Re: how ehidium bromide interacts with DNA?

The ethidium 
bromide (EtBr) slips between the bases of the RNA (which is exactly 
analogous to 
the interaction with DNA, as I recall). The 3D-structure of ethidium 
bromide complexed with RNA is given here: http://www.liv.ac.uk/~bat
es/EtBrframe.html

The bonding is similar to the bonding between the layers of graphite: i.e. 
stacks of aromatic rings. In addition, judging from the 3D structure 
above, EtBr seems to be able to hydrogen-bond from its free amine groups 
to the oxygens of the phosphate backbone.

The reason this causes the molecule to fluoresce is explained well here:
"Ethidium bromide looks a bit like a base pair and inserts into double 
stranded DNA between base pairs. It is a powerful mutagen producing a 
point mutation. Ethidium bromide on its own is weakly fluorescent. 
Fluorescence occurs because an electron is excited to an upper level (in 
this case by uv 365nm); when the electron falls back to a lower energy 
level, that difference in energy is given out as light quanta of lower 
energy (visible orange light in this case). The fluorescence of free 
ethidium bromide in solution is low because the electron can trickle 
between the two energy levels in stages using vibrational energy levels. 
This alternative pathway reduces number of electrons that follow the 
fluorescence pathway and so the yield is weak. When ethidium bromide is 
bound to DNA it is held more rigidly so the pathway giving out low energy 
quanta is less probable and the fluorescent pathway is favoured" http://ww
w.bch.ed.ac.uk/paul/TEACHING/MAC1h/DNA/mac_p2.htm

Ewen McLaughlin