IGEM:Harvard/2006/vlau/Notebook/2006-7-25

Pre-Working Stocks & Working Stocks

1. Rxn Mixtures

Description	Plate Locations	Total
c4.0.2: core top lid oligos	box 4_A: row F (7-12), row G (1-12), row H (1-12); box 4_B: row A (1-3)	33
c4.0.3: core bottom lid oligos	box 4_B: row A (4-12), row B (1-12), row C (1-12)	33

Working Stocks	Description	Pre-Working Stocks	Water	Total
c4.0Fb.core	latch design 1, inside biotin	1 (66 μL, 2 (33 μL), 3 (33 μL), 4b (4 μL)	64 μL	200 μL
c4.0Fb.latches	latch design 1, inside biotin	8 (4 μL), 11 (2 μL), 12 (2 μL)	-	-
c4.0Gb.core	latch design 1, outside biotin	1 (66 μL, 2 (33 μL), 3 (33 μL), 6b (4 μL)	64 μL	200 μL
c4.0Gb.latches	latch design 1, outside biotin	8 (4 μL), 11 (2 μL), 12 (2 μL)	-	-
c4.0Hb.core	latch design 2, inside biotin	1 (66 μL, 2 (33 μL), 3 (33 μL), 4b (4 μL)	64 μL	200 μL
c4.0Hb.latches	latch design 2, inside biotin	9 (4 μL), 13 (2 μL), 14 (2 μL), 23 (4 μL), 24 (2 μL), 25 (2 μL)	-	-
c4.0Ib.core	latch design 2, outside biotin	1 (66 μL, 2 (33 μL), 3 (33 μL), 6b (4 μL)	64 μL	200 μL
c4.0Ib.latches	latch design 2, oustide biotin	9 (4 μL), 13 (2 μL), 14 (2 μL), 23 (4 μL), 24 (2 μL), 25 (2 μL)	-	-

2. Protocol

   - mixed 10 μL of each 50 μM stock oligo to make pre-working stocks
   - mixed listed pre-working stocks to make working stocks where final concentration of each oligo is 250 nM

Folding Rxns w/ Biotinylated Oligos

1. Reagents (for c4.0Fb, c4.0Gb, c4.0Hb, c4.0Ib)

  - 9 μL p7308 scaffold = (10 nM)/(44 nM) * 40 μL
  - 16 μL oligos = (100 nM)/(250 nM) * 40 μL
  - 4 μL 10x folding buffer (500 mM HEPES pH 7.5, 500 mM NaCl, 100 mM MgCl2)
  - 11 μL dH2O
  - total volume: 40 μL

2. Negative Controls

  - 1st (no oligos): 9 μL scaffold, 16 μL dH2O, 4 μL buffer, 11 μL dH2O
  - 2nd (no scaffold): 9 μL dH2O, 16 μL oligos, 4 μL buffer, 11 μL dH2O