science.sciencemag.org/content/37
1/6531/
eabd6179
/suppl/DC1
Supplementary
Material
s for
Absolute and arbitrary orientation of single
-molecule shapes
Ashwin
Gopinath*, Chris
Thachuk, Anya
Mitskovets, Harry A.
Atwater
, David
Kirkpatrick
,
Paul W. K. Rothemund
*
*Corresponding author.
Email:
agopi@mit.edu (A.G.); pwkr@dna.caltech.edu (P.W.K.R.
)
Published
19 Febr
uary
2021,
Science
371
, eabd6179
(20
21)
DOI:
10.1126/science.
abd6179
This PDF file includes:
Materials and Methods
Figs. S1 to S17
References
and Notes
Contents
Materials and Methods
..........................................................................................
3
DNA origami designs, preparation and purification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3
Placement chip fabrication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5
Photonic crystal fabrication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5
FDTD simulations of PCCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5
Origami placement experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6
Ethanol drying . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
Troubleshooting placement experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
8
AFM characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
TOTO-3 binding and optical experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
Figs. S
1
through S
17
...........................................................................................
12
2
Materials and Methods
DNA origami designs, preparation and purification
Designs.
Here, all origami were designed with caDNAno (ref. 61,
http://cadnano.org/
) to position all staple ends on the
same face of the origami so that single-stranded 20T extensions to 5’ staple ends would all project from the same face of the
origami. All caDNAno design files and lists of staples are included as a supplementary zip archive:
AA-designs+scripts.zip
.
For right triangle designs, we list two versions of each staple: one is as designed from caDNAno and the other is with 20T
extension on the 5’ end. The three origami used in this work are as follows:
1.
Right-handed right triangle (RRT):
Staples on the right-hand face of this triangle were extended. The caDNAno design
and staple list files are
RRT.json
,
RRT-Staples.xls
and
RRT-T20-Staples.xls
.
2.
Left-handed right triangle (LRT):
This design is similar to that for the right-handed right triangle, except that staple ends
have been shifted by half a DNA turn so that they fall onto the left-hand face of the triangle. The caDNAno design and
staple list files are
LRT.json
,
LRT-Staples.xls
and
LRT-T20-Staples.xls
.
3.
Small moon:
CaDNAno design and staple list files are
small-moon.json
and
small-moon-staples.xslx
; staples
are extended with 20T on their 5’ ends.
Preparation.
Staple strands (Integrated DNA Technologies, 100
μ
M each in water) and the scaffold strand (single-stranded
M13mp18, 400 nM from Bayou Biolabs for right triangles; p8064, 100 nM from Tilibit for small moons) were mixed together to
target concentrations of 100 nM (each staple) and 40 nM, respectively (a 2.5:1 staple:scaffold ratio) in 10 mM Tris Base, 1 mM
EDTA buffer (adjusted to pH 8.35 with HCl) with 12.5 mM magnesium chloride (TE/Mg
2+
). 50
μ
L volumes of staple/scaffold
mixture were heated to 90