OhioMOd2013:Methods/origamifolding

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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

The pre-stock is a pool of oligonucleotides that contain specific components of the origami structure. They are therefore sub-sets to the intended structure. We divide the staples into specific pre-stocks so that in the event we change a specific component to the origami structure, then only that single working stock will need to be changed. Here is an example pipetting guide that is used to prepare the pre-stocks. This guide includes from what plate and range of wells the staples were taken from, the name of the pre-stock, the number of oligos, their associated concentration, and what element of the structure the pre-stock is part of.

index	plate	from well	to well	name	no of oligos	conc.(μM)	element
p01	p085	A1	H12	CoreP085	96	1.04	core 1	p02	p086	A1	D5	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