Biomod/2013/OSU/protocol/folding reaction

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Revision as of 23:39, 6 October 2013


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Folding Reaction

A folding reaction is a mixture containing scaffold DNA, staple DNA, water, a buffer mastermix, and magnesium ions. The folding involves subjecting the sample mixture to thermal denaturation followed by renaturing. We will usually have the folding reactions occur in PCR strip tubes of either 50-100 μL aliquots.

Pre-stocks

A folding reaction is a mixture containing scaffold DNA, staple DNA, water, a buffer mastermix, and magnesium ions. The folding involves subjecting the sample mixture to thermal denaturation followed by renaturing. We will usually have the folding reactions occur in PCR strip tubes of either 50-100 μL aliquots.

Index Plate From Well To Well Name No. of Oligos Conc. (um) Element
p01 p085 A1 H12 CoreP085 96 1.04 core 1
p02 p085 A1 H12 CoreP086 41 2.44 core 2
p03 p086 E1 F1 Neighbors 13 7.69 Neighbors
p04 p086 G1 H1 Polymers 13 7.69 Replaced by polymers

Working Stocks

After pipetting the pre-stocks (hint: use multi-channel pipette) we will now take aliquots from each pre-stock to form the working stock. Here is an example sheet used.

Pre-stock Source # [uL] [uL]
CoreP085 96 1 96 1 96
CoreP086 41 1 41 1 41
Neighbors 13 1 13 0 0
Polymers 13 1 13 0 0
ddH20 37 63
Sum Volume 200 200
Concentration 500 nM 500 nM

Prepare Folding Reaction

Now that we have our working stock, we must decide whether to use 10 nM or 20 nM of our scaffold concentration, and whether hte final volume will be 50 μL or 100 μL. By default the FOBXM buffer solution and the MgCl2 magnesium screen will have already been prepared.


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