">28718-90-3</a></span><sup> <span typeof="mw:File"><span></span></span><span style="display:none">Y</span></sup></li></ul></div>

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<td><div style="display: inline-block; line-height: 1.2em; padding: .1em 0;">3D model (<a href="JSmol" class="mw-redirect" title="JSmol">JSmol</a>)</div>

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<td><div class="plainlist"><ul><li><span title="chemapps.stolaf.edu (3D interactive model)"><a rel="nofollow" class="external text" href="https://chemapps.stolaf.edu/jmol/jmol.php?model=%5BN%40H%5D%3DC%28N%29c3ccc%28c2cc1ccc%28cc1%5BnH%5D2%29C%28%3D%5BN%40H%5D%29N%29cc3">Interactive image</a></span></li><li><span title="chemapps.stolaf.edu (3D interactive model)"><a rel="nofollow" class="external text" href="https://chemapps.stolaf.edu/jmol/jmol.php?model=%5BH%5D%2FN%3DC%28%2Fc1ccc%28cc1%29c2cc3ccc%28cc3%5BnH%5D2%29%2FC%28%3DN%2F%5BH%5D%29%2FN%29%5CN">Interactive image</a></span></li></ul></div>

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<td><a href="ChEBI" title="ChEBI">ChEBI</a>

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<td><div class="plainlist"><ul><li><span title="www.ebi.ac.uk"><a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=51231">CHEBI:51231</a></span><sup> <span typeof="mw:File"><span></span></span><span style="display:none">Y</span></sup></li></ul></div>

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<td><a href="ChEMBL" title="ChEMBL">ChEMBL</a>

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<td><div class="plainlist"><ul><li><span title="www.ebi.ac.uk"><a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/chembl/explore/compound/ChEMBL48217">ChEMBL48217</a></span><sup> <span typeof="mw:File"><span></span></span><span style="display:none">Y</span></sup></li></ul></div>

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<td><a href="ChemSpider" title="ChemSpider">ChemSpider</a>

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<td><div style="display: inline-block; line-height: 1.2em; padding: .1em 0;"><a href="PubChem" title="PubChem">PubChem</a> <abbr title="Compound ID">CID</abbr></div>

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<td><div style="display: inline-block; line-height: 1.2em; padding: .1em 0;"><a href="CompTox_Chemicals_Dashboard" title="CompTox Chemicals Dashboard">CompTox Dashboard</a> <span style="font-weight:normal">(<abbr title="U.S. Environmental Protection Agency">EPA</abbr>)</span></div>

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<td><div class="plainlist"><ul><li><span title="comptox.epa.gov"><a rel="nofollow" class="external text" href="https://comptox.epa.gov/dashboard/chemical/details/DTXSID50963757">DTXSID50963757</a> </span></li></ul></div>

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<div style="line-height: 1.6em; font-weight: bold; text-align:left; font-weight:normal;"><div><a href="International_Chemical_Identifier" title="International Chemical Identifier">InChI</a></div></div>

<ul class="mw-collapsible-content" style="margin-top: 0; margin-bottom: 0; line-height: inherit; list-style: none; margin-left: 0; word-break:break-all;"><li style="line-height: inherit; margin: 0"><div style="border-top:1px solid #ccc; padding:0.2em 0 0.2em 1.5em; text-align:left;"><div style="word-wrap:break-word; text-indent:-1.5em; font-size:97%; line-height:120%;">InChI=1S/C16H15N5/c17-15(18)10-3-1-9(2-4-10)13-7-11-5-6-12(16(19)20)8-14(11)21-13/h1-8,21H,(H3,17,18)(H3,19,20)<sup> <span typeof="mw:File"><span></span></span><span style="display:none">Y</span></sup></div><div style="word-wrap:break-word; text-indent:-1.5em; font-size:97%; line-height:120%;">Key: FWBHETKCLVMNFS-UHFFFAOYSA-N<sup> <span typeof="mw:File"><span></span></span><span style="display:none">Y</span></sup></div></div></li><li style="line-height: inherit; margin: 0"><div style="border-top:1px solid #ccc; padding:0.2em 0 0.2em 1.5em; text-align:left;"><div style="word-wrap:break-word; text-indent:-1.5em; font-size:97%; line-height:120%;">InChI=1/C16H15N5/c17-15(18)10-3-1-9(2-4-10)13-7-11-5-6-12(16(19)20)8-14(11)21-13/h1-8,21H,(H3,17,18)(H3,19,20)</div><div style="word-wrap:break-word; text-indent:-1.5em; font-size:97%; line-height:120%;">Key: FWBHETKCLVMNFS-UHFFFAOYAH</div></div></li></ul>

