Size selective DNA precipitation protocol - source code

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Current revision (02:20, 27 April 2010) (view source)
 
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Fluid dna = new_fluid("DNA sample", "DNA to be separated (e.g. PCR reaction mixture)");
Fluid dna = new_fluid("DNA sample", "DNA to be separated (e.g. PCR reaction mixture)");
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Fluid peg = new_fluid("PEG/MgCl2", "30% (w/v) PEG 8000/30 mM MgCl2 (concentration of PEG 8000  
+
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)");
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                                                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 te = new_fluid("TE buffer", "10 mM TRIS-HCl, 1 mM EDTA, pH 8.0");
Fluid buffer = new_fluid("buffer of choice");
Fluid buffer = new_fluid("buffer of choice");
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next_step();
next_step();
measure_fluid(buffer, eppendorf);
measure_fluid(buffer, eppendorf);
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comment("Add appropriate volume of buffer.");
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to_do("Add appropriate volume of buffer.");
dissolve(eppendorf);
dissolve(eppendorf);

Current revision

#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);
	to_do("Add appropriate volume of buffer.");
	dissolve(eppendorf);

	end_protocol();
}
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