IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-7-24

Precipitation tests

• Made 10 mL solution with Dr. Shih's protocol.
• Tested (which DNA?) with the PEG precipitation protocol.

Streptavidin binding assay

• For the future...
• Double asterisks indicate need for purified nanostructures
• Total volume for each reaction: 13 μL

lane	streptavidin (0.5 μM) (μL)	p7308 scaffold (44 nM) (μL)	oligos (250 nM) (μL)	nanostructures (10 nM) (μL)	water (μL)	10x Tris-gly loading dye (μL)
2	1.0	-	-	-	12.0	2
3	-	11.4	-	-	1.6	2
4	1.0	11.4	-	-	0.6	2
5	-	-	4.0 (a b-working stock)	-	9.0	2
6	1.0	-	4.0 (same b-working stock)	-	8.0	2
7	1.0	-	-	10.0** (3.2.A)	2.0	2
8	1.0	-	-	10.0** (3.2.Eb or 4.0 Ib	2.0	2
9	1.0	-	-	10.0** (3.2.Ib or 4.0.Ib)	2.0	2
10	1.0	-	-	10.0** (3.2.Db or 4.0.Db)	2.0	2
11	1.0	-	-	10.0** (3.2.Hb or 4.0.Hb)	2.0	2
12	1.0	-	-	10.0** (3.2.Lb)	2.0	2

Make c3.2 working stocks

Final concentration of each oligo in working stocks is 250 nM.

working stock	description	pre-working stocks (according to chart)	water	total
c3.2.Db	-latches +aptamers_in	1 (94 μL), 2 (28 μL), 3 (30 μL), 5 (3 μL), 6b (3 μL), 8 (2 μL), 9 (0 μL)	40 μL	200 μL
c3.2.Eb	-latches +aptamers_out	1 (94 μL), 2 (28 μL), 3 (30 μL), 4 (3 μL), 7b (3 μL), 8 (2 μL), 9 (0 μL)	40 μL	200 μL
c3.2.H.core	+latch2 +aptamers_in	1 (94 μL), 2 (28 μL), 3 (30 μL), 5 (3 μL), 6b (3 μL), 10 (2 μL), 12 (2 μL), 13 (0 μL), 15 (2 μL)	36 μL	200 μL
c3.2.H.latches	+latch2 +aptamers_in	16 (4 μL)	-	-
c3.2.I.core	+latch2 +aptamers_out	1 (94 μL), 2 (28 μL), 3 (30 μL), 4 (3 μL), 7b (3 μL), 10 (2 μL), 12 (2 μL), 13 (0 μL), 15 (2 μL)	36 μL	200 μL
c3.2.I.latches	+latch2 +aptamers_out	16 (4 μL)	-	-
c3.2.Lb	-latches +aptamers_all	1 (94 μL), 2 (28 μL), 3 (30 μL), 6b (3 μL), 7b (3 μL), 8 (2 μL), 9 (0 μL)	40 μL	200 μL