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<div style="line-height: 1.6em; font-weight: bold; text-align:left; font-weight:normal;"><div><a href="Simplified_molecular-input_line-entry_system" class="mw-redirect" title="Simplified molecular-input line-entry system">SMILES</a></div></div>

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<th colspan="2" style="background: #f8eaba;color:inherit; text-align: center;">Properties

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<td><div style="display: inline-block; line-height: 1.2em; padding: .1em 0;"><a href="Chemical_formula" title="Chemical formula">Chemical formula</a></div>

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<td><a href="Molar_mass" title="Molar mass">Molar mass</a>

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<td colspan="2" style="text-align:left; background:#f8eaba; color:inherit; border:1px solid #a2a9b1;"><div style="display: inline-block; line-height: 1.2em; padding: .1em 0;">Except where otherwise noted, data are given for materials in their <a href="Standard_state" title="Standard state">standard state</a> (at 25 °C [77 °F], 100 kPa).</div>

<div style="margin-top: 0.3em;"><div style="text-align:center;"><span typeof="mw:File"><span></span></span><span style="display:none">Y</span> <span class="reflink nourlexpansion"><a class="external text external" href="https://en.wikipedia.org/w/index.php?title=Special:ComparePages&rev1=443556310&page2=DAPI">verify</a></span> (what is <sup><span typeof="mw:File"><span></span></span><span style="display:none">Y</span><span typeof="mw:File"><span></span></span><span style="display:none">N</span></sup> ?)

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<div style="margin-top: 0.3em; text-align: center;">Infobox references</div>

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<p><b>DAPI</b> (pronounced 'DAPPY', /ˈdæpiː/), or <b>4′,6-diamidino-2-phenylindole</b>, is a <a href="Fluorescence" title="Fluorescence">fluorescent</a> <a href="Staining_(biology)" class="mw-redirect" title="Staining (biology)">stain</a> that binds strongly to <a href="Adenine" title="Adenine">adenine</a>–<a href="Thymine" title="Thymine">thymine</a>-rich regions in <a href="DNA" title="DNA">DNA</a>. It is used extensively in <a href="Fluorescence_microscopy" class="mw-redirect" title="Fluorescence microscopy">fluorescence microscopy</a>. As DAPI can pass through an intact <a href="Cell_membrane" title="Cell membrane">cell membrane</a>, it can be used to stain both live and <a href="Fixation_(histology)" title="Fixation (histology)">fixed</a> cells, though it passes through the membrane less efficiently in live cells and therefore provides a marker for membrane viability.

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<div class="mw-heading mw-heading2"><h2 id="History">History</h2></div>

<p>DAPI was first synthesised in 1971 in the laboratory of Otto Dann as part of a search for drugs to treat <a href="Trypanosomiasis" title="Trypanosomiasis">trypanosomiasis</a>. Although it was unsuccessful as a drug, further investigation indicated it bound strongly to DNA and became more fluorescent when bound. This led to its use in identifying <a href="Mitochondria" class="mw-redirect" title="Mitochondria">mitochondrial</a> DNA in <a href="Ultracentrifugation" class="mw-redirect" title="Ultracentrifugation">ultracentrifugation</a> in 1975, the first recorded use of DAPI as a fluorescent DNA stain.<sup id="cite_ref-Kapuscinski1995_1-0" class="reference"><a href="#cite_note-Kapuscinski1995-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup>

</p><p>Strong fluorescence when bound to DNA led to the rapid adoption of DAPI for fluorescent staining of DNA for <a href="Fluorescence_microscopy" class="mw-redirect" title="Fluorescence microscopy">fluorescence microscopy</a>. Its use for detecting DNA in <a href="Plant" title="Plant">plant</a>, <a href="Metazoa" class="mw-redirect" title="Metazoa">metazoa</a> and <a href="Bacteria" title="Bacteria">bacteria</a> cells and <a href="Virus" title="Virus">virus</a> particles was demonstrated in the late 1970s, and quantitative staining of DNA inside cells was demonstrated in 1977. Use of DAPI as a DNA stain for <a href="Flow_cytometry" title="Flow cytometry">flow cytometry</a> was also demonstrated around this time.<sup id="cite_ref-Kapuscinski1995_1-1" class="reference"><a href="#cite_note-Kapuscinski1995-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup>

