Size selective DNA precipitation protocol - source code

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Revision as of 05:50, 19 November 2009 by Vaishnavi Ananth (Talk | contribs)
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#include "BioCoder.h"

void main()
{
	start_protocol("Size specific DNA precipitation");

	Fluid dna = new_fluid("DNA sample", "DNA to be separated (e.g. PCR reaction mixture)");
	Fluid peg = new_fluid("PEG/MgCl2", "30% (w/v) PEG 8000/30 mM MgCl2 (concentration of PEG 8000 
                                                 can be varied to shift the size of the percipitated DNA.
                                                 The concentration used here will remove DNA fragments with 
                                                 less than 300bp)");
	Fluid te = new_fluid("TE buffer", "10 mM TRIS-HCl, 1 mM EDTA, pH 8.0");
	Fluid buffer = new_fluid("buffer of choice");

	Container eppendorf = new_container(EPPENDORF);

	//* Mix 50 μL of sample with 150 µL of TE
	first_step();
	measure_fluid(dna, vol(50, UL), eppendorf);
	measure_fluid(te, vol(150, UL), eppendorf);
	tap(eppendorf);

	//* Add 100 µL of PEG/MgCl2
	next_step();
	measure_fluid(peg, vol(10, UL), eppendorf);

	//* Vortex
	next_step();
	vortex(eppendorf);

	//* Centrifuge 15 min at 10.000 rcf at roomtemperature
	next_step();
	centrifuge_pellet(eppendorf, speed(10000, G), RT, time(15, MINS));

	//* Carefully remove supernatant not to disturb the pellet, which will be invisible
	next_step();
	comment("Carefully remove supernatant not to disturb the pellet, which will be invisible.");

	//* Dissolve the pellet in a appropriate amount of buffer of choice 
	next_step();
	measure_fluid(buffer, eppendorf);
	comment("Add appropriate volume of buffer.");
	dissolve(eppendorf);

	end_protocol();
}
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