Biomod/2011/TUM/TNT/Glossary: Difference between revisions

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<h3>DAPI</h3> (4',6-diamidino-2-phenylindole):  
<h3>DAPI</h3> (4',6-diamidino-2-phenylindole):  
DAPI is an unfused aromatic ring system linked by bonds with torsional freedom which allow the molecules to adopt appropriate conformation to fit the helical curvature of the groove without significant perturbation of the DNA. DAPI has demonstrated DNA binding via intercalation with poly[d(GC)]. It is a nonclasical intercalator.  
DAPI is an unfused aromatic ring system linked by bonds with torsional freedom which allow the molecules to adopt appropriate conformation to fit the helical curvature of the groove without significant perturbation of the DNA. DAPI has demonstrated DNA binding via intercalation with poly[d(GC)]. It is a nonclasical intercalator. ([http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras/References#DNA_binders Strekowski et.al.)]


http://upload.wikimedia.org/wikipedia/commons/thumb/b/b4/DAPI.svg/300px-DAPI.svg.png
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b4/DAPI.svg/300px-DAPI.svg.png




<h3>DNA association binding constants</h3>
<h3>DNA dissociation constants</h3>
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<td><b>Compound</b></td><td><b>Binding mode</b></td><td><b>KD (nM)</b></td>
<td><b>Compound</b></td><td><b>Binding mode</b></td><td><b>K<sub>D</sub></b></td>
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<td>DAPI</td><td>intercalation</td><td>1.2×105</td>
<td>DAPI</td><td>intercalation</td><td>8.3 µM</td>
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</tr>
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<td>Spermine</td><td>groove binding</td><td>4.8 uM</td>
<td>Spermine</td><td>groove binding</td><td>4.8 µM</td>
</tr>
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<td>Ethidium bromide</td><td>intercalation</td><td>12.0 uM</td>  
<td>Ethidium bromide</td><td>intercalation</td><td>12.0 µM</td>  
</tr>
</tr>
</table>
</table>
([http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras/References#DNA_binders Strekowski et.al.)]




 
<h3>Ethidium bromide</h3>Ethidium bromide is a classical intercalator. It is a fused-ring aromatic molecule with positive charges on an attached side chain and/or the ring system itself. The planar ring system stacks well with base pairs in the intercalation. Ethidium bromide intercalates from the minor groove of the duplex complex. ([http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras/References#DNA_binders Strekowski et.al.)]
<h3>Ethidium bromide</h3>Ethidium bromide is a classical intercalator. It is a fused-ring aromatic molecule with positive charges on an attached side chain and/or the ring system itself. The planar ring system stacks well with base pairs in the intercalation. Ethidium bromide intercalates from the minor groove of the duplex complex.


http://upload.wikimedia.org/wikipedia/commons/thumb/0/0a/Ethidium_bromide.svg/200px-Ethidium_bromide.svg.png
http://upload.wikimedia.org/wikipedia/commons/thumb/0/0a/Ethidium_bromide.svg/200px-Ethidium_bromide.svg.png
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<h3>Spermine</h3> Spermine is a polyamine, which is protonated under physiological conditions and therefore interacts strongly with DNA. All  theoretical and experimental results (see: Noncovalent interactions with DNA: An overview) can be rationalized in terms of the concept of the negative potentials in the DNA macromolecule. It has been concluded that the highest concentration of the negative potentials is in the grooves of the DNA duplexes rather than on the backbones, despite the location of the anionic phosphates within these backbones. The negative potentials are stronger in the major groove than in the minor groove at GC sequences. Accordingly, a flexible cationic molecule of protonatedspermine forms a complex within the DNA <b>major</b> groove with GC sequences following the negative potential concentration.
<h3>Spermine</h3> Spermine is a polyamine, which is protonated under physiological conditions and therefore interacts strongly with DNA. All  theoretical and experimental results (see: Noncovalent interactions with DNA: An overview) can be rationalized in terms of the concept of the negative potentials in the DNA macromolecule. It has been concluded that the highest concentration of the negative potentials is in the grooves of the DNA duplexes rather than on the backbones, despite the location of the anionic phosphates within these backbones. The negative potentials are stronger in the major groove than in the minor groove at GC sequences. Accordingly, a flexible cationic molecule of protonatedspermine forms a complex within the DNA <b>major</b> groove with GC sequences following the negative potential concentration. ([http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras/References#DNA_binders Strekowski et.al.)]


http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Spermine.svg/500px-Spermine.svg.png
http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Spermine.svg/500px-Spermine.svg.png

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