IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-8-31

Streptavidin Depletion Assay

Biotinylated oligos arrived today - yay! Proceeded according to previously written procedure.

Reconstitution

oligo name	nmoles in tube	EB necessary for 200uM (uL)
c5.0.8.1ra	79.7	398.5
c5.0.8.2ra	144.4	722
c5.0.8.5ra	136.9	684.5
c5.0.9.1ra	138.4	692
c5.0.9.2ra	55.8	279
c5.0.9.3ra	124.7	623.5
cc5.0.9.4ra	121.3	606.5
c5.0.9.5ra	162.7	813.5

Stocks Made

• Pre-Working Stock

• • Added these oligos in the following proportions to respective tubes for c5.0.8(b)r and c5.0.9(b)r
    • 2.5uL of each (biotinylated and unbiotinylated) c5.0.8.#r and c5.0.9.#r oligo in respective tubes
    • 7.5uL of dH2O for each (8*7.5 for c5.0.8 = 60uL, 8*7.5 for c5.0.9 = 60uL)

• Working Stocks c5.0.E(b)r"' (outside biotinylation) and c5.0.F(b)r"' (inside biotinylation)

• • Made as given here.

Folding

• Folded, using FOLDINGD protocol, 3 rxns each of A (lidless), E(b), F(b).

Per Reaction:
-----------
9.4uL of p7308 ~42nM
11uL of H2O
4uL of 10x folding buffer, 30mM MgCl2
16uL of working stock

Gel

• 2% agarose, 0.5x TBE, 10mM MgCl2, 5uL EtBr
• Ran at 75V for 1hr30m in 0.5x TBE