Team:EPF-Lausanne/Protocols/MITOMI protein DNA

{{:Team:EPF-Lausanne/Templates/ProtocolHeader|title=MITOMI: Protein-DNA Interaction}}

made on 16.05.2011

== Purpose ==

To detect potential protein-DNA interactions

== Chip ==

MITOMI device bonded to epoxy slide spotted with DNA samples, bonded at 40C overnight (alternatively @room temperature)

== Method ==

<p>•	Load all control lines with dH2O, at ~5 psi, check that all valves work</p>
	 <p> '' Usually “B” valves are starting to load earlier (leave the button unpressurised prior to the pressure increase, it tends to stick to the slide.)</p>
	 <p>  Increase the pressure in both “A” and “B” valves till ~13-15 psi and make sure that you can see that all chambers are separated. If no – increase the pressure''</p>
<p>•	2mg/ml BSA-bio @ 5psi for 20 minutes; chambers (B3): closed</p>
<p>•	'' You can prepare the ITT mix meanwhile and put it at 25C for 3-4 hours (it takes that long to express your TF with a GFP tag)'' </p>
<p>•	PBS for ~2 minutes (or as long as the preparation for next step takes)</p>
<p>•	500ug/ml NA PBS for 20 minutes</p>
<p>•	PBS for ~5 minutes</p>
<p>•	Close button, continue PBS for 1-2minutes making sure button is closed</p>
<p>•	2mg/ml BSA biotin for 20 minutes</p>
<p>•	PBS for 10 minutes</p>
<p>•	Antibody-GFP-biotin in PBS for 4-5 minutes</p>
<p>•	open button, continue antibody for 20 minutes</p>
<p>•	PBS for ~10 minutes</p>
<p>•	flow the expression mix with expressed protein for 10-15 minutes, when  ~2-3 cm of mix left in the inlet tube :</p>
<p>•	Close outlet B4 and open B3 (isolates spotted DNA in a chamber) and load chambers with the same expression mix</p>
<p>             	''To do so you should close the outlet first (“B4”) and continue flow. Stop the flow as soon as all your chambers with DNA will be filled. Do not wait for too long or DNA will diffuse to the neighbor chamber''</p>
<p>•	close chambers</p>
<p>•	close sandwich</p>
<p>•	open chamber</p>
<p>•	incubate TF with target DNA at RT for 30-60 minutes (to reach a thermodynamic equilibrium)</p>
<p>•	scan using Arrayworx</p>
<p> Use 1 sec exposure time</p>
<p>•	close button</p>
<p>•	close chamber</p>
<p>•	open sandwich</p>
<p>•	PBS for 10-15 minutes</p>
<p>•	scan using Arrayworx to detect the interacting sequences</p>

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