</p><p>When bound to double-stranded DNA, DAPI has an absorption maximum at a wavelength of 358 nm (<a href="Ultraviolet" title="Ultraviolet">ultraviolet</a>) and its emission maximum is at 461 nm (blue). Therefore, for fluorescence microscopy, DAPI is excited with ultraviolet light and is detected through a blue/cyan filter. The emission peak is fairly broad.<sup id="cite_ref-DAPI_Nucleic_Acid_Stain_2-0" class="reference"><a href="#cite_note-DAPI_Nucleic_Acid_Stain-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> DAPI will also bind to <a href="RNA" title="RNA">RNA</a>, though it is not as strongly fluorescent. Its emission shifts to around 500 nm when bound to RNA.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup>

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<p>DAPI's blue emission is convenient for microscopists who wish to use multiple fluorescent stains in a single sample. There is some fluorescence overlap between DAPI and green-fluorescent molecules like <a href="Fluorescein" title="Fluorescein">fluorescein</a> and <a href="Green_fluorescent_protein" title="Green fluorescent protein">green fluorescent protein</a> (GFP) but the effect of this is small.

</p><p>Outside of analytical fluorescence light microscopy DAPI is also popular for labeling of <a href="Cell_cultures" class="mw-redirect" title="Cell cultures">cell cultures</a> to detect the DNA of contaminating <i><a href="Mycoplasma" title="Mycoplasma">Mycoplasma</a></i> or <a href="Virus" title="Virus">virus</a>. The labelled <i>Mycoplasma</i> or virus particles in the <a href="Growth_medium" title="Growth medium">growth medium</a> fluoresce once stained by DAPI making them easy to detect.<sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup>

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<div class="mw-heading mw-heading2"><h2 id="Modelling_of_absorption_and_fluorescence_properties">Modelling of absorption and fluorescence properties</h2></div>

<p>This DNA fluorescent probe has been effectively modeled<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> using the <a href="Time-dependent_density_functional_theory" title="Time-dependent density functional theory">time-dependent density functional theory</a>, coupled with the IEF version of the <a href="Polarizable_continuum_model" title="Polarizable continuum model">polarizable continuum model</a>. This quantum-mechanical modeling has rationalized the absorption and fluorescence behavior given by minor groove binding and <a href="Intercalation_(biochemistry)" title="Intercalation (biochemistry)">intercalation</a> in the DNA pocket, in term of a reduced structural flexibility and polarization.

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<div class="mw-heading mw-heading2"><h2 id="Live_cells_and_toxicity">Live cells and toxicity</h2></div>

<p>DAPI can be used for fixed cell staining. The concentration of DAPI needed for live cell staining is generally very high; it is rarely used for live cells.<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> It is labeled non-toxic in its MSDS<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> and though it was not shown to have mutagenicity to <i>E. coli</i>,<sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> it is labelled as a known mutagen in manufacturer information.<sup id="cite_ref-DAPI_Nucleic_Acid_Stain_2-1" class="reference"><a href="#cite_note-DAPI_Nucleic_Acid_Stain-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> As it is a small DNA binding compound, it is likely to have some <a href="Carcinogenic" class="mw-redirect" title="Carcinogenic">carcinogenic</a> effects and care should be taken in its handling and disposal.

</p>

<div class="mw-heading mw-heading2"><h2 id="Alternatives">Alternatives</h2></div>

<p>The <a href="Hoechst_stain" title="Hoechst stain">Hoechst stains</a> are similar to DAPI in that they are also blue-fluorescent DNA stains which are compatible with both live- and fixed-cell applications, as well as visible using the same equipment filter settings as for DAPI.

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<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

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</style><cite id="CITEREFKapuscinski1995" class="citation journal cs1">Kapuscinski, J. (September 1995). "DAPI: a DNA-specific fluorescent probe". <i>Biotech. Histochem</i>. <b>70</b> (5): <span class="nowrap">220–</span>233. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.3109%2F10520299509108199">10.3109/10520299509108199</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/8580206">8580206</a>.</cite></span>

</li>

<li id="cite_note-DAPI_Nucleic_Acid_Stain-2"><span class="mw-cite-backlink">^ <a href="#cite_ref-DAPI_Nucleic_Acid_Stain_2-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-DAPI_Nucleic_Acid_Stain_2-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text">Invitrogen, <a rel="nofollow" class="external text" href="http://probes.invitrogen.com/media/pis/mp01306.pdf">DAPI Nucleic Acid Stain</a> <a rel="nofollow" class="external text" href="https://web.archive.org/web/20090306113851/http://probes.invitrogen.com/media/pis/mp01306.pdf">Archived</a> 2009-03-06 at the <a href="Wayback_Machine" title="Wayback Machine">Wayback Machine</a>. accessed 2009-12-08.</span>

