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

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Contents

Precipitation tests

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)
21.0---12.02
3-11.4--1.62
41.011.4--0.62
5--4.0 (a b-working stock)-9.02
61.0-4.0 (same b-working stock)-8.02
71.0--10.0** (3.2.A)2.02
81.0--10.0** (3.2.Eb or 4.0 Ib2.02
91.0--10.0** (3.2.Ib or 4.0.Ib)2.02
101.0--10.0** (3.2.Db or 4.0.Db)2.02
111.0--10.0** (3.2.Hb or 4.0.Hb)2.02
121.0--10.0** (3.2.Lb) 2.02

3.2

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 μL200 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 μL200 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 μL200 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 μL200 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 μL200 μL

Folding reaction

Reagents (each expt in respective 0.2 mL PCR tube)

Experiment Scaffold Oligos Folding buffer dH2O total volume
3.2.Db9 μL p730816 μL (250 nM)4 μL 10x11 μL40 μL
3.2.Eb9 μL p730816 μL (250 nM)4 μL 10x11 μL40 μL
3.2.Hb9 μL p730816 μL (250 nM)4 μL 10x11 μL40 μL
3.2.Ib9 μL p730816 μL (250 nM)4 μL 10x11 μL40 μL
3.2.Lb9 μL p730816 μL (250 nM)4 μL 10x11 μL40 μL
-oligos9 μL p7308-4 μL 10x27 μL40 μL

Annealing protocol

  • start at 80[[:Category:{{{1}}}|{{{1}}}]]
  • 60 cycles: wait 2 minutes, decrease 1[[:Category:{{{1}}}|{{{1}}}]]
  • hold at 4[[:Category:{{{1}}}|{{{1}}}]]
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