IGEM:Harvard/2006/Folding DNA nanostructures

Six-helix bundles

• 4.5 μL p7308 scaffold (44 nM)
• 2 μL oligos (990 nM)
• 2 μL 10x folding buffer (500 mM HEPES pH 7.5, 500 mM NaCl, 100 mM MgCl₂)
• 11.5 μL dH₂O

Our structures

• 4.5 μL p7308 scaffold (44 nM)
• 8 μL oligos (250 nM)
• 2 μL 10x folding buffer (500 mM HEPES pH 7.5, 500 mM NaCl, 100 mM MgCl₂)
• 5.5 μL dH₂O

Annealing protocols

Don't use higher than 50 μL volumes in any one tube, because thermal cycling is unreliable otherwise

• 90[[:Category:{{{1}}}|{{{1}}}]] 5' → 65[[:Category:{{{1}}}|{{{1}}}]] 20' → 55[[:Category:{{{1}}}|{{{1}}}]] 20' → 45[[:Category:{{{1}}}|{{{1}}}]] 20' → 37[[:Category:{{{1}}}|{{{1}}}]] 30'

or

• start at 80[[:Category:{{{1}}}|{{{1}}}]], decrement 1[[:Category:{{{1}}}|{{{1}}}]] every 2 min. for 60 cycles.

Gel Analysis

• Run 2% agarose gel, supplemented to 10 mM MgCl₂
• Also supplement 1x TBE to 11 mM MgCl₂
• Run at low voltage (80V) for 1 hour (longer if necessary)

File:SMD-gel060612a.jpg

1% agarose 10 mM MgCl₂

Lane	Contents	Loading Buffer
0	1kb DNA ladder (10 μL)	10x loading dye (1.1 μL)
1	control: +scaffold -oligos (10 μL)	10x loading dye (1.1 μL)
2	control: -scaffold +oligos (10 μL)	10x loading dye (1.1 μL)
3	folded nanotubes (10 μL)	10x loading dye (1.1 μL)