</li>

<li id="cite_note-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-3">^</a></b></span> <span class="reference-text">Scott Prahl, <a rel="nofollow" class="external text" href="http://omlc.ogi.edu/spectra/PhotochemCAD/html/dapi(H2O).html">DAPI</a>. accessed 2009-12-08.</span>

</li>

<li id="cite_note-4"><span class="mw-cite-backlink"><b><a href="#cite_ref-4">^</a></b></span> <span class="reference-text"><cite id="CITEREFKapuscinski2017" class="citation journal cs1">Kapuscinski, J (2017). <a rel="nofollow" class="external text" href="https://doi.org/10.1177%2F38.9.1696951">"Interactions of nucleic acids with fluorescent dyes: spectral properties of condensed complexes"</a>. <i>Journal of Histochemistry & Cytochemistry</i>. <b>38</b> (9): <span class="nowrap">1323–</span>1329. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1177%2F38.9.1696951">10.1177/38.9.1696951</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/1696951">1696951</a>.</cite></span>

</li>

<li id="cite_note-5"><span class="mw-cite-backlink"><b><a href="#cite_ref-5">^</a></b></span> <span class="reference-text"><cite id="CITEREFRussellNewmanWilliamson1975" class="citation journal cs1">Russell, W. C.; Newman, Carol; Williamson, D. H. (1975). "A simple cytochemical technique for demonstration of DNA in cells infected with mycoplasmas and viruses". <i>Nature</i>. <b>253</b> (5491): <span class="nowrap">461–</span>462. <a href="Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/1975Natur.253..461R">1975Natur.253..461R</a>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1038%2F253461a0">10.1038/253461a0</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/46112">46112</a>. <a href="S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:25224870">25224870</a>.</cite></span>

</li>

<li id="cite_note-6"><span class="mw-cite-backlink"><b><a href="#cite_ref-6">^</a></b></span> <span class="reference-text"><cite id="CITEREFBiancardiBiverSeccoMennucci2013" class="citation journal cs1">Biancardi, Alessandro; Biver, Tarita; Secco, Fernando; Mennucci, Benedetta (2013). "An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools". <i>Phys. Chem. Chem. Phys</i>. <b>15</b> (13): <span class="nowrap">4596–</span>603. <a href="Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2013PCCP...15.4596B">2013PCCP...15.4596B</a>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1039%2FC3CP44058C">10.1039/C3CP44058C</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/23423468">23423468</a>.</cite></span>

</li>

<li id="cite_note-7"><span class="mw-cite-backlink"><b><a href="#cite_ref-7">^</a></b></span> <span class="reference-text"><cite id="CITEREFZinkSadoniStelzer2003" class="citation journal cs1">Zink D, Sadoni N, Stelzer E (2003). "Visualizing Chromatin and Chromosomes in Living Cells. Usually for the live cells staining Hoechst Staining is used. DAPI gives a higher signal in the fixed cells compare to Hoechst Stain but in the live cells Hoechst Stain is used". <i>Methods</i>. <b>29</b> (1): <span class="nowrap">42–</span>50. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2FS1046-2023%2802%2900289-X">10.1016/S1046-2023(02)00289-X</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/12543070">12543070</a>.</cite></span>

</li>

<li id="cite_note-8"><span class="mw-cite-backlink"><b><a href="#cite_ref-8">^</a></b></span> <span class="reference-text"><a rel="nofollow" class="external text" href="https://web.archive.org/web/20120305183437/http://www.kpl.com/docs/msds/710301.pdf">DAPI MATERIAL SAFETY DATA SHEET</a>. kpl.com</span>

</li>

<li id="cite_note-9"><span class="mw-cite-backlink"><b><a href="#cite_ref-9">^</a></b></span> <span class="reference-text"><cite id="CITEREFOhtaTokishitaYamagata2001" class="citation journal cs1">Ohta T, Tokishita S, Yamagata H (2001). "Ethidium bromide and SYBR Green I enhance the genotoxicity of UV-irradiation and chemical mutagens in <i>E. coli</i>". <i>Mutat. Res</i>. <b>492</b> (<span class="nowrap">1–</span>2): <span class="nowrap">91–</span>7. <a href="Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2001MRGTE.492...91O">2001MRGTE.492...91O</a>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2FS1383-5718%2801%2900155-3">10.1016/S1383-5718(01)00155-3</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/11377248">11377248</a>.</cite></span>

</li>

</ol></div>

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