Paul W. K. Rothemund- Folding DNA to create nanoscale shapes and patterns: Supplementary Notes 1-11

8/3/2019 Paul W. K. Rothemund- Folding DNA to create nanoscale shapes and patterns: Supplementary Notes 1-11

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The rst pass design can be output either as a line diagram (as in Supplementary Fig. S1 step 3) or as adetailed diagram showing the sequence of the scaffold layed out along the folding path, and the sequence of thestaples where they appear in the nal folded structure (Supplementary Fig. S2). In the detailed design diagramstaple strands are indexed by xy position of the adjacent crossover and the designation a or b depending onwhether the staple falls to the left or right of the crossover, respectively. Here names are of the form sXtYPwhere X is the x position, Y is the y position, and P the position with respect to the adjacent crossover.

4. Renement of the helical domain lengths to minimize strain in the design. In a third sort of diagram(Supplementary Fig. S3), the computer program displays the predicted twist at each base position as a color(assuming the spacing of crossovers represents an exact number of half turns). Red indicates that the base at aparticular position is pointing up, blue that it is pointing down. At crossover points, strand backbone positionsshould fall at the tangent point between helices; thus bases from the helix above a crossover should be blueand those from the helix below a crossover should be red. (More specically, the color of bases at the crossovershould be spaced equally clockwise and counterclockwise of the colors blue and red, that themselves shouldoccur exactly at the tangent point.) All of the crossovers internal to the design are spaced 16 bases apart andrelated by a glide symmetry that should balance strain. This can be observed for the two types of crossovers(+, major-groove up and - major-groove down) that occur internally in a shape, shown in both the boxedregions and at the lower left of Supplementary Fig. S3. (A naive view is that the bases of the crossover willactually be centered around the tangent point between helices. In reality, twist strain might be relieved bydistortion of the crossover but the idea is that if so, such a distortion will be balanced by that of neighboringsymmetrically-placed crossovers.)Ideally, at all other crossovers in the design, the orientation of bases would be similar to that desired for the

balanced internal crossovers. However, because of the non-integral number of bases in a single turn, and themajor-minor groove angle, it is not possible to put all crossovers in this optimal orientation. Crossovers alongthe edges of the shape, in particular, must be adjusted to minimize strain. The program computes a strainenergy along the edges of the design, and so positions of predicted high strain can be identied. (For a givenstrand passing through a crossover, the computed strain energy is just the sum of the squared angular deviationfrom the tangent point for the base before and the base after the crossover.)By hand, helical domain lengths are changed by single bases until the strain energy is minimized. The map of twists aids in this process. For example, high twist strain occurs in a couple scaffold crossovers in the rst passdesign (marked by s labels inside ovals in Supplementary Fig. S3). These crossovers were initially designedto be 5 bases away from the nearest internal crossover (a - crossover). At bottom right, the situation for onesuch crossover may be compared to that which would occur if the distance to the nearest internal crossoverwere changed to 6 bases, as well as the ideal situation for this type of crossover, that of a + type crossover.

The 6-base distance creates the least strain.Once the appropriate adjustments are decided, a matrix of adjustments is input to the design program, withthe original design (Supplementary Fig. S4, design {ADJUSTMENTS}, top). The matrix gives adjustments forthe left and right edges of each helical domain in the design, columns C1 and C2 for domains to the left of theseam and columns C3 and C4 for columns to the right of the seam. The program updates design lengths(Supplementary Fig. S4, bottom) accordingly and a second pass diagram is generated (Supplementary Fig. S5).

5. Breaking and merging of strands. The merging of strands is specied by giving a pairwise list of the namesto be merged (i.e. s-2t9b and s-1t8a ) along with the name of the new strand (i.e. s-1t8e ). The programchecks to see that all strands to be merged have adjacent 3 and 5 bases. The position of strands to be brokenis specied by the name of a strand and the position along its length at which it is to be broken. The patternof merges is not unique. Supplementary Fig. S6, Supplementary Fig. S8, and Supplementary Fig. S10 showthree different diagrams (full sequence, line drawing, and crossover map) of a design that features bridging

staple strands across the seam. Supplementary Fig. S7, Supplementary Fig. S9, and Supplementary Fig. S11show three different diagrams (full sequence, line drawing, and crossover map) of a design that has no bridgingstaples. Diagrams are interleaved to allow comparison of the differences between these two designs. Using aPDF viewer, ip back and forth between two diagrams of the same type to see the effect of different mergepatterns. Particularly interesting are the crossover maps, Supplementary Fig. S10 and Supplementary Fig. S11.The addition of bridging staples creates a characteristic pattern of bars down the center of the design whichis observed in experiments that using bridging staples (and not observed in experiments that dont use bridgingstaples.) Supplementary Fig. S12 highlights the the basic type of grid underlying each merge pattern and theimplications for applying pixels to the pattern.

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The design method given here is a generalization of that developed by Nadrian Seeman for creating rigid moleculesout of parallel helical domains (here helices are technically antiparallel in the standard terminology), which wasrst elaborated for the creation of double-crossover molecules (molecules with two parallel helices, ref. 16) and laterextended to triple crossover molecules (molecules with three parallel helices, 24 ). The main principle used in theseworks is that crossovers may be used to hold helices rigidly in a parallel orientation . More specically,wherever the twist of two parallel helices bring the backbones of the two helices sufficiently close,reciprocal strand exchange can be used to incorporate a crossover. Further, an amazing aspect of theprinciple is that such a crossover does not disturb base pairing in either helix; the crossover appears to contain onlysingle phosphate from each strand. The basic principle can be extended to many general schemes with a variety

of crossover spacings and crossover types (parallel or antiparallel), as was mentioned in ref. 16. Here I explore ascheme that uses a regular grid of antiparallel crossovers (spaced an odd number of half-turns apart) in the bulk of ashape but on the edges and seams of a shape admits the placement of a crossovers with arbitrary offsets (in integralnumbers of turns) from the underlying crossover grid.

The composition of double crossovers into periodic two dimensional crystals 25 showed that, through the use of sticky-end interactions, arbitrary numbers of helices could be held in a parallel arrangement by crossovers. Becausethe natural equilibrium length for a single turn of DNA appears to be close to 10.5 base pairs 26, 27 , and because DNAbackbones are not symmetrically spaced around the helix (there is a major and minor groove), designs of such twodimensional DNA nanostructures (which must use integral numbers of DNA bases) invariably incorporate featuresthat should cause strain. That is, the design assumes a DNA geometry slightly different than that of a single isolatedhelix with 10.5 bases per turn with normal major/minor groove angles. This difficulty appears to have manifesteditself experimentally. A number of 2D DNA nanostructures form tubes rather than sheets 15 , 22 .

The solution to this problem was rst articulated to me by Erik Winfree, and was implicit in the design of DAO-

E double crossover lattices 25 : crossovers (and nicks) in extended structures of parallel helices should beplaced so that they have symmetries which balance strain. This principle is described at length in ref. 15and its supplemental materials; it is also often described as corrugation 22 . The principle has demonstrably inhibitedtube formation in at least one system 22 .

For DNA origami this criterion was used in the placement of crossovers; after merging it does not hold truefor nicks in some designs. The use of 16 bases to represent 1.5 turns of DNA (in the 1.5-turn crossover spacingstructures) or 26 bases to represent 2.5 turns of DNA (in the 2.5-turn crossover spacing structures) means that thehelical domains between crossovers are slightly overtwisted or undertwisted, respectively. To balance this strain,alternating columns of staple crossovers are related by a glide symmetrythe local conguration of crossovers in onecolumn is identical to that of crossovers in the next column over after a translation and a ip (a rotation about oneof the crossovers in-plane axes). Cross-section 1 of Fig. 1d shows the presumed orientation of backbones through onecolumn of crossovers in the lattice, and the top two helices of cross-section 2, the presumed orientation of crossovers inan adjacent column 1.5 turns away (alternatively the diagrams for + and - crossovers in Supplementary Fig. S3).This symmetry should tend to balance strain in the origami and cause them to be, on average, at. (So far, noexperimental evidence has demonstrated that the origami are at, however).

The use of a glide symmetry means that large regions of a DNA origami should have balanced strain. However, atseams and edges this is not necessarily true, even where a seam or edge lines up with the underlying crossover lattice.At seams or edges, because DNA has a major and minor groove, a crossover involving staple strands is in tensionwith an adjacent crossover involving the scaffold strand. Such a conguration of crossovers in tension has neverbefore been used in DNA nanostructures. For example, in Fig. 1d the cross-section through a seam (cross-section 2)has been drawn so that the staple crossover is relaxed (top two helices of three) and the scaffold crossover (bottomtwo helices of three) is highly strained. Perhaps both crossovers assume some intermediate conformation.

How the strain is actually relieved is unknown, the nal base pairs of each helix may be distorted. Strain atseams or edges does not appear to cause any gross defects in the origami; bases at the end of the helices are highlyavailable for stacking against other DNA origami which suggests that the last base pair does form and assumes aplanar conguration. If, in the future, strain associated defects should be detected at edges, then one or two scaffoldbases could be left unpaired and allowed to form a hairpin that should relax the crossover.

Another place that the design of scaffolded DNA origami currently breaks with normal DNA nanotechnology isin its use of a wide range of sequences for its antiparallel crossovers. Customarily, crossover sequences are drawnfrom one of a few sequences that both form an immobile branched junction 28 and have well-characterized geometry.Such junctions have been designed with minimal symmetry so that the junction cannot branch migrate back andforth. Because the crossover sequences in the DNA origami demonstrated here are determined by the M13mp18 DNAsequence, and hundreds of them are used, a few probably have symmetries that would allow them to branch migrate afew bases; the crossover sequences have not been inspected for such properties. Further, different crossover sequencesshow a varying tendency to assume one of two different stacked-X conformers 29, 30 , one of which is incompatible with

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the DNA origamis intended structure at every crossover.It is hoped that the juxtaposition of multiple crossovers in DNA origami inhibits both branch migrations and

conformer isomerizations; isomerization or migration to an undesired form at one junction would tend to increasestrain between adjacent junctions. A study of a pair of symmetric antiparallel junctions juxtaposed with an asym-metric antiparallel junction has shown that the asymmetric junction can prevent the adjacent symmetric junctionsfrom branch migrating 31 . But the same study showed that two symmetric antiparallel junctions juxtaposed nextto eachother can branch migrate. Thus it seems possible that several symmetric junctions near eachother mightconspire and migrate. Indeed it seems likely that some local rearrangements of junctions in origami happen; sincethey are likely to be smaller than a few nanometers, they cannot be observed by AFM. Eventually higher resolution

structural information on DNA origami will determine if such isomerizations occur. Importantly, I note that there isno reason why better characterized, well-behaved junction sequences should not be incorporated into DNA origamidesigns if it helps to create more precise structure. The incorporation of specic crossover sequences will require theuse of a synthetic scaffold rather than a natural one, a practical incovenience for very long scaffolds.

A note on seams: while most seams presented here are vertically aligned (for simplicity and convenience in design),and this necessitates the use of bridges to strengthen seams, it is in possible to create staggered seams (as E. Winfreehas suggested) so that staple strands naturally cross and bridge the seam vertically (between two adjacent helices)and no creation of horizontal bridges would be required. In these cases the addition of horizontal bridges acrosssome parts of the seam might still add addtional strength. A small instance of staggered seams occurs in the smileyface design. Above the right hand eye a small 2-helix seam appears that, because it is not aligned with other seamswould not necessarily need bridges. An experiment in which the staples at this position were rearranged to removehorizontal bridging gave smileys of (not surprisingly) similar quality.

A note on folding paths and arbitrary shapes: there may be additional constraints on DNA origami that limit

the family of shapes that can be approximated a little. In particular, shapes with lots of long thin projections orthin waists connecting two different parts of the shape may not form very well. As presented here, the minimumallowable width of a vertically oriented structure (such as a tall thin rectangle), if the scaffold rasters progesses in onedirection vertically, is 1.5 turns, or about 5.4 nm wide. I have not tested the formation of such a narrow structure.The narrowest equivalent structure occurs at the jaw hinge of the smiley, 4.5 turns wide, about 16 nm wide. Whilemost smileys are well formed, a signicant number have dislocations along these 4.5 turn waists and it appears to bea weak spot.

In some shapes it is desired that a strand pass both back and forth through a narrow waist so that it may accessdifferent portions of the shape. For example, consider a vertically oriented hourglass shape. If it is desired thata circular scaffold be used, then the scaffold must pass both up and down the narrow waist of the hourglass. Aspresented here, the minimal allowable width of the waist, which would accomodate the scaffold going up and down,would be 3 turns or about 11 nm. This width is the width of the top 4 helices of the star and because they do notimage well, it seems that such a narrow waist may be oppy (in isolation). Clearly the analogous waist down thecenter of the smiley, which is 6 turns or 22 nm wide forms well and is mechanically stable in the context of the largerstructure. Note that it is asymmetric an is composed of 1.5 turn and 4.5 turn wide vertical rasters.

Similarly, consider a horizontally oriented hourglass. For a circular scaffold to pass both left and right through thewaist of the hourglass would require two helices, and so in principle the waist could be about 5 nm wide. However,I am unsure how well such a skinny waist would form. Again the smiley gives the best example of the smallest suchwaist so far. Below each eye is a four helix waist, about 11 nm wide which forms well and is stable.

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0

1. Block diagram 2. Folding path 3. First pass design

+1

-1

0

0

+1

-1

0

Program outputs first pass design:

% C0 C1 C2 C3 C4design_turns = [

[3 1.5 0 0 1.5]; %H1[3 1.5 0 0 1.5]; %H2

[5 2.5 0 0 2.5]; %H3[5 2.5 0 0 2.5]; %H4[7 3.5 0 0 3.5]; %H5[7 3.5 0 0 3.5]; %H6[9 4.5 0 0 4.5]; %H7[9 4.5 0 0 4.5]; %H8[9 4.5 0 0 4.5]; %H9[9 4.5 0 0 4.5]; %H10[9 4.5 0 0 4.5]; %H11[9 4.5 0 0 4.5]; %H12

];

design_lengths =C0 C1 C2 C3 C4

32 16 0 0 16 %H132 16 0 0 16 %H254 27 0 0 27 %H354 27 0 0 27 %H474 37 0 0 37 %H574 37 0 0 37 %H696 48 0 0 48 %H796 48 0 0 48 %H896 48 0 0 48 %H996 48 0 0 48 %H1096 48 0 0 48 %H1196 48 0 0 48 %H12

=

10.6 bases, 3.63 nm32 bases 3 turns~~

Block includesinter-helix gap.

