Size selective DNA precipitation protocol - source code: Difference between revisions
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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)"); | ||
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)"); | ||
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"); |
Revision as of 22:53, 19 November 2009
#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();
}