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<h3>Ethidium bromide</h3> 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.
<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


<h3>FOB</h3> is short for folding buffer. It contains 50mM Tris and 10mM EDTA. FOBxM refers to FOB without MgCl<sub>2</sub>, whereas FOB20 is FOB with 20mM MgCl<sub>2</sub>
<h3>FOB</h3>FOB is short for folding buffer. It contains 50mM Tris and 10mM EDTA. FOBxM refers to FOB without MgCl<sub>2</sub>, whereas FOB20 is FOB with 20mM MgCl<sub>2</sub>






<h3>Intercalation</h3> is known to occur without interfering with hydrogen bonding of the base pairs and obeys the nearest neighbor exclusion principle. When DNA is saturated with intercalators, every second potential intercalation site on the helix remains empty. In order for intercalation to ensue, theDNAbase pairs separate 3.4 °A to form a cavity for the incoming planar ligand through localized left-handed unwinding of the duplex. The normal twist of B-formDNA is 36◦ (10 base pairs per one turn of 360◦). In order to accommodate the ligand, a reduction of this rotation occurs. The unwinding angle varies with the geometry of the ligand–DNA complex.
<h3>Intercalation</h3>Intercalation is known to occur without interfering with hydrogen bonding of the base pairs and obeys the nearest neighbor exclusion principle. When DNA is saturated with intercalators, every second potential intercalation site on the helix remains empty. In order for intercalation to ensue, theDNAbase pairs separate 3.4 °A to form a cavity for the incoming planar ligand through localized left-handed unwinding of the duplex. The normal twist of B-formDNA is 36◦ (10 base pairs per one turn of 360◦). In order to accommodate the ligand, a reduction of this rotation occurs. The unwinding angle varies with the geometry of the ligand–DNA complex.


In spite of the wealth of structural data known for intercalation complexes, the origin of the intercalation forces is not fully understood. Intercalation has been generally considered to be the result of a hydrophobic interaction in which a hydrophobic aromatic molecule is drawn to a hydrophobic environment of the base pairs from the hydrophilic aqueous environment.
In spite of the wealth of structural data known for intercalation complexes, the origin of the intercalation forces is not fully understood. Intercalation has been generally considered to be the result of a hydrophobic interaction in which a hydrophobic aromatic molecule is drawn to a hydrophobic environment of the base pairs from the hydrophilic aqueous environment.

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