Supplementary Figure S1: First three steps of origami design.

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3 2 1 0 1 2 3

s-3t0b s-1t0a s-1t0b s1t0a s1t0b s3t0a

< < < --- GGAGAGGG< < GTAATTAC--- < < --- --- --- ---CCTCTCCC---CGCGCGTT-------GGCCGATT---CATTAATG--- --- --- --- >

/ < < < GCGCGCAA------- CCGGCTAA< < < \

| s-2t1a ) ( s-2t1b s0t1a s0t1b s2t1a ) ( s2t1b |

\ > > > GTATTGGG------- CCTGTCGT> > > /

< --- --- --- ---GCCAAACG---CATAACCC< > CGGTTTGC> \ / > GCCAGCTG > >

( s-3t2b s-1t2a ) ( s-1t2b | | s1t2a ) ( s1t2b s3t2a )

< < CACTTTTC TTTTTGGT< / \ < GACCTTTC GCCCGTCA< <

> --- --- CTG---GTGAAAAG---AAAAACCA---CCCTGGCG> >TTTCCCGA---CTGGAAAG---CGGGCAGT---GAG --- --- >

/ < GAC< < GGGACCGC------- AAAGGGCT< < CTC < \

| s-2t3a ) ( s-2t3B s0t3a s0t3b s2t3A ) ( s2t3b |

\ > TGA> > TTGCCCTT------- GAGCTAAC> > GCG > /

< --- --- ACT---CTGCCCGT---TGTCGACT---AACGGGAA< > GACGGGCA ACAGCTGA> \ / > TCACATTA ATTGCGTT> >


< < GTTGAGAG AGTCCCGG< / \ < CCGTGGGG TCCGAAAT< <

> --- GGACC---GCTTGCTG---CAACTCTC---TCAGGGCC---AGGCGGTG> >ACTCATTA---GGCACCCC---AGGCTTTA---CACTTTAT---GCTTC --- >

/ < CCTGG CGAACGAC< < TCCGCCAC------- TGAGTAAT< < GTGAAATA CGAAG < \


\ > ACGCT GGTTTGCC> > CTGTTTGA------- TGTTATCC> > AACATACG AGCCG > /

< --- TGCGA---CCAAACGG---GGTCGTCC---GCTTTTAG---GACAAACT< > CCAGCAGG CGAAAATC> \ / > GCTCACAA TTCCACAC> >


CCGATAAG< < TAAAACGG CTAAAGCC< / \ < GTCCTTTG TCGATACT< < CTCGAGCC

>GGCTATTC---TTTTGATT---TATAAGGG---ATTTTGCC---GATTTCGG---AACCACCA> >ATTTCACA---CAGGAAAC---AGCTATGA---CCATGATT---ACGAATTC---GAGCTCGG>

/ < AAAACTAA ATATTCCC < < TTGGTGGT------- TAAAGTGT< < GGTACTAA TGCTTAAG< \


\ > GGTTGAGT GTTGTTCC> > CCACTATT------- GTGCCAAG> > TCGACTCT AGAGGATC> /

AGTTTGGA ACAAGAGT> \ / > CTTGCATG CCTGCAGG> > CCCGGGTA


GGGACTAT< < AACTGCAA CCTCAGGT< / \ < CAAAATGT TGCAGCAC< < GCAATGGG >CCCTGATA---GACGGTTT---TTCGCCCT---TTGACGTT---GGAGTCCA---CGTTCTTT> >TGGCCGTC---GTTTTACA---ACGTCGTG---ACTGGGAA---AACCCTGG---CGTTACCC>

/ < CTGCCAAA AAGCGGGA< < GCAAGAAA------- ACCGGCAG< < TGACCCTT TTGGGACC< \


\ > CACTACGT GAACCATC> > TTGGGGTC------- TATTACGC> > GATGTGCT GCAAGGCG> /

ACCCAAAT CAAGTTTT> \ / > CAGCTGGC GAAAGGGG> > ATTAAGTT


TTAGCCCC< < GCTAAATC ACGAAATG< / \ < CGGGCGTG GCTAGCGG< < GTCGGACT

>AATCGGGG---GCTCCCTT---TAGGGTTC---CGATTTAG---TGCTTTAC---GGCACCTC> >GCGAAGAG---GCCCGCAC---CGATCGCC---CTTCCCAA---CAGTTGCG---CAGCCTGA>

/ < CGAGGGAA ATCCCAAG< < CCGTGGAG------- CGCTTCTC< < GAAGGGTT GTCAACGC< \


\ > GACGGGGA AAGCCGGC> > GAAGGGAA------- CCGGCACC> > ACCAGGCA AAGCGCCA> /

> GAACGTGG--- CGAGAAAG> > GCTTCTGG--- TGCCGGAA> > TTCGCCAT

/ < < < ------- < < < \


\ > > > ------- > > > /

< --- --- --- --- --- < < --- --- --- --- --- > > \ / > > >


< <

< / \ <

< <

> --- --- --- --- --- > > --- --- --- --- --- >

/ < < < ------- < < < \


\ > > > ------- > > > /

< --- --- --- --- --- < < --- --- --- --- --- > > \ / > > >


< < < / \ < < <

> --- --- --- --- --- > > --- --- --- --- --- >

/ < < < ------- < < < \


\ > > > ------- > > > /

< --- --- --- --- --- < < --- --- --- --- --- > > \ / > > >


< < < / \ < < --- --- --- --- --- > > --- --- --- --- --- >/ < < < ------- < < < \


\ > > > ------- > > > /

< --- --- --- --- --- < < --- --- --- --- --- > > \ / > > >


< < < / \ < < --- --- --- --- --- > > --- --- --- --- --- >

/ < < < ------- < < < \


\ > > > ------- > > > /

< --- --- --- --- --- < < --- --- --- --- --- > > \ / > > >


< < < / \ < < --- --- --- --- --- > > --- --- --- --- --- >

/ < < < ------- < < < \


\ > > > ------- > > > /

< --- --- --- --- --- < < --- --- --- --- --- > > --- > > --- > >

/ < < < GCGCAACC------- GGCTAAGT< < < \


\ > > > GCGTATTG------- AACCTGTC> > > /

< --- --- --- ---CCGCCAAA---CGCATAAC< > GGCGGTTT> \ / > GTGCCAGC > >


< < CTTTTCTT TTTGGTGG< / \ < CCTTTCGC CCGTCACT< <

> --- --- GGT---GAAAAGAA---AAACCACC---CTGGCGCC> >TCCCGACT---GGAAAGCG---GGCAGTGA---GCG --- --- >

/ < CCA< < GACCGCGG------- AGGGCTGA< < CGC < \


\ > AGT> > GATTGCCC------- GTGAGCTA> > TTG > /

< --- --- TCA---CTCTGCCC---GTTGTCGA---CTAACGGG< > GAGACGGG CAACAGCT> \ / > ACTCACAT TAATTGCG> >


< < TGAGAGAG TCCCGGTC< / \ < GTGGGGTC CGAAATGT< <

> --- GACCGC---TTGCTGCA---ACTCTCTC---AGGGCCAG---GCGGTGAA> >TCATTAGG---CACCCCAG---GCTTTACA---CTTTATGC---TTCCGG --- >

/ < CTGGCG AACGACGT< < CGCCACTT------- AGTAATCC< < GAAATACG AAGGCC < \


\ > CACGCT GGTTTGCC> > CTGTTTGA------- AAATTGTT> > ACACAACA TACGAG > /

< --- GTGCGA---CCAAACGG---GGTCGTCC---GCTTTTAG---GACAAACT< > CCAGCAGG CGAAAATC> \ / > ATCCGCTC ACAATTCC> >


CCGATAAG< < TAAAACGG CTAAAGCC< / \ < TTTGTCGA TACTGGTA< < AGCCATGG

>GGCTATTC---TTTTGATT---TATAAGGG---ATTTTGCC---GATTTCGG---AACCACCA> >CACACAGG---AAACAGCT---ATGACCAT---GATTACGA---ATTCGAGC---TCGGTACC>

/ < AAAACTAA ATATTCCC < < TTGGTGGT------- GTGTGTCC< < CTAATGCT TAAGCTCG< \


\ > GGTTGAGT GTTGTTCC> > CCACTATT------- GCCAGTGC> > CAGGTCGA CTCTAGAG> /

AGTTTGGA ACAAGAGT> \ / > CAAGCTTG CATGCCTG> > GATCCCCG


GGGACTAT< < AACTGCAA CCTCAGGT< / \ < ATGTTGCA GCACTGAC< < TGGGTTGA >CCCTGATA---GACGGTTT---TTCGCCCT---TTGACGTT---GGAGTCCA---CGTTCTTT> >CGTCGTTT---TACAACGT---CGTGACTG---GGAAAACC---CTGGCGTT---ACCCAACT>

/ < CTGCCAAA AAGCGGGA< < GCAAGAAA------- GCAGCAAA< < CCTTTTGG GACCGCAA< \


\ > CACTACGT GAACCATC> > TTGGGGTC------- TCGCTATT> > GGGGGATG TGCTGCAA> /

ACCCAAAT CAAGTTTT> \ / > ACGCCAGC TGGCGAAA> > GGCGATTA


TTAGCCCC< < GCTAAATC ACGAAATG< / \ < CGTGGCTA GCGGGAAG< < GACTTACC

>AATCGGGG---GCTCCCTT---TAGGGTTC---CGATTTAG---TGCTTTAC---GGCACCTC> >AGAGGCCC---GCACCGAT---CGCCCTTC---CCAACAGT---TGCGCAGC---CTGAATGG>

/ < CGAGGGAA ATCCCAAG< < CCGTGGAG------- TCTCCGGG< < GGTTGTCA ACGCGTCG< \


\ > GACGGGGA AAGCCGGC> > GAAGGGAA------- CTTTCCGG> > GGAAACCA GGCAAAGC> /

> GAACGTGG--- CGAGAAAG> > CACCGCTT--- CTGGTGCC> > GCCATTCG


| s-2t1a ) ( s-2t1b s2t1a ) ( s2t1b |



( s-3t2b s-1t2e ) ( s-1t2i | | s1t2i ) ( s3t2a )




| s-2t3a ) ( s-2t3g s2t3c ) ( s2t3b |



( s-3t4b ) ( s-1t4i | | s1t4i ) ( s1t4f s3t4a )




| s-2t5a ) ( ) ( s2t5b |



( s-1t6e ) ( s-1t6i | | s1t6i ) ( s1t6f s3t6e )




| ) ( ) ( |



( s-3t8g s-1t8e ) ( s-1t8i | | s1t8i ) ( s1t8f s3t8e )



| ) ( ) ( |



( s-3t10f s-1t10e ) ( s-1t10i | | s1t10i ) ( s1t10f s3t10g )




| ) ( ) ( |


> GAACGTGG--- CGAGAAAG> > CACCGCTT--- CTGGTGCC> > GCCATTCG


| s-2t1a ) ( s-2t1b s0t1f s2t1a ) ( s2t1b |



( s-3t2b s-1t2e ) ( | | s1t2e ) ( s3t2a )




| s-2t3a ) ( s-2t3g s0t3f s2t3c ) ( s2t3b |



( s-3t4b ) ( | | s1t4e ) ( s3t4a )




| s-2t5a ) ( s0t5f s2t5g ) ( s2t5b |



( s-1t6e ) ( | | s1t6e ) ( s3t6e )




| s-2t7f ) ( s0t7f s2t7f ) ( |



( s-1t8e ) ( | | s1t8e ) ( s3t8e )



| s-2t9f ) ( s0t9f s2t9f ) ( |



( s-1t10f ) ( | | s1t10g ) ( s3t10g )




| ) ( ) ( |


> GAACGTGG--- CGAGAAAG> > CACCGCTT--- CTGGTGCC> > GCCATTCG 276 bases8 helices tall

a b

Supplementary Figure S14: Schematics for 1/ 3 of the square (8 helices) in Fig. 2a used in the rst origami experiments(Supplemental Note S5.3). a Block diagram. Designed for 2.5-turn spacing blocks have 5 different offsets with respect to theunderlying lattice of crossovers, hence the 5 different hues of blocks in different columns. As in other block diagrams, orangeblock/red block boundaries have an offset of 0 turns with respect to the underlying lattice of crossovers. b Folding path. Acircular scaffold is used.

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26.5 turns wide at 10.4 bases/turn -> 276 bases26 helices tall

a b

Supplementary Figure S16: Schematics for the square in Fig. 2a. a Block diagram. Designed for 2.5-turn spacing, blockshave 5 different offsets with respect to the underlying lattice of crossovers, hence the ve different hues of blocks in differentcolumns. As in other block diagrams, orange block/red block boundaries have an offset of 0 turns with respect to the underlyinglattice of crossovers. The red square highlights our prediction for how well the design is expected to approximate a square. bFolding path.

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Supplementary Figure S17: Crossover induced structure of square.

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1y_1C; GAGCCCCCGATTTAGAGCTTGACGGGx3y_1C; CAAGTTTTTTGGGGTCGAGGTGCCGTx5y_1C; CGAAAAACCGTCTATCAGGGCGATGGx7y_1C; AGTTTGGAACAAGAGTCCACTATTAAx9y_1C; AATCGGCAAAATCCCTTATAAATCAAAAGAATAG

x0y0A; CTGGGGTGCCTAATGAGTGAGCGTGGCGAGAAAGGAAGGGAAx0y0B; GAAAGCCGGCGAACTAACTCACATTAx2y0A; CCAGTCGGGAAACGGAACCCTAAAGGx2y0B; AAAGCACTAAATCCTGTCGTGCCAGCx4y0A; GGGAGAGGCGGTTCCATCACCCAAATx4y0B; CCCACTACGTGAATGCGTATTGGGCGx6y0A; GAGACGGGCAACACAACGTCAAAGGGx6y0B; AGAACGTGGACTCGCTGATTGCCCTTx8y0A; GCAAGCGGTCCACTGAGTGTTGTTCCx8y0B; CCCGAGATAGGGTGCTGGTTTGCCCC

x1y1A; ATTGCGTTGCGCTCTCACAATTCCACx1y1B; AAATTGTTATCCGCACTGCCCGCTTTx3y1A; TGCATTAATGAATCTCGAATTCGTAAx3y1B; CCCGGGTACCGAGCGGCCAACGCGCGx5y1A; CCAGGGTGGTTTTTGCCAAGCTTGCAx5y1B; AAACGACGGCCAGTCTTTTCACCAGTx7y1A; CACCGCCTGGCCCGTTGGGTAACGCCx7y1B; GCAAGGCGATTAATGAGAGAGTTGCAx9y1A; AGCAGGCGAAAATTCTTCGCTATTACx9y1B; GAAGGGCGATCGGTGCGGGCCCCTGTTTGATGGTGGTTCCGA

x0y2A; CGCGTCTGGCCTTCCTGTAGCCGGAAGCATAAAGTGTAAAGCx0y2B; ACAACATACGAGCCAGCTTTCATCAAx2y2A; GTCGGATTCTCCGTGTTTCCTGTGTGx2y2B; TCATGGTCATAGCTGGGAACAAACGGx4y2A; CGTTGGTGTAGATACTCTAGAGGATCx4y2B; TGCCTGCAGGTCGGGGCGCATCGTAAx6y2A; GACGACAGTATCGTCACGACGTTGTAx6y2B; AGGGTTTTCCCAGGCCTCAGGAAGATx8y2A; GCTTCTGGTGCCGAGGGGGATGTGCTx8y2B; GCCAGCTGGCGAAGAAACCAGGCAAA

x1y3A; CATTAAATGTGAGTAAATCAGCTCATx1y3B; ATTAAATTTTTGTCGAGTAACAACCCx3y3A; CGGATTGACCGTATATTTAAATTGTA

x3y3B; TTGTATAAGCAAAATGGGATAGGTCAx5y3A; CCGTGCATCTGCCCCCCGGTTGATAAx5y3B; TCAATCATATGTAAGTTTGAGGGGACx7y3A; CGCACTCCAGCCAACAAGAGAATCGAx7y3B; GAGTCTGGAGCAAGCTTTCCGGCACCx9y3A; GCGCCATTCGCCATTTTGAGAGATCTx9y3B; AATGCCGGAGAGGGTAGCTATTTCAGGCTGCGCAACTGTTGG

x0y4A; CAATAAATCATACAGGCAAGGGGAACGCCATCAAAAATAATTx0y4B; TTTTTAACCAATACAAAGAATTAGCAx2y4A; TAAAGCTAAATCGTGTTAAAATTCGCx2y4B; AACGTTAATATTTGTTGTACCAAAAAx4y4A; GGAGAAGCCTTTAAAAAACAGGAAGAx4y4B; TCAGAAAAGCCCCTTTCAACGCAAGGx6y4A; TTTTAAATGCAATTAAAACTAGCATGx6y4B; TGAACGGTAATCGGCCTGAGTAATGTx8y4A; AAGGCCGGAGACAGGTCATTGCCTGAx8y4B; ACAAAGGCTATCAGTCAAATCACCAT

x1y5A; AAATTAAGCAATAGCTGAAAAGGTGGx1y5B; ATTTGGGGCGCGAAAGCCTCAGAGCAx3y5A; CATTATGACCCTGATTTCGCAAATGGx3y5B; GACCATTAGATACTAATACTTTTGCGx5y5A; ATAAAAATTTTTACAGTTGATTCCCAx5y5B; TCATTCCATATAAGAACCCTCATATAx7y5A; GTAGGTAAAGATTTGTTTTAAATATGx7y5B; CTGTAGCTCAACACAAAAGGGTGAGAx9y5A; CAATATGATATTCTTTTGCGGATGGCx9y5B; CTCCTTTTGATAAGAGGTCATAACCGTTCTAGCTGATAAATT

x0y6A; ATGTTTAGACTGGATAGCGTCAATAGTAGTAGCATTAACATCx0y6B; CATCAATTCTACTCAATACTGCGGAAx2y6A; CTCAAATGCTTTATAGCTATATTTTCx2y6B; TCAATAACCTGTTAACAGTTCAGAAAx4y6A; AGGTCTTTACCCTGTAGATTTAGTTTx4y6B; ATTCTGCGAACGAGACTATTATAGTCx6y6A; GATTAAGAGGAAGGTGTCTGGAAGTTx6y6B; CAACTAAAGTACGCCCGAAAGACTTCx8y6A; AAAGCGAACCAGAGCTGAATATAATGx8y6B; TTAGAGCTTAATTCCGGAAGCAAACT

x1y7A; TCGTCATAAATATCGAGAGGCTTTTGx1y7B; AAAACCAAAATAGTCATTGAATCCCCx3y7A; ACGAGAATGACCAAGCAACACTATCAx3y7B; GAGGCATAGTAAGTAAATCAAAAATCx5y7A; AGAAGCAAAGCGGATTCAACTAATGCx5y7B; TTAGGAATACCACATTGCATCAAAAAx7y7A; AAATATCGCGTTTACAACATTATTACx7y7B; ACGAACTAACGGATAATTCGAGCTTCx9y7A; CCAACAGGTCAGGCCAGTCAGGACGTx9y7B; TTTAAGAACTGGCTCATTATAATTAGAGAGTACCTTTAATTG

x0y8A; CCGGAACGAGGCGCAGACGGTGCCAGAGGGGGTAATAGTAAAx0y8B; CAAAAGAAGTTTTCAATCATAAGGGAx2y8A; ACAGATGAACGGTCCAGACGACGATAx2y8B; TAACCCTCGTTTAGTACAGACCAGGCx4y8A; AGTAATCTTGACACAAAAGGAATTACx4y8B; AGATACATAACGCAGAACCGGATATTx6y8A; TGCTCATTCAGTGCATCAGTTGAGATx6y8B; AGGTAGAAAGATTAATAAGGCTTGCCx8y8A; TAAATTGGGCTTGCTACGTTAATAAAx8y8B; TGGGAAGAAAAATAGATGGTTTAATT

x1y9A; ACCGAACTGACCAGCCTGATAAATTGx1y9B; GATTTGTATCATCACTTTGAAAGAGGx3y9A; GCATAGGCTGGCTCCCAGCGATTATAx3y9B; CTCATCTTTGACCGACCTTCATCAAGx5y9A; CATTACCCAAATCCAACCTAAAACGA

x5y9B; ACTACGAAGGCACAACGTAACAAAGCx7y9A; CTGACGAGAAACATGAGGAAGTTTCCx7y9B; AAAGACTTTTTCACCAGAACGAGTAGx9y9A; TCAACTTTAATCAGGAACGAGGGTAGx9y9B; TCAGCAGCGAAAGACAGCATCTTGTGAATTACCTTATGCGAT

x0y10A; AACTTTCAACAGTTTCAGCGGGACCTGCTCCATGTTACTTAGx0y10B; TGTCGAAATCCGCAGTGAGAATAGAAx2y10A; ATAATTTTTTCACAAAGTACAACGGAx2y10B; CCAAGCGCGAAACGTTGAAAATCTCCx4y10A; TAATTGTATCGGTATACACTAAAACAx4y10B; AAGAGGCAAAAGATTATCAGCTTGCTx6y10A; GATACCGATAGTTAATACGTAATGCCx6y10B; ATTAAACGGGTAAGCGCCGACAATGAx8y10A; ATATATTCGGTCGGGCTTTGAGGACTx8y10B; CAACGGCTACAGACTGAGGCTTGCAG

x1y11A; AGGAACAACTAAATTTCCAGACGTTAx1y11B; AAGTTTTGTCGTCGGAATTGCGAATAx3y11A; AAAAAAAAGGCTCCATTCCACAGACAx3y11B; ACAACGCCTGTAGCAAAAGGAGCCTTx5y11A; TTCGAGGTGAATTCATGTACCGTAACx5y11B; CCCAATAGGAACCTCTTAAACAGCTTx7y11A; CAACAACCATCGCACCCTCAGAGCCAx7y11B; CCTCAGAACCGCCCCACGCATAACCGx9y11A; GGAGTTAAAGGCCACTCAGGAGGTTT

x9y11B; CCGGAATAGGTGTATCACCGTGCTTTTGCGGGATCGTCACCC

x0y12A; GGAAAGCGCAGTCTCTGAATTCTGTATGGGATTTTGCTAAACx0y12B; GTAAATGAATTTTTACCGTTCCAGTAx2y12A; CAGGAGTGTACTGGCGTAACGATCTAx2y12B; GCCCTCATAGTTAGTAATAAGTTTTAx4y12A; GCCCGTATAAACAACCAGTACAAACTx4y12B; ACTGAGTTTCGTCGTTAATGCCCCCTx6y12A; AACATGAAAGTATCAGGGATAGCAAGx6y12B; CCACCCTCATTTTTAAGAGGCTGAGAx8y12A; CGGGGTTTTGCTCTCAGAACCGCCACx8y12B; AGTACCGCCACCCAGTACCAGGCGGA

x1y13A; AGCGTCATACATGTTGGCCTTGATATx1y13B; GCAGGTCAGACGAGCTTTTGATGATAx3y13A; ACGGGGTCAGTGCCACCACCAGAGCCx3y13B; CCGCCACCAGAACCTTGAGTAACAGTx5y13A; GCCTATTTCGGAACCCTCAGAACCGCx5y13B; CTCAGAGCCGCCACCTATTATTCTGAx7y13A; CTCCTCAAGAGAAAAAATCACCGGAAx7y13B; TCTTTTCATAATCGGATTAGGATTAGx9y13A; TAAGTGCCGTCGACGGCATTTTCGGTx9y13B; CAGACTGTAGCGCGTTTTCATGAGGGTTGATATAAGTATAGC

x0y14A; TTATTTTGTCACAATCAATAGAATCCTCATTAAAGCCAGAATx0y14B; TCACAAACAAATAAAAATTCATATGGx2y14A; GACATTCAACCGAACAGGAGGTTGAGx2y14B; GCCGCCAGCATTGTTGAGGGAGGGAAx4y14A; TAAAGGTGAATTAACCACCCTCAGAGx4y14B; CACCCTCAGAGCCTCACCGTCACCGAx6y14A; GCAAAATCACCAGCGGAACCGCCTCCx6y14B; CCAGAGCCACCACTAGCACCATTACCx8y14A; TGAAACCATCGATTTAGCGTTTGCCAx8y14B; CATAGCCCCCTTAAGCAGCACCGTAA

x1y15A; TTTACCAGCGCCAAAAGGTGGCAACAx1y15B; AAAATACATACATAAGACAAAAGGGCx3y15A; GGTAAATATTGACATTAAGACTCCTTx3y15B; AAGAACTGGCATGGGAAATTATTCATx5y15A; CTTGAGCCATTTGAAGGAAACCGAGGx5y15B; ACAAAGTTACCAGGGAATTAGAGCCAx7y15A; ATTAGCAAGGCCGTACCGAAGCCCTTx7y15B; GCAATAGCTATCTGAAACGTCACCAAx9y15A; TCAGTAGCGACAGGAGTTAAGCCCAAx9y15B; GAGAGATAACCCACAAGAATTAATCAAGTTTGCCTTTAGCGT

x0y16A; AATCAAGATTAGTTGCTATTTCAAAGACACCACGGAATAAGTx0y16B; TATAAAAGAAACGTGCACCCAGCTACx2y16A; TAACGAGCGTCTTTTAGCAAACGTAGx2y16B; ATTACGCAGTATGTCCAGAGCCTAATx4y16A; ATTATTTATCCCAACGGAATACCCAAx4y16B; AAACGCAATAATAATCCAAATAAGAAx6y16A; GAAAATAGCAGCCAGCAGATAGCCGAx6y16B; TTTAAGAAAAGTATTTACAGAGAGAAx8y16A; GACGGGAGAATTAAAACAATGAAATAx8y16B; TAATAAGAGCAAGACTGAACACCCTG

x1y17A; AATTTTATCCTGAAGGCGTTTTAGCGx1y17B; TTCTAAGAACGCGATCTTACCAACGCx3y17A; TTGCCAGTTACAACAATAGCAAGCAAx3y17B; TCATTACCGCGCCAATAAACAGCCATx5y17A; ACGATTTTTTGTTTCGAGAACAAGCA

x5y17B; AGTACCGCACTCATAACGTCAAAAATx7y17A; TAACATAAAAACACTGTCTTTCCTTAx7y17B; AATCAATAATCGGGGGAAGCGCATTAx9y17A; AACAAAGTCAGAGAAATAATATCCCAx9y17B; TAGATAAGTCCTGAACAAGAAGGTAATTGAGCGCTAATATCA

x0y18A; AATAAGAATAAACACCGGAATGCGGGAGGTTTTGAAGCCTTAx0y18B; AACCTCCCGACTTCATAATTACTAGAx2y18A; TATACAAATTCTTGGCTTATCCGGTAx2y18B; ATCAGATATAGAAACCAGTATAAAGCx4y18A; AGAATCGCCATATTTCATCGTAGGAAx4y18B; AGCCGTTTTTATTTTAACAACGCCAAx6y18A; GAGCCAGTAATAAGGGTATTAAACCAx6y18B; TCATTCCAAGAACGAGAATATAAAGTx8y18A; CCAGACGACGACAGCATGTAGAAACCx8y18B; TCCTAATTTACGAATAAACAACATGT

x1y19A; AAAAGCCTGTTTATAAATTTAATGGTx1y19B; TCATCTTCTGACCGTATCATATGCGTx3y19A; CAACGCTCAACAGGAACGCGAGAAAAx3y19B; ATCGCAAGACAAATAGGGCTTAATTGx5y19A; CATGTAATTTAGGTGGGTTATATAACx5y19B; CTCCGGCTTAGGTCAGAGGCATTTTCx7y19A; ACCGACAAAAGGTTTTATCAAAATCAx7y19B; AGTCAATAGTGAAAAAGTAATTCTGTx9y19A; TCAGCTAATGCAGTGAAAACATAGCG

x9y19B; TTAATTTTCCCTTAGAATCCTAACGCGCCTGTTTATCAACAA

x0y20A; TTTAACGTCAGATGAATATACCGTGTGATAAATAAGGCGTTAx0y20B; TTGAAATACCGACAGTAACAGTACCTx2y20A; TTCGCCTGATTGCATTTTAGTTAATTx2y20B; CTTTTTCAAATATTTTGAATACCAAGx4y20A; TTCATTTCAATTATGATGCAAATCCAx4y20B; TATATGTAAATGCCCTGAGCAAAAGAx6y20A; CAAAATTAATTACCTACCTTTTTAACx6y20B; TAGGTCTGAGAGAATTTAACAATTTCx8y20A; CAGTACATAAATCAGACGCTGAGAAGx8y20B; ATAGCTTAGATTAAATATATGTGAGT

x1y21A; TTTACATCGGGAGTTATTTGCACGTAx1y21B; TACCATATCAAAAAAACAATAACGGAx3y21A; TTACAAAATCGCGGTTTGGATTATACx3y21B; TATAATCCTGATTCAGAGGCGAATTAx5y21A; AGATGATGAAACACATCATATTCCTGx5y21B; GGAGCGGAATTATAACATCAAGAAAAx7y21A; ATTTGAATTACCTGTAACATTATCATx7y21B; TTTAAAAGTTTGATTTTTAATGGAAAx9y21A; GAATAACCTTGCTGACAACTCGTATTx9y21B; ATTAGACTTTACAAACAATTCTCTGTAAATCGTCGCTATTAA

x0y22A; AATACCGAACGAACCACCAGCGAAATTGCGTAGATTTTCAGGx0y22B; AAACAGAAATAAAAGAAGATAAAACAx2y22A; GCCTGCAACAGTGAAGGGTTAGAACCx2y22B; TTCTGAATAATGGCCACGCTGAGAGCx4y22A; TCACCTTGCTGAAGGCAATTCATCAAx4y22B; ATTATCAGATGATCCTCAAATATCAAx6y22A; GCAAATCAACAGTGAAACCACCAGAAx6y22B; TTTGCGGAACAAATGAAAGGAATTGAx8y22A; AGCACTAACAACTGAACGTTATTAATx8y22B; AAATCCTTTGCCCAATAGATTAGAGC

x1y23A; GAGGTGAGGCGGTTTAGTCTTTAATGx1y23B; TTTTGAATGGCTACAGTATTAACACCx3y23A; CAGCAGCAAATGACTGACCTGAAAGCx3y23B; AGATAGAACCCTTAAAATCTAAAGCAx5y23A; ACCCTCAATCAATTCACACGACCAGTx5y23B; GCAGATTCACCAGATCTGGTCAGTTGx7y23A; GGAAGGTTATCTATTTTGACGCTCAAx7y23B; GGAAATACCTACAAAATATCTTTAGGx9y23A; CGTCAATAGATAAAATATTACCGCCAx9y23B; CTTGCTGGTAATATCCAGAACTACATTTGAGGATTTAGAAGT

x0y24A; GCGCTTAATGCGCCGCTACAGCCCTAAAACATCGCCATTAAAx0y24B; CGCGAACTGATAGGGCGCGTACTATGx2y24A; GCTTTCCTCGTTAGCACAGACAATATx2y24B; GTAAGAATACGTGGAATCAGAGCGGGx4y24A; ATTTTAGACAGGATTCTGGCCAACAGx4y24B; AATAAAAGGGACAACGGTACGCCAGAx6y24A; TGAGGCCACCGAGATTATTTACATTG

x6y24B; TCGTCTGAAATGGTAAAAGAGTCTGTx8y24A; AATACTTCTTTGAGAAAAACGCTCATx8y24B; GCCATTGCAACAGTTAGTAATAACAT

x1y25C; GTTGCTTTGACGAGCACGTATAACGTx3y25C; AGCTAAACAGGAGGCCGATTAAAGGGx5y25C; ATCCTGAGAAGTGTTTTTATAATCAGx7y25C; CCATCACGCAAATTAACCGTTGTAGCx9y25C; CACTTGCCTGAGTAGAAGAACTCAAACTATCGGC

Supplementary Figure S18: Sequences for the square.

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Supplementary Figure S20: Crossover diagram for the rectangle.

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Plate number: 1r1t0g,A1,CAAGCCCAATAGGAACCCATGTACCGTAACACr1t10e,B1,TCTTACCAGCCAGTTACAAAATAAATGAAATAr1t10f,C1,CCTAATTTACGCTAACGAGCGTCTATATCGCGr1t12e,D1,CTAATTTATCTTTCCTTATCATTCATCCTGAAr1t12f,E1,ATCGGCTGCGAGCATGTAGAAACCAGCTATATr1t14e,F1,AATTACTACAAATTCTTACCAGTAATCCCATCr1t14f,G1,GCGTTATAGAAAAAGCCTGTTTAGAAGGCCGGr1t16e,H1,TAGAATCCCTGAGAAGAGTCAATAGGAATCATr1t16f,A2,TTAAGACGTTGAAAACATAGCGATTTAAATCAr1t18e,B2,TTTAACGTTCGGGAGAAACAATAATTTTCCCTr1t18f,C2,CTTTTACACAGATGAATATACAGTAAGCGCCAr1t20e,D2,GGATTTAGCGTATTAAATCCTTTGTTTTCAGG

r1t20f,E2,CGACAACTAAGTATTAGACTTTACAGCCGGAAr1t22e,F2,TAGCCCTACCAGCAGAAGATAAAAACATTTGAr1t22f,G2,ACGAACCAAAACATCGCCATTAAATGGTGGTTr1t24h,H2,CGGCCTTGCTGGTAATATCCAGAACGAACTGAr1t2e,A3,TGCCTTGACTGCCTATTTCGGAACAGGGATAGr1t2f,B3,AATGCCCCGTAACAGTGCCCGTATGTGAATTTr1t4e,C3,AACCAGAGACCCTCAGAACCGCCAGGGGTCAGr1t4f,D3,GAGCCGCCCCACCACCGGAACCGCCTAAAACAr1t6e,E3,ATTGAGGGTAAAGGTGAATTATCAATCACCGGr1t6f,F3,TTATTCATAGGGAAGGTAAATATTCATTCAGTr1t8e,G3,GCAATAGCGCAGATAGCCGAACAATTCAACCGr1t8f,H3,AAAAGTAATATCTTACCGAAGCCCAACACTATr3t0g,A4,CTCAGAGCCACCACCCTCATTTTCCTATTATTr3t10e,B4,TATTTTGCTCCCAATCCAAATAAGTGAGTTAAr3t10f,C4,ATTATTTAACCCAGCTACAATTTTCAAGAACGr3t12e,D4,TAAGTCCTACCAAGTACCGCACTCTTAGTTGCr3t12f,E4,GGTATTAAGAACAAGAAAAATAATTAAAGCCAr3t14e,F4,AGGCGTTACAGTAGGGCTTAATTGACAATAGAr3t14f,G4,ACGCTCAAAATAAGAATAAACACCGTGAATTTr3t16e,H4,CTGTAAATCATAGGTCTGAGAGACGATAAATAr3t16f,A5,ATCAAAATCGTCGCTATTAATTAACGGATTCGr3t18e,B5,ACAGAAATCTTTGAATACCAAGTTCCTTGCTTr3t18f,C5,CCTGATTGAAAGAAATTGCGTAGACCCGAACGr3t20e,D5,AGATTAGATTTAAAAGTTTGAGTACACGTAAAr3t20f,E5,TTATTAATGCCGTCAATAGATAATCAGAGGTG

r3t22e,F5,GAATGGCTAGTATTAACACCGCCTCAACTAATr3t22f,G5,AGGCGGTCATTAGTCTTTAATGCGCAATATTAr3t24h,H5,CCGCCAGCCATTGCAACAGGAAAAATATTTTTr3t2e,A6,AGTGTACTTGAAAGTATTAAGAGGCCGCCACCr3t2f,B6,CTGAAACAGGTAATAAGTTTTAACCCCTCAGAr3t4e,C6,GTTTGCCACCTCAGAGCCGCCACCGATACAGGr3t4f,D6,GCCACCACTCTTTTCATAATCAAACCGTCACCr3t6e,E6,AGCGCCAACCATTTGGGAATTAGATTATTAGCr3t6f,F6,GACTTGAGAGACAAAAGGGCGACAAGTTACCAr3t8e,G6,GCCCAATACCGAGGAAACGCAATAGGTTTACCr3t8f,H6,GAAGGAAAATAAGAGCAAGAAACAACAGCCATr5t0g,A7,CCCTCAGAACCGCCACCCTCAGAACTGAGACTr5t10e,B7,AGGTTTTGAACGTCAAAAATGAAAGCGCTAATr5t10f,C7,TTTTGTTTAAGCCTTAAATCAAGAATCGAGAAr5t12e,D7,AATGCAGACCGTTTTTATTTTCATCTTGCGGGr5t12f,E7,CAAGCAAGACGCGCCTGTTTATCAAGAATCGCr5t14e,F7,AATGGTTTACAACGCCAACATGTAGTTCAGCTr5t14f,G7,CATATTTAGAAATACCGACCGTGTTACCTTTTr5t16e,H7,AAATCAATGGCTTAGGTTGGGTTACTAAATTTr5t16f,A8,TAACCTCCATATGTGAGTGAATAAACAAAATCr5t18e,B8,AACCTACCGCGAATTATTCATTTCCAGTACATr5t18f,C8,GCGCAGAGATATCAAAATTATTTGACATTATCr5t20e,D8,CTAAAATAGAACAAAGAAACCACCAGGGTTAGr5t20f,E8,ATTTTGCGTCTTTAGGAGCACTAAGCAACAGTr5t22e,F8,GCGTAAGAGAGAGCCAGCAGCAAAAAGGTTATr5t22f,G8,GCCACGCTATACGTGGCACAGACAACGCTCATr5t24h,H8,GGAAATACCTACATTTTGACGCTCACCTGAAAr5t2e,A9,TAAGCGTCGAAGGATTAGGATTAGTACCGCCAr5t2f,B9,CCTCAAGAATACATGGCTTTTGATAGAACCACr5t4e,C9,TCGGCATTCCGCCGCCAGCATTGACGTTCCAGr5t4f,D9,CACCAGAGTTCGGTCATAGCCCCCGCCAGCAAr5t6e,E9,TCACAATCGTAGCACCATTACCATCGTTTTCAr5t6f,F9,AATCACCAAATAGAAAATTCATATATAACGGAr5t8e,G9,ATCAGAGAAAGAACTGGCATGATTTTATTTTGr5t8f,H9,ATACCCAAGATAACCCACAAGAATAAACGATTr7t0g,A10,TATCACCGTACTCAGGAGGTTTAGCGGGGTTTr7t10e,B10,GAGGCGTTAGAGAATAACATAAAAGAACACCCr7t10f,C10,CTTTACAGTTAGCGAACCTCCCGACGTAGGAAr7t12e,D10,CCAGACGAGCGCCCAATAGCAAGCAAGAACGCr7t12f,E10,TCATTACCCGACAATAAACAACATATTTAGGCr7t14e,F10,TTTTAGTTTTTCGAGCCAGTAATAAATTCTGTr7t14f,G10,AGAGGCATAATTTCATCTTCTGACTATAACTAr7t16e,H10,TTGAATTATGCTGATGCAAATCCACAAATATAr7t16f,A11,TATGTAAACCTTTTTTAATGGAAAAATTACCTr7t18e,B11,TGGATTATGAAGATGATGAAACAAAATTTCATr7t18f,C11,GAGCAAAAACTTCTGAATAATGGAAGAAGGAGr7t20e,D11,ATCAACAGTCATCATATTCCTGATTGATTGTTr7t20f,E11,CGGAATTATTGAAAGGAATTGAGGTGAAAAATr7t22e,F11,GCCAACAGTCACCTTGCTGAACCTGTTGGCAAr7t22f,G11,CTAAAGCAAGATAGAACCCTTCTGAATCGTCTr7t24h,H11,GAAATGGATTATTTACATTGGCAGACATTCTGr7t2e,A12,GGAAAGCGACCAGGCGGATAAGTGAATAGGTGr7t2f,B12,TGCTCAGTCAGTCTCTGAATTTACCAGGAGGTr7t4e,C12,TGCCTTTAGTCAGACGATTGGCCTGCCAGAATr7t4f,D12,TGAGGCAGGCGTCAGACTGTAGCGTAGCAAGGr7t6e,E12,ACGCAAAGGTCACCAATGAAACCAATCAAGTTr7t6f,F12,CCGGAAACACACCACGGAATAAGTAAGACTCCr7t8e,G12,TGAACAAACAGTATGTTAGCAAACTAAAAGAAr7t8f,H12,TTATTACGGTCAGAGGGTAATTGAATAGCAGC

Plate number: 2r9t0f,A1,TATAAGTATAGCCCGGCCGTCGAGr9t10f,B1,GCGCATTAGCTTATCCGGTATTCTAAATCAGAr9t12f,C1,TATAGAAGCGACAAAAGGTAAAGTAGAGAATAr9t14f,D1,TAAAGTACCGCGAGAAAACTTTTTATCGCAAGr9t16f,E1,ACAAAGAAATTAATTACATTTAACACATCAAGr9t18f,F1,AAAACAAATTCATCAATATAATCCTATCAGATr9t20f,G1,GATGGCAAAATCAATATCTGGTCACAAATATCr9t22j,H1,AAACCCTCACCAGTAATAAAAGGGATTCACCAGTCACACGr9t2f,A2,AGGGTTGAATAAATCCTCATTAAATGATATTCr9t4f,B2,ACAAACAAAATCAGTAGCGACAGATCGATAGCr9t6f,C2,AGCACCGTTAAAGGTGGCAACATAGTAGAAAAr9t8f,D2,TACATACAGACGGGAGAATTAACTACAGGGAA

r-1t0g,E2,TGAGTTTCGTCACCAGTACAAACTTAATTGTAr-1t10e,F2,TTTTAATTGCCCGAAAGACTTCAATTCCAGAGr-1t10f,G2,AAGAGGAACGAGCTTCAAAGCGAAGATACATTr-1t12e,H2,TTTCATTTGGTCAATAACCTGTTTAATCAATAr-1t12f,A3,TCGCAAATGGGGCGCGAGCTGAAATAATGTGTr-1t14e,B3,AGACAGTCATTCAAAAGGGTGAGATATCATATr-1t14f,C3,AGGTAAAGAAATCACCATCAATATAATATTTTr-1t16e,D3,GCTCATTTTCGCATTAAATTTTTGAGCTTAGAr-1t16f,E3,GTTAAAATTTTAACCAATAGGAACCCGGCACCr-1t18e,F3,TTCGCCATTGCCGGAAACCAGGCAAACAGTACr-1t18f,G3,GCTTCTGGTCAGGCTGCGCAACTGTGTTATCCr-1t20e,H3,GCATAAAGTTCCACACAACATACGAAACAATTr-1t20f,A4,GCTCACAATGTAAAGCCTGGGGTGGGTTTGCCr-1t22e,B4,CCGAAATCCGAAAATCCTGTTTGAAATACCGAr-1t22f,C4,CCAGCAGGGGCAAAATCCCTTATAAAGCCGGCr-1t24h,D4,GAACGTGGCGAGAAAGGAAGGGAACAAACTATr-1t2e,E4,CTTAAACATCAGCTTGCTTTCGAGAAACAGTTr-1t2f,F4,TCGGTTTAGCTTGATACCGATAGTCCAACCTAr-1t4e,G4,CTCATCTTGAGGCAAAAGAATACACTCCCTCAr-1t4f,H4,AAACGAAATGACCCCCAGCGATTATTCATTACr-1t6e,A5,GAATAAGGACGTAACAAAGCTGCTGACGGAAAr-1t6f,B5,CCAAATCACTTGCCCTGACGAGAACGCCAAAAr-1t8e,C5,CATAACCCGAGGCATAGTAAGAGCTTTTTAAGr-1t8f,D5,GGAATTACTCGTTTACCAGACGACAAAAGATTr-3t0g,E5,TGTAGCATTCCACAGACAGCCCTCATCTCCAA

r-3t10e,F5,GAAGCAAAAAAGCGGATTGCATCAGATAAAAAr-3t10f,G5,TCAGAAGCCTCCAACAGGTCAGGATCTGCGAAr-3t12e,H5,TCAATTCTTTTAGTTTGACCATTACCAGACCGr-3t12f,A6,CGAGTAGAACTAATAGTAGTAGCAAACCCTCAr-3t14e,B6,ACCGTTCTAAATGCAATGCCTGAGAGGTGGCAr-3t14f,C6,TATATTTTAGCTGATAAATTAATGTTGTATAAr-3t16e,D6,AAATAATTTTAAATTGTAAACGTTGATATTCAr-3t16f,E6,GCAAATATCGCGTCTGGCCTTCCTGGCCTCAGr-3t18e,F6,GGCGATCGCACTCCAGCCAGCTTTGCCATCAAr-3t18f,G6,GAAGATCGGTGCGGGCCTCTTCGCAATCATGGr-3t20e,H6,GTGAGCTAGTTTCCTGTGTGAAATTTGGGAAGr-3t20f,A7,TCATAGCTACTCACATTAATTGCGCCCTGAGAr-3t22e,B7,GAATAGCCGCAAGCGGTCCACGCTCCTAATGAr-3t22f,C7,GAGTTGCACGAGATAGGGTTGAGTAAGGGAGCr-3t24h,D7,CCCCGATTTAGAGCTTGACGGGGAAATCAAAAr-3t2e,E7,CAATGACACTCCAAAAGGAGCCTTACAACGCCr-3t2f,F7,AAAAAAGGACAACCATCGCCCACGCGGGTAAAr-3t4e,G7,GCGAAACATGCCACTACGAAGGCATGCGCCGAr-3t4f,H7,ATACGTAAAAGTACAACGGAGATTTCATCAAGr-3t6e,A8,ACGAGTAGTGACAAGAACCGGATATACCAAGCr-3t6f,B8,AGTAATCTTAAATTGGGCTTGAGAGAATACCAr-3t8e,C8,CCAAAATATAATGCAGATACATAAACACCAGAr-3t8f,D8,CATTCAACGCGAGAGGCTTTTGCATATTATAGr-5t0g,E8,CGTAACGATCTAAAGTTTTGTCGTGAATTGCGr-5t10e,F8,TACCTTTAAGGTCTTTACCCTGACAAAGAAGTr-5t10f,G8,CAAAAATCATTGCTCCTTTTGATAAGTTTCATr-5t12e,H8,CAATAAATACAGTTGATTCCCAATTTAGAGAGr-5t12f,A9,TCCATATACATACAGGCAAGGCAACTTTATTTr-5t14e,B9,GGTAGCTAGGATAAAAATTTTTAGTTAACATCr-5t14f,C9,CAACGCAATTTTTGAGAGATCTACTGATAATCr-5t16e,D9,CTTTCATCCCCAAAAACAGGAAGACCGGAGAGr-5t16f,E9,AGAAAAGCAACATTAAATGTGAGCATCTGCCAr-5t18e,F9,CAGCTGGCGGACGACGACAGTATCGTAGCCAGr-5t18f,G9,GTTTGAGGGAAAGGGGGATGTGCTAGAGGATCr-5t20e,H9,ACTGCCCGCCGAGCTCGAATTCGTTATTACGCr-5t20f,A10,CCCGGGTACTTTCCAGTCGGGAAACGGGCAACr-5t22e,B10,AGTTTGGAGCCCTTCACCGCCTGGTTGCGCTCr-5t22f,C10,AGCTGATTACAAGAGTCCACTATTGAGGTGCCr-5t24h,D10,GTAAAGCACTAAATCGGAACCCTAGTTGTTCCr-5t2e,E10,ATATATTCTTTTTTCACGTTGAAAATAGTTAGr-5t2f,F10,AATAATAAGGTCGCTGAGGCTTGCAAAGACTTr-5t4e,G10,CGCCTGATGGAAGTTTCCATTAAACATAACCGr-5t4f,H10,TTTCATGAAAATTGTGTCGAAATCTGTACAGAr-5t6e,A11,TTTCAACTATAGGCTGGCTGACCTTGTATCATr-5t6f,B11,CCAGGCGCTTAATCATTGTGAATTACAGGTAGr-5t8e,C11,TTTGCCAGATCAGTTGAGATTTAGTGGTTTAAr-5t8f,D11,AAAGATTCAGGGGGTAATAGTAAACCATAAATr-7t0g,E11,ACGTTAGTAAATGAATTTTCTGTAAGCGGAGTr-7t10e,F11,TTTTTGCGCAGAAAACGAGAATGAATGTTTAGr-7t10f,G11,AAACAGTTGATGGCTTAGAGCTTATTTAAATAr-7t12e,H11,CAAAATTAAAGTACGGTGTCTGGAAGAGGTCAr-7t12f,A12,TGCAACTAAGCAATAAAGCCTCAGTTATGACCr-7t14e,B12,TCAGGTCACTTTTGCGGGAGAAGCAGAATTAGr-7t14f,C12,CTGTAATATTGCCTGAGAGTCTGGAAAACTAGr-7t16e,D12,ACCCGTCGTCATATGTACCCCGGTAAAGGCTAr-7t16f,E12,CATGTCAAGATTCTCCGTGGGAACCGTTGGTGr-7t18e,F12,ATTAAGTTCGCATCGTAACCGTGCGAGTAACAr-7t18f,G12,TAGATGGGGGGTAACGCCAGGGTTGTGCCAAGr-7t20e,H12,GCCAGCTGCCTGCAGGTCGACTCTGCAAGGCG

Plate number: 3r-7t20f,A1,CTTGCATGCATTAATGAATCGGCCCGCCAGGGr-7t22e,B1,TGGACTCCCTTTTCACCAGTGAGACCTGTCGTr-7t22f,C1,TGGTTTTTAACGTCAAAGGGCGAAGAACCATCr-7t24h,D1,ACCCAAATCAAGTTTTTTGGGGTCAAAGAACGr-7t2e,E1,AAAGGCCGAAAGGAACAACTAAAGCTTTCCAGr-7t2f,F1,GAGAATAGCTTTTGCGGGATCGTCGGGTAGCAr-7t4e,G1,GCTCCATGAGAGGCTTTGAGGACTAGGGAGTTr-7t4f,H1,ACGGCTACTTACTTAGCCGGAACGCTGACCAAr-7t6e,A2,CGATTTTAGAGGACAGATGAACGGCGCGACCTr-7t6f,B2,CTTTGAAAAGAACTGGCTCATTATTTAATAAAr-7t8e,C2,ACTGGATAACGGAACAACATTATTACCTTATGr-7t8f,D2,ACGAACTAGCGTCCAATACTGCGGAATGCTTT

r-9t10e,E2,ATATAATGCATTGAATCCCCCTCAAATCGTCAr-9t12e,F2,GCTAAATCCTGTAGCTCAACATGTATTGCTGAr-9t14e,G2,AGAGAATCGGTTGTACCAAAAACAAGCATAAAr-9t16e,H2,GATTGACCGATGAACGGTAATCGTAGCAAACAr-9t18e,A3,CACGACGTGTAATGGGATAGGTCAAAACGGCGr-9t20e,B3,GGGAGAGGTGTAAAACGACGGCCATTCCCAGTr-9t22e,C3,TATCAGGGCGGTTTGCGTATTGGGAACGCGCGr-9t24e,D3,CGATGGCCCACTACGTAAACCGTCr-9t2i,E3,CAGCGAAAAACTTTCAACAGTTTCTGGGATTTTGCTAAACr-9t4e,F3,ACGGTCAAGACAGCATCGGAACGAACCCTCAGr-9t6e,G3,GGACGTTGTCATAAGGGAACCGAAAGGCGCAGr-9t8e,H3,TAAATATTGGAAGAAAAATCTACGACCAGTCArt-rem1,A4,AACATCACTTGCCTGAGTAGAAGAACTrt-rem2,B4,TGTAGCAATACTTCTTTGATTAGTAATrt-rem3,C4,AGTCTGTCCATCACGCAAATTAACCGTrt-rem4,D4,ATAATCAGTGAGGCCACCGAGTAAAAGrt-rem5,E4,ACGCCAGAATCCTGAGAAGTGTTTTTrt-rem6,F4,TTAAAGGGATTTTAGACAGGAACGGTrt-rem7,G4,AGAGCGGGAGCTAAACAGGAGGCCGArt-rem8,H4,TATAACGTGCTTTCCTCGTTAGAATCrt-rem9,A5,GTACTATGGTTGCTTTGACGAGCACGrt-rem10,B5,GCGCTTAATGCGCCGCTACAGGGCGC

Supplementary Figure S21: Sequences for the rectangle.

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a

b c

Supplementary Figure S22: More design details for the star a, Original block diagram assuming that each block (1 turn of DNA) would have an aspect ration of roughly 1:1 (3.5 nm per turn:3.5 nm per helix) based on the inter-helix gap for 2.5 turnspacing. In reality 1.5-turn spacing appears to have a ratio of roughly 1.2:1 (3.6 nm per turn:3 nm per helix) and so the stars

were somewhat squat b . c reproduces the folding path for reference. In a , turns that occur between columns of red blocksand orange blocks have offset 0 with respect to the underlying crossover lattice. Other turns on the left and right outer edgeshave +1 or -1 offsets depending on which side of the star they occur. Purple and green half-blocks show that turns (in thescaffold) made on the seam or on the interior of the bottom left and right star arms are made an odd number of 1 / 2 turns(DNA half-turns) away from turns (in the scaffold) on the outer edges.

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Supplementary Figure S23: Crossover diagram for the star (top) and high resolution AFM (bottom, taken by E. Winfree)which shows the crossover structure in great detail. Defects are probably tip damage. White arrow points to a section of helixthat does not image well and appears to be a hole. On edges where helices can move unimpeded by neighbors helices oftendisappear at high tapping amplitude.

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Plate number: 1s10t15f,A1,AAAGACAAGCAAGGCCGGAAACGTs10t17f,B1,AGAGAGAACCACAAGAATTGAGTTCCAGCGCCs11t14e,C1,AGCACCATTACCATTAAAGGGCGAs11t16e,D1,CATTCAACATATCAGAGAGATAACTAACATAAs11t18g,E1,AAACAGGGAACAAGCAAGCCGTTTTACCGCACTCATCGAGs11t18h,F1,AAGCGCATTAGACGGGGGGTAATTGAGCGCTACGATTGAGs12t15f,G1,GGAGGGAACAGCAAAATCACCAGTs13t14e,H1,ATTTGGGAATTAGAGCGGTAAATAs13t16g,A2,TTGACGGACCTGAACAAAGTCAGAAGAATTAACTGAACACs13t16h,B2,AATTATTCATTAAAGGGTCACCGACTTGAGCCs14t15b,C2,ATCACCTGAATTs1t0h,D2,TATAGCCCGGAATAGGTGTATCACCGTACTCA

s1t10i,E2,CGTTCCAGGGAAAGCGCAGTCTCTTTCAACAGs1t12i,F2,CAGGAGGTCACCAGAGCCGCCGCCAAAAGGAGs1t14i,G2,CCAGAGCCTTTTCATAATCAAAATATATTCGGs1t16i,H2,TTAAGACTGAATACCCAAAAGAACGAACCGGAs1t18i,A3,TTATCCTGGCTATTTTGCACCCAGTAATAGTAs1t20i,B3,ATGTTCAGGTCCAGACGACGACAACTCAACATs1t22i,C3,ACCTAAATTATTTTAGTTAATTTCACCAAAAAs1t24i,D3,AATTTTCCTTCTGTAAATCGTCGCAGAGATCTs1t26i,E3,TTGAATACCAATAACGGATTCGCCAAATCAGCs1t28i,F3,ATGATGGCTATCATCATATTCCTGGGGGACGAs1t2i,G3,GATATAAGCGGATAAGTGCCGTCGCACCCTCAs1t30i,H3,ATCTAAAAAGTTGAAAGGAATTGAGTTGTAAAs1t32g,A4,GCGCGAACTGACAGTTGGCAAATCAACTATCTTTAs1t4i,B4,GTACCAGGTTAGGATTAGCGGGGTCCCTCAGAs1t6i,C4,TTAAGAGGCTATTATTCTGAAACAGTACCGTAs1t8i,D4,TTGAGTAAATAAGTTTTAACGGGGCGTAACGAs2t11f,E4,GTCAGACGTCATTAAAGCCAGAATTAAGCGTCs2t13f,F4,AACCGCCTCCGCCACCAGAACCACTGAGGCAGs2t15f,G4,CGCAGTATATTAGCGTTTGCCATCACCACCGGs2t17f,H4,CAACGCTAAAACGCAATAATAACGCCTTATTAs2t19f,A5,GAACGCGCTAAATCAAGATTAGTTAATCTTACs2t21f,B5,TTGAAATAAAGGTAAAGTAATTCTCTAATGCAs2t23f,C5,CCTTGAAAAAAACTTTTTCAAATATTAATGGTs2t25f,D5,AAAATCGCGAGTGAATAACCTTGCCTTAGAATs2t27f,E5,AATATAATTTTACATCGGGAGAAACAAGTTAC

s2t29f,F5,GGAGCACTCCAGAAGGAGCGGAATAATTCATCs2t5g,G5,CAAGAGAAGGAs2t7b,H5,TGCCCCAGTTAAs2t7g,A6,GTATAAACCTGCCTATTTCGGAACCTGAGACTCCTs2t9b,B6,ATGATACTTTTGs2t9f,C6,ATACATGGCAGGAGTGTACTGGTACAGTGCCCs3t10e,D6,ACAAACAAATAAATCCATTGGCCTs3t12e,E6,TGATATTCGCCACCACCCTCAGAGCCCTCAGAs3t14e,F6,GCCGCCACCGGTCATAGCCCCCTTGTTAGCAAs3t16e,G6,ACGTAGAACAGAAGGAAACCGAGGACGAGCGTs3t18e,H6,CTTTCCAGGGAGGTTTTGAAGCCTCTGTTTATs3t20e,A7,CAACAATATATAAAGTACCGACAACCGACCGTs3t22e,B7,GTGATAAAAGACAAAGAACGCGAGACATAGCGs3t24e,C7,ATAGCTTAATAAATCAATATATGTGCAGAGGCs3t26e,D7,GAATTATTTACAGTAACAGTACCTCCTGATTGs3t28e,E7,TTTGGATTCGGAACAAAGAAACCAAACAACTAs3t30e,F7,ATAGATTATCAATCAATATCTGGTTAGCCCTAs3t32h,G7,AAACATCGATTTTTGAATGGCTATTAGTCTTTAATs3t34a,H7,ATGGAAACGCTCs4t13g,A8,CCACCCTCAGAs4t15g,B8,CATAAAGGTTTTCATCGGCATTTTCCTCAGAACCGs4t17f,C8,TTGCCAGTAGCCGAACAAAGTTACAATACATAs4t19f,D8,CTGAACAAAACCTCCCGACTTGCGAGCCTAATs4t21f,E8,TAAATAAGGCCAGTAATAAGAGAAGATAAGTCs4t23f,F8,CGCTGAGATGCAAATCCAATCGCATAAGGCGTs4t25f,G8,TTACCTGATTAATGGAAACAGTACGATTAAGAs4t27f,H8,GAATAATGTAACGTCAGATGAATACATTTCAAs4t29f,A9,AATAGATATAACATTATCATTTTGATACTTCTs4t31f,B9,AATACCGACTCAAATATCAAACCCGAGCCGTCs4t33f,C9,ATTTTGACACGTGGCACAGACAATCCATTAAAs4t35f,D9,CATTGCAACAGGAAAAATACCTACs5t14e,E9,GTCAGACTGTAGCGCGTGGCAACAs5t16e,F9,TATAAAAGAGAAAAGTAAGCAGATTACAAAATs5t18e,G9,AAACAGCCGCGAGGCGTTTTAGCGGAAAAATAs5t20e,H9,ATATCCCAGCAGAGGCATTTTCGAAATAAACAs5t22e,A10,CCGGAATCTATATGTAAATGCTGAAGAGTCAAs5t24e,B10,TAGTGAATATTTGAATTACCTTTTGCAAAAGAs5t26e,C10,AGATGATGCGTAGATTTTCAGGTTGAAGGGTTs5t28e,D10,AGAACCTAATTTTAAAAGTTTGAGATACATTTs5t30e,E10,GAGGATTTCATCACCTTGCTGAACACGAACCAs5t32e,F10,CCAGCAGACTGAAAGCGTAAGAATGCTCAATCs5t34e,G10,GTCTGAAACAATATTACCGCCAGCs5t36a,H10,GAGTCTGTAAAAs6t15f,A11,AGACACCACAAGTTTGCCTTTAGCs6t17f,B11,TATCCCAAACCGAAGCCCTTTTTAAAACGCAAs6t19f,C11,TACGAGCACCGGTATTCTAAGAACATATTATTs6t21f,D11,TAGAAAAACCAACATGTAATTTAGTCCTAATTs6t23f,E11,ATCATAGGGGTTGGGTTATATAACATAATTACs6t25b,F11,ATTAATAACAAAs6t25f,G11,ATCAAGAATACATTTAACAATTTCTTATCAAAs6t27b,H11,TAAAACTGCACG

s6t27f,A12,AAATTATTAGAAATAAAGAAATTGAAACAAACs6t29f,B12,TAGACTTTTGCCCGAACGTTATTACCATATCAs6t31f,C12,CAGAGGTGAATGAAAAATCTAAAGAGAAGTATs6t33f,D12,TTACATTGATAGAACCCTTCTGACAGATAAAAs6t35f,E12,CGCAAATTCTGGTAATATCCAGAATGGATTATs6t37f,F12,TCAGTGAGGCCACCGAGTCCATCAs7t14e,G12,TCAGTAGCGACAGAATCGGAATAAs7t16e,H12,GTTTATTTTAGCAATAGCTATCTTTCCAAATA

Plate number: 2s7t18e,A1,AGAAACGAGATATAGAAGGCTTATTGTAGAAAs7t20e,B1,CCAATCAAGCCATATTTAACAACGGCCTGTTTs7t22g,C1,AGTATCATTTTAACCTCCGGCTTATCTGAGAGACTACCTTs7t22h,D1,ATGCGTTATACAAATTGGCTTAATTGAGAATCTAATCGGCs7t28e,E1,CTCGTATTAAATCCTTACAAACAAs7t30e,F1,TTCGACAACTGAGAGCCAGCAGCAAGGCGGTCs7t32e,G1,AGTATTAAATTCTGGCCAACAGAGGCAGATTCs7t34e,H1,ACCAGTCACAAACTATCGGCCTTGAACCGTTGs7t36e,A2,TAGCAATAAGAAGTGTTTTTATAAs7t38a,B2,AATCAGCGTTAGs8t15f,C2,TCAATAGAGATAGCAGCACCGTAAs8t17f,D2,TTAACGTCGCAAGAAACAATGAAATGTCACAA

s8t19f,E2,TGTCTTTCAATAGCAAGCAAATCATTTTTTGTs8t31g,F2,ACAGTGCCACGs8t33h,G2,ATAAAAGGGACCACCGCCTGCAs8t35b,H2,CACTTGTAACATs8t35g,A3,ATTAGTAACCTGAGTAGAAGAACTCACGACCAGTAs8t37f,B3,CTAAACAGGTACGCCAGAATCCTGCTTCTTTGs8t39f,C3,TATAACGTGCTTTCCTAGCGGGAGs9t14e,D3,CACCAATGAAACCATCAAATTCATs9t16e,E3,ATGGTTTAAAGCCCAATAATAAGAAAAAATGAs9t18e,F3,AAATAGCAAATCATTACCGCGCCCCTTATCATs9t20g,G3,TCCAAGAACAACGCTCAACAGTAGCTTACCAGTATAAAGCs9t20h,H3,CGGGTATTAAACCAAGTTATTTTCATCGTAGGGCCTTTACs9t36e,A4,ATTTTAGACAGGAACGGAGGCCGAs9t38g,B4,TTAAAGGGTGCTTTGACGAGCACGGGGCGCGTACTATGGTs-10t15f,C4,ATAAATTGACGTAATGCCACTACGs-10t17f,D4,TCATCAGTGGCTCATTATACCAGTATCGCCTGs-11t14e,E4,AAGGCACCAACCTAAAAACGGAGAs-11t16g,F4,TTTGTATCCAGGACGTTGGGAAGACAACATTATTACAGGTs-11t20g,G4,TTAAGAGGAAGCCCGAGATTGCATCAAAAAGAAGAAAGATs-12t15f,H4,CAAAGTACACGAAAGAGGCAAAAGs-13t14g,A5,AATACACTAAAACACTCCAGCGATTATACCAAs-13t18g,B5,AAACGAACTAACGGAAAAAATCTACGTTAATAGCGCGAAAs-14t15a,C5,TGACCCCATCTTs-1t10e,D5,TGTATGGGGAGTGAGAATAGAAAGTTCACGTTs-1t10i,E5,TTTCAGCGATTTTGCTAAACAACTGAATTTAC

s-1t12e,F5,GAAAATCTTGTATCGGTTTATCAGATGACAACs-1t12i,G5,CCTTTAATCCAAAAAAAAGGCTCCAGCATTGAs-1t14e,H5,AACCATCGGCTTGCAGGGAGTTAATGGCTGACs-1t14i,A6,TCGCTGAGCCCACGCATAACCGATCACCGGAAs-1t16e,B6,CTTCATCAACCCAAATCAACGTAAGGCTTTTGs-1t16i,C6,TATTCATTAGAGTAATCTTGACAATGGCATGAs-1t18e,D6,CAAAAGAAAGACTGGATAGCGTCCTTAGAGCTs-1t18i,E6,AAATGTTTGTTTTGCCAGAGGGGGCTACAATTs-1t20e,F6,TAATTGCTTATGCAACTAAAGTACAAAGCCTCs-1t20i,G6,GTTTTAAAGAATATAATGCTGTAGTAAACAACs-1t22e,H6,AGAGCATACCCTGTAATACTTTTGTAAATTAAs-1t22i,A7,CATTATGAAAGCTAAATCGGTTGTATCTTCTGs-1t24e,B7,TGCCGGAGTATCAGGTCATTGCCTTATTTTGTs-1t24i,C7,ACAAAGGCAGGGTAGCTATTTTTGTATTAATTs-1t26e,D7,TAAAATTCTAACCAATAGGAACGCGGCGCATCs-1t26i,E7,TCATTTTTGCATTAAATTTTTGTTTGATTGCTs-1t28e,F7,GTAACCGTTCGGCCTCAGGAAGATTTGGGTAAs-1t28i,G7,CGACAGTAGCATCTGCCAGTTTGAATTATCAGs-1t2i,H7,GAACCGCCGGAGGTTTAGTACCGCAGAGGGTTs-1t30g,A8,CGCCAGGGCAGTGCCAAGCTTGCAGCTCACTGCCCs-1t30i,B8,ACGACGGCTTTTCCCAGTCACGACGGAAGGTTs-1t32h,C8,GCTTTCCAGTCGGGAAACCTGTCGTGCACATTAATs-1t4g,D8,CCTCATTTTCAs-1t4i,E8,GCCACCACACCCTCAGAACCGCCATTTGCTCAs-1t6i,F8,ACACTGAGCCCAATAGGAACCCATTGAAAGTAs-1t8e,G8,TCCACAGATTTGTCGTCTTTCCAGGAATTTTCs-1t8i,H8,TCTAAAGTCAGCCCTCATAGTTAGTCAGTGCCs-2t11f,A9,ATAATTTTGAACAACTAAAGGAATs-2t13f,B9,CGCCGACACTTGCTTTCGAGGTGATGCGAATAs-2t15f,C9,GCATAGGCAGGCCGCTTTTGCGGGGATAGTTGs-2t17f,D9,TAGCGAGACAAAGCTGCTCATTCAGACCAGGCs-2t19f,E9,CGGATGGCAATACTGCGGAATCGTAACCAAAAs-2t21f,F9,TAAGCAATGGTGTCTGGAAGTTTCCATTTTTGs-2t23f,G9,CTAGCTGACGGGAGAAGCCTTTATAGCAAAATs-2t25f,H9,AACGTTAAGAGAGTCTGGAGCAAACAACCGTTs-2t27f,A10,TGTAGATGCATCAAAAATAATTCGAAATTGTAs-2t29f,B10,CGATTAAGCGCACTCCAGCCAGCTCACGTTGGs-2t31f,C10,TGCGTTGCTGCCTGCAGGTCGACTCTGCAAGGs-2t5g,D10,GGGATAGCAAGTTTCGTCACCAGTACATGTAGCATs-2t7a,E10,AACGCCAACTACs-2t9a,F10,GTAAATACGTTAs-3t12g,G10,ATTTCTTAAACs-3t16e,H10,GGTGTACAGTGAATAAGGCTTGCCACCAGACGs-3t18e,A11,ACGATAAACATAAATATTCATTGACCTTTTGAs-3t20e,B11,TAAGAGGTATTCCATATAACAGTTGGCAAGGCs-3t22e,C11,AAAGAATTTTCAACGCAAGGATAACCATCAATs-3t24e,D11,ATGATATTCAAGAGAATCGATGAAGTATAAGCs-3t26e,E11,AAATATTTCGTCTGGCCTTCCTGTCCGTAATGs-3t28e,F11,GGATAGGTTTCCGGCACCGCTTCTGCGAAAGGs-3t30e,G11,GGGATGTGCTAGAGGATCCCCGGGATGAGTGAs-3t32e,H11,GCTAACTCCAGCTGCATTAATGAAGCAAGCGG

s-3t34b,A12,CCCCAGGGTTTGs-3t34e,B12,TCCACGCTCAGGCGAAAATCCTGTs-4t13g,C12,AGCTTGATACCATCGTCACCCTCAGCAAGATGAACs-4t15f,D12,AAGAGGACGCGAAAGACAGCATCGs-4t17f,E12,CCTCGTTTCTGACGAGAAACACCAAACTTTGAs-4t19f,F12,TAATTGCTATCCCCCTCAAATGCTATCATAACs-4t21f,G12,ATCATACAGATTCCCAATTCTGCGAGTACCTTs-4t23f,H12,TCAAATCAAAATTTTTAGAACCCTTCCAATAA

Plate number: 3s-4t25f,A1,GGAAGATTCGGTAATCGTAAAACTGGAGACAGs-4t27f,B1,CGGATTGAAGCCAGCTTTCATCAACAAAAACAs-4t29f,C1,GCCAGCTGGGTGCCGGAAACCAGGACAAACGGs-4t31f,D1,GGTGCCTATACCGAGCTCGAATTCGCTATTACs-4t33f,E1,GAGTTGCATCGGCCAACGCGCGGGAAGCCTGGs-4t35f,F1,TTGATGGTGGTTCCGACCCTGAGAs-5t14e,G1,GAACGAGGGTAGCAACGGGAACCGs-5t16e,H1,AACTGACCGAACGAGTAGTAAATTTAGTAAGAs-5t18e,A2,GCAACACTTTAAACAGTTCAGAAACAGGTCAGs-5t20e,B2,GATTAGAGAACGAGTAGATTTAGTAGTAGTAGs-5t22e,C2,CATTAACACATATATTTTAAATGCAAGGGTGAs-5t24e,D2,GAAAGGCCAGCATGTCAATCATATATAATCAG

s-5t26e,E2,AAAAGCCCCATTAAATGTGAGCGACGGATTCTs-5t28e,F2,CCGTGGGACAAAGCGCCATTCGCCCGGTGCGGs-5t30e,G2,GCCTCTTCGTAATCATGGTCATAGGGAAGCATs-5t32e,H2,AAAGTGTAGAGAGGCGGTTTGCGTGCCCTTCAs-5t34e,A3,CCGCCTGGAATCGGCAAAATCCCTTGGACTCCs-5t36b,B3,AAAAACAGGGCGs-5t36e,C3,AACGTCAACGTCTATCAGGGCGATs-6t15f,D3,AATCATAAGGCTACAGAGGCTTTGs-6t17f,E3,ACGAGGCAGGGCTTGAGATGGTTTAGACGGTCs-6t19f,F3,AACTCCAAACGAGAATGACCATAAAAGGAATTs-6t21f,G3,CTACTAATTTGACCATTAGATACACGGAAGCAs-6t25a,H3,CGGTTGGTACCCs-6t27a,A4,ACCCGTGTAACAs-6t29f,B4,AGGGCGATATTCAGGCTGCGCAACs-6t31f,C4,TACGAGCCCTGTTTCCTGTGTGAATGTTGGGAs-6t33f,D4,AGCTGATTATTGGGCGCCAGGGTGACACAACAs-6t35f,E4,AAAGAACGTATAAATCAAAAGAATCGGGCAACs-6t37f,F4,GGCCCACTACGTGAACCCACTATTs-7t14e,G4,AGGACTAAAGACTTTTAGCCGGAAs-7t16e,H4,CGAGGCGCAATTTCAACTTTAATCAGATACATs-7t18e,A5,AACGCCAAATCAAAAATCAGGTCTTCAAAGCGs-7t20g,B5,AACCAGACTTTCGCAAATGGTCAACGAGCTGAAAAGGTGGs-7t24g,C5,GTAGGTAAAGATTCAAAATGCCTGAGTAATGTCATCAATTs-7t30g,D5,ATTGTTATCCGs-7t36e,E5,ACAAGAGTCATCACCCAAATCAAGATCGGAAC

s-7t38b,F5,CCGATTGAGCCCs-7t38e,G5,CCTAAAGGTAGAGCTTGACGGGGAs-8t15f,H5,TGTTACTTTCATGAGGAAGTTTCCs-8t17f,A6,ACTAATGCATTGTGAATTACCTTACTGCTCCAs-8t19f,B6,TTCGAGCTTTACCCTGACTATTATCACATTCAs-8t31h,C6,CTCACAATTCCGTTTTTCTTTTs-8t33g,D6,CACCAGTGAGAAGCCCGAGATAGGGTTAGTTTGGAs-8t35a,E6,TGTTCCGAGTGTs-8t37f,F6,AGCACTAATTTTTTGGGGTCGAGGs-9t14e,G6,ATTAAACGGGTAAAATTGTCGAAAs-9t16e,H6,TCCGCGACTGCGATTTTAAGAACTTGAGATTTs-9t18g,A7,AGGAATACAGTCAGAAGCAAAGCGAAGACTTCAAATATCGs-9t22g,B7,ATTTTCATTTGGGGCGTAACCTGTTTAGCTATCGTTTTAAs-9t40g,C7,CGAGAAAGGAAGGGAAAAGCCGGCGAACGTGGTGCCGTAAst-rem1,D7,GCGCTTAATGCGCCGCTACA

Supplementary Figure S24: Sequences for the star.

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a b

c

Supplementary Figure S25: More design details of the 3-hole disk (smiley). a, Block diagram. b, Reproduction of thefolding path. c, Block diagram with all colors and notations removed. In a , turns that occur between columns of red blocksand orange blocks have offset 0 with respect to the underlying crossover lattice. Other turns on the left and right outer edgeshave +1 or -1 offsets depending on which side of the smiley they occur. Purple and green half-blocks show that scaffold turnsmade at most seams or on the interior of voids are an odd number of 1 / 2 DNA turns away from scaffold turns on the outeredges. A pair of columns with alternating light and dark orange and red blocks marks a seam of 0 offset, placed 1.5 turns tothe left of the central seam.

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Supplementary Figure S26: Crossover diagram for the disk with holes (smiley) with a high resolution zoom out of Fig. 2: d3for comparison of ne structure. Some tip damage has occurred to the right eye of the righthand smiley.

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Supplementary Figure S27: Diagram showing how the smileys stick together to maximize the number of blunt end stackinginteractions. Compare to previous Supplementary Fig. S26.

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25 turns wide at 10.4 bases/turn -> 260 bases9 helices / domain, 27 helices in alll

a b

Supplementary Figure S29: Schematics for the triangle Fig. 2e. a Block diagram. Designed for 2.5-turn spacing blocks have5 different offsets with respect to the underlying lattice of crossovers, hence the 5 different hues of blocks in different columns.As in other block diagrams, orange block/red block boundaries have an offset of 0 turns with respect to the underlying latticeof crossovers. b Folding path.

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Supplementary Figure S30: Crossover diagram for the equilateral composed of rectangular domains.

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Plate number: 1e0t11d,A1,CATAGTTAGCGTAAATCGATGAACGGe0t13c,B1,GCCGACAATGACACTGTAATACTTTTe0t13d,C1,GAGCAAACAAGAGACGATCTAAAGTTe0t15c,D1,ACTCATCTTTGACTCATTCCATATAAe0t15d,E1,AAACATTATGACCACAACCATCGCCCe0t17c,F1,AATCAACGTAACATATTATAGTCAGAe0t17d,G1,GTGTCTGGAAGTTCCCCAGCGATTATe0t19c,H1,CTAATGCAGATACATAACGCCAAAAGe0t19d,A2,TCTTTACCCTGACAAGCTGCTCATTCe0t1d,B2,CAATAGTGAATTTTGCTCAGTACCAGe0t21d,C2,TAACAACCCGTCGAATCGCGCAGAGGe0t23c,D2,CCAGCTGGCGAAAAGAAGGAGCGGAAe0t23d,E2,TACCAAGTTACAAGATTCTCCGTGGGe0t25c,F2,AGCTAACTCACATACCTCAAATATCAe0t25d,G2,CAAAGAAACCACCGGGGGATGTGCTGe0t27c,H2,CGGCAAAATCCCTTAAAAGGGACATTe0t27d,A3,ATCACCTTGCTGATAATTGCGTTGCGe0t29c,B3,GAAAGGAAGGGAAATAATCAGTGAGGe0t29d,C3,ACACGACCAGTAATATAAATCAAAAGe0t3c,D3,GTATCATATGCGTATTCACAAACAAAe0t3d,E3,ATTAGCGGGGTTTATCAAAATCATAGe0t5c,F3,CCATCCTAATTTAATCAAGTTTGCCTe0t5d,G3,GATTGGCCTTGATTATACAAATTCTTe0t7c,H3,CTATTTTGCACCCAAGTTTATTTTGTe0t7d,A4,CAGTAGCGACAGACGAGCATGTAGAAe0t9c,B4,AGAGAGATAACCCACAAGAATTGAGTe0t9d,C4,GACACCACGGAATAGCTACAATTTTAe1t10e,D4,TAAGCCCAATAATAAGAGCAAGAAACe1t12a,E4,TAATCGTAAAACTGCCTGAGAGTCTGe1t12b,F4,CTATCAGGTCATTAGCATGTCAATCAe1t14a,G4,GCGGGAGAAGCCTTCGGTTGTACCAAe1t14b,H4,GCATAAAGCTAAATTATTTCAACGCAe1t16a,A5,CAGTTGATTCCCACAACTAAAGTACGe1t16b,B5,TGTTTTAAATATGATTCTGCGAACGAe1t18a,C5,AGCAAAGCGGATTATCAAAAATCAGGe1t18b,D5,AGAATGACCATAAGCATCAAAAAGATe1t20e,E5,GAATTACGAGGCATAGTAAGAGCAACe1t22a,F5,CGAATTATTCATTTGATTGCTTTGAAe1t22b,G5,TAACGGATTCGCCTCAATTACCTGAGe1t24a,H5,TTATCATCATATTTCATTTTGCGGAAe1t24b,A6,TTGAGTAACATTACCTGATTATCAGAe1t26a,B6,AACCCTCAATCAAAAAAATCTAAAGCe1t26b,C6,CCAGCAGCAAATGTATCTGGTCAGTTe1t28a,D6,CTGGCCAACAGAGAGATTCACCAGTCe1t28b,E6,TATTTACATTGGCATAGAACCCTTCTe1t2a,F6,GCGGATAAGTGCCGAGAAGGATTAGGe1t2b,G6,TGAGACTCCTCAAGTCGAGAGGGTTGe1t30e,H6,CCACCGAGTAAAAGAGTCTGTCCATCe1t4a,A7,TAAATCCTCATTAAGGCAGGTCAGACe1t4b,B7,TGACAGGAGGTTGAAGCCAGAATGGAe1t6a,C7,TTAGCGTCAGACTGCAGCACCGTAATe1t6b,D7,GAAACCATCGATAGTAGCGCGTTTTCe1t8a,E7,CACAATCAATAGAAAAGAAACGCAAAe1t8b,F7,GTGGCAACATATAAAATTCATATGGTe2t11e,G7,TATGTACCCCGGTTGATAATCAGAAAe2t13a,H7,AGGATAAAAATTTAGATCTACAAAGGe2t13b,A8,AGCTATTTTTGAGTTAGAACCCTCATe2t15a,B8,GTAGATTTAGTTTATAAAGCCTCAGAe2t15b,C8,GCAAAATTAAGCAGACCATTAGATACe2t17a,D8,TAAGAGGAAGCCCCTGTAGCTCAACAe2t17b,E8,GCTGAATATAATGGAAAGACTTCAAAe2t19a,F8,ACTATCATAACCCAGTTCAGAAAACGe2t19b,G8,AAATGCTTTAAACTCGTTTACCAGAC

e2t1e,H8,ATATAAGTATAGCCCGGAATAGGTGTe2t21e,A9,CAAAAGAAGATGATGAAACAAACATCe2t23a,B9,TGATGGCAATTCATCGGGAGAAACAAe2t23b,C9,AGTACCTTTTACATCAATATAATCCTe2t25a,D9,GGCAAATCAACAGTAATTTTAAAAGTe2t25b,E9,GCCCGAACGTTATTTGAAAGGAATTGe2t27a,F9,GACCTGAAAGCGTGCCACGCTGAGAGe2t27b,G9,CGCCTGCAACAGTAAGAATACGTGGCe2t29a,H9,ACGCAAATTAACCGTCTGAAATGGATe2t29b,A10,TTGACGCTCAATCGTTGTAGCAATACe2t3a,B10,AAGCGCAGTCTCTAGTATTAAGAGGCe2t3b,C10,TCTGAAACATGAAGAATTTACCGTTCe2t5a,D10,ATCGGCATTTTCGCCGCCGCCAGCATe2t5b,E10,ACCACCACCAGAGGTCATAGCCCCCTe2t7a,F10,TTACCAGCGCCAAAAACGTCACCAATe2t7b,G10,TTAGCAAGGCCGGAGACAAAAGGGCGe2t9a,H10,AATGAAATAGCAATACATACATAAAGe2t9b,A11,CAAACGTAGAAAATAGCTATCTTACCe3t10e,B11,GAAGCCCTTTTTAAGAAAAGTAAGCAe3t12a,C11,AGCCCCAAAAACATGCCGGAGAGGGTe3t12b,D11,GCTGATAAATTAAGGAAGATTGTATAe3t14a,E11,ATATTTTAAATGCAGGCAAAGAATTAe3t14b,F11,AATCATACAGGCAAATGCCTGAGTAAe3t16a,G11,ATTTCGCAAATGGTTAGAGCTTAATTe3t16b,H11,TTTTGCGGATGGCTCAATAACCTGTTe3t18a,A12,TATCGCGTTTTAATTGAATCCCCCTCe3t18b,B12,TCATAAATATTCATTCGAGCTTCAAAe3t20e,C12,GACGATAAAAACCAAAATAGCGAGAGe3t22a,D12,AAGAAAACAAAATAATATACAGTAACe3t22b,E12,TTAACGTCAGATGTAATTACATTTAAe3t24a,F12,GATTGTTTGGATTTATTAAATCCTTTe3t24b,G12,ATTCGACAACTCGATACTTCTGAATAe3t26a,H12,AGGAAGGTTATCTTCAGTATTAACAC

Plate number: 2e3t26b,A1,AGAGGTGAGGCGGAAAATATCTTTAGe3t28a,B1,ACAGACAATATTTAAATACCTACATTe3t28b,C1,AAAACGCTCATGGTTGAATGGCTATTe3t2a,D1,ATCACCGTACTCACGGAACCTATTATe3t2b,E1,CCCCTGCCTATTTGGAGGTTTAGTACe3t30e,F1,TTCTTTGATTAGTAATAACATCACTTe3t4a,G1,CAGTAAGCGTCATAGCCGCCACCAGAe3t4b,H1,CCACCACCCTCAGACATGGCTTTTGAe3t6a,A2,TATTAGCGTTTGCAGCACCATTACCAe3t6b,B2,CAAAATCACCAGTCATCTTTTCATAAe3t8a,C2,ACATTCAACCGATCGCAGTATGTTAGe3t8b,D2,AGACTCCTTATTATGAGGGAGGGAAGe4t11e,E2,AGCAAATATTTAAATTGTAAACGTTAe4t13a,F2,TGTGTAGGTAAAGTTCAACCGTTCTAe4t13b,G2,CATCAATATGATAATTCAAAAGGGTGe4t15a,H2,TAGCTATATTTTCTTAACATCCAATAe4t15b,A3,AATAGTAGTAGCAATTTGGGGCGCGAe4t17a,B3,GCGAACCAGACCGGATAAGAGGTCATe4t17b,C3,AATTGCTCCTTTTGAAGCAAACTCCAe4t19a,D3,GCTTTTGCAAAAGTACTGCGGAATCGe4t19e,E3,GGATAGCGTCCAAAAGTTTTGCCAGAGGGGGTAATAGTAe4t1e,F3,CGCCACCCTCAGAACCGCCACCCTCAe4t21e,G3,CAATTTCATTTGAATTACCTTTTTTAe4t23a,H3,ATGGAAGGGTTAGTAGATTTTCAGGTe4t23b,A4,TAAAGAAATTGCGAACCTACCATATCe4t25a,B4,GAGCACTAACAACGACTTTACAAACAe4t25b,C4,TTTAGAAGTATTATAATAGATTAGAGe4t27a,D4,AGTCTTTAATGCGCAGAAGATAAAACe4t27b,E4,AACGAACCACCAGCGAACTGATAGCCe4t29a,F4,GCCTGAGTAGAAGCATTGCAACAGGAe4t29e,G4,TATTACCGCCAGCAACTCAAACTATCGGCCTTGCTGGTAe4t3a,H4,TGATACAGGAGTGAAACAGTTAATGCe4t3b,A5,ACAGTGCCCGTATTACTGGTAATAAGe4t5a,B5,TCAAAATCACCGGGCCACCCTCAGAGe4t5b,C5,CACCCTCAGAACCAACCAGAGCCACCe4t7a,D5,GTAAATATTGACGGAATTAGAGCCAGe4t7b,E5,TTGAGCCATTTGGGAAATTATTCATTe4t9a,F5,GATAGCCGAACAAACTGGCATGATTAe4t9e,G5,AATACCCAAAAGAAGTTACCAGAAGGAAACCGAGGAAACe5t12a,H5,ATATTTTGTTAAAACAGTCAAATCACe5t14a,A6,AGAAAGGCCGGAGCATCAATTCTACTe5t16a,B6,GCTGAAAAGGTGGAGAGAGTACCTTTe5t18a,C6,ACAGGTCAGGATTAAATGTTTAGACTe5t22a,D6,ATGGAAACAGTACCGTAAAACAGAAAe5t24a,E6,AAAATTATTTGCAATACATTTGAGGAe5t26a,F6,CCGTCAATAGATAATTAAAAATACCGe5t28a,G6,CTAAAACATCGCCATATCCAGAACAAe5t2a,H6,GAACCGCCACCCTAGTGCCTTGAGTAe5t4a,A7,TTTTAACGGGGTCCCCTCAGAGCCGCe5t6a,B7,ACCGGAACCGCCTCACCGTCACCGACe5t8a,C7,AAAGGTGAATTATGCAATAATAACGGe-1t10e,D7,TCAGAGGGTAATTGAGCGCTAATATCe-1t12a,E7,GCCTGTAGCATTCAGACGTTAGTAAAe-1t12b,F7,TTGTCGTCTTTCCCACAGACAGCCCTe-1t14a,G7,TTAAACAGCTTGAATATTCGGTCGCTe-1t14b,H7,ACGCATAACCGATTACCGATAGTTGCe-1t16a,A8,AAAGAGGCAAAAGCAAAGTACAACGGe-1t16b,B8,ACCAAGCGCGAAAAATACACTAAAACe-1t18a,C8,GACAAGAACCGGATGCCCTGACGAGAe-1t18b,D8,AGTGAATAAGGCTTATTCATTACCCAe-1t20e,E8,TTGAGATTTAGGAATACCACATTCAAe-1t22a,F8,TTTCATCAACATTTTGACCGTAATGGe-1t22b,G8,AACAAACGGCGGAAAATGTGAGCGAG

e-1t24a,H8,TCGGTGCGGGCCTTTGGGTAACGCCAe-1t24b,A9,CAAGGCGATTAAGCTTCGCTATTACGe-1t26a,B9,GTAAAGCCTGGGGTTCCAGTCGGGAAe-1t26b,C9,CTCACTGCCCGCTTGCCTAATGAGTGe-1t28a,D9,ATCCTGTTTGATGAGGGTTGAGTGTTe-1t28b,E9,AATAGCCCGAGATGTGGTTCCGAAATe-1t2a,F9,GCTTAGATTAAGACCTTTTTAACCTCe-1t2b,G9,GTCTGAGAGACTACGCTGAGAAGAGTe-1t30e,H9,ACGGGGAAAGCCGGCGAACGTGGCGAe-1t4a,A10,CATAATTACTAGACAACGCTCAACAGe-1t4b,B10,ACCAGTATAAAGCAAAAGCCTGTTTAe-1t6a,C10,AAGTCCTGAACAACGGCTGTCTTTCCe-1t6b,D10,ACCAATCAATAATGAAAAATAATATCe-1t8a,E10,TTGAAGCCTTAAACAACGCTAACGAGe-1t8b,F10,TCCTGAATCTTACTCAAGATTAGTTGe-2t11e,G10,GTTTCGTCACCAGTACAAACTACAACe-2t13a,H10,ATCAGCTTGCTTTTGGGATTTTGCTAe-2t13b,A11,TGAATTTTCTGTACGAGGTGAATTTCe-2t15a,B11,CACTACGAAGGCAAGTTAAAGGCCGCe-2t15b,C11,GAGGCTTGCAGGGCCAACCTAAAACGe-2t17a,D11,GGCTGACCTTCATCGCCTGATAAATTe-2t17b,E11,AGATTTGTATCATCAAGAGTAATCTTe-2t19a,F11,TTATTACAGGTAGGTAGTAAATTGGGe-2t19b,G11,AACACCAGAACGAAAAGATTCATCAGe-2t1e,H11,TTAGAATCCTTGAAAACATAGCGATAe-2t21e,A12,TCGCGTCTGGCCTTCCTGTAGCCAGCe-2t23a,B12,GGCTGCGCAACTGGGTGTAGATGGGCe-2t23b,C12,GATAGGTCACGTTTTGGGAAGGGCGAe-2t25a,D12,CAACATACGAGCCCACGACGTTGTAAe-2t25b,E12,GGGTTTTCCCAGTGGAAGCATAAAGTe-2t27a,F12,ACGCTGGTTTGCCGCTGCATTAATGAe-2t27b,G12,ACCTGTCGTGCCACCAGCAGGCGAAAe-2t29a,H12,AAAGGGAGCCCCCACAAGAGTCCACT

Plate number: 3e-2t29b,A1,GTTCCAGTTTGGAGATTTAGAGCTTGe-2t3a,B1,CGTTAAATAAGAAGTTATATAACTATe-2t3b,C1,CGGCTTAGGTTGGTAAACACCGGAATe-2t5a,D1,AACGCGCCTGTTTAGAATCGCCATATe-2t5b,E1,TAGGGCTTAATTGATCAACAATAGATe-2t7a,F1,GCGAACCTCCCGAAACGGGTATTAAAe-2t7b,G1,TTATCATTCCAAGCTTGCGGGAGGTTe-2t9a,H1,GAATTAACTGAACCCTAATTTGCCAGe-2t9b,A2,CGTCTTTCCAGAGACCCTGAACAAAGe-3t10e,B2,AAAACAGGGAAGCGCATTAGACGGGAe-3t12a,C2,TAGGAACCCATGTAGTTTCAGCGGAGe-3t12b,D2,AACAACTTTCAACACCGTAACACTGAe-3t14a,E2,AAAGGAGCCTTTATCACCCTCAGCAGe-3t14b,F2,TTTTGCGGGATCGATTGTATCGGTTTe-3t16a,G2,CATTAAACGGGTACGACCTGCTCCATe-3t16b,H2,GTGTCGAAATCCGAAATACGTAATGCe-3t18a,A3,CGGTGTACAGACCAATTTCAACTTTAe-3t18b,B3,CTTGAGATGGTTTAGGCGCATAGGCTe-3t20e,C3,TAATAAAACGAACTAACGGAACAACAe-3t22a,D3,CCAATAGGAACGCGCATCTGCCAGTTe-3t22b,E3,GCATCGTAACCGTCATCAAAAATAATe-3t24a,F3,CCAGGCAAAGCGCGCCAAGCTTGCATe-3t24b,G3,AACGACGGCCAGTCATTCGCCATTCAe-3t26a,H3,AATTGTTATCCGCCGGGGAGAGGCGGe-3t26b,A4,ATCGGCCAACGCGTCACAATTCCACAe-3t28a,B4,CCTGAGAGAGTTGGACTCCAACGTCAe-3t28b,C4,ATTAAAGAACGTGCAGCAAGCGGTCCe-3t2a,D4,AATCGTCGCTATTTGCAAATCCAATCe-3t2b,E4,ATGTAAATGCTGAAATTAATTTTCCCe-3t30e,F4,GCCGTAAAGCACTAAATCGGAACCCTe-3t4a,G4,AAATACCGACCGTCATGTAATTTAGGe-3t4b,H4,TTAACAACGCCAAGTGATAAATAAGGe-3t6a,A5,ATAAACAACATGTTCATCGAGAACAAe-3t6b,B5,CCAAGTACCGCACTCAGCTAATGCAGe-3t8a,C5,GTATTCTAAGAACAGCCATATTATTTe-3t8b,D5,TTACAAAATAAACGCGAGGCGTTTTAe-4t11e,E5,CTCATTTTCAGGGATAGCAAGCCCAAe-4t13a,F5,TGAAAATCTCCAAGAACAACTAAAGGe-4t13b,G5,TGAGAATAGAAAGAAAAAAGGCTCCAe-4t15a,H5,TAAAGACTTTTTCCGGAACGAGGGTAe-4t15b,A6,CGAAAGACAGCATATGAGGAAGTTTCe-4t17a,B6,ACCAACTTTGAAAAACGAGGCGCAGAe-4t17b,C6,GTTACTTAGCCGGGAGGACAGATGAAe-4t19b,D6,ATCATTGTGAATTGAAAAATCTACGTe-4t1e,E6,TGTGAGTGAATAACCTTGCTTCTGTAe-4t21e,F6,TTTTGTTAAATCAGCTCATTTTTTAAe-4t23a,G6,TCCGGCACCGCTTACAGTATCGGCCTe-4t23b,H6,TGAGGGGACGACGCTGGTGCCGGAAAe-4t25a,A7,CATGGTCATAGCTCTCTAGAGGATCCe-4t25b,B7,GCCTGCAGGTCGAGTTTCCTGTGTGAe-4t27a,C7,CAGCTGATTGCCCCGCCAGGGTGGTTe-4t27b,D7,TTTGCGTATTGGGTTCACCGCCTGGCe-4t29b,E7,AAGGGCGAAAAACTTGGGGTCGAGGTe-4t3a,F7,TCTTCTGACCTAACGCGAGAAAACTTe-4t3b,G7,GCAAGACAAAGAAATTTAATGGTTTGe-4t5a,H7,AAAGTAATTCTGTGAGCCAGTAATAAe-4t5b,A8,CAGAGGCATTTTCCCAGACGACGACAe-4t7a,B8,CAAATCAGATATAATTTTCATCGTAGe-4t7b,C8,GCAAGCCGTTTTTGAAGGCTTATCCGe-4t9b,D8,ATCCCAATCCAAAAGAGAATAACATAe-5t10e,E8,AAAAATGAAAATAGCAGCCTTTACAGTAAGAAACGATTTe-5t12b,F8,AATTGCGAATAATCAGAGCCACCACCe-5t14b,G8,GCAACGGCTACAGAATTTTTTCACGT

e-5t16b,H8,CGGTCAATCATAAAGGCTTTGAGGACe-5t18b,A9,TTAAGAACTGGCTGGGAACCGAACTGe-5t20e,B9,CATTATACCAGTCAGGACGTTGGGAAACCTTATGCGATTe-5t22b,C9,CAGGAAGATCGCAATTCGCATTAAATe-5t24b,D9,CCGGGTACCGAGCCTCCAGCCAGCTTe-5t26b,E9,TTTCTTTTCACCATCGAATTCGTAATe-5t28b,F9,GATGGCCCACTACGTGAGACGGGCAAe-5t2b,G9,TTTCAAATATATTATAAATCAATATAe-5t30e,H9,GTGAACCATCACCCAAATCAAGTTTTCGTCTATCAGGGCe-5t4b,A10,GAGAATATAAAGTTTAGTTAATTTCAe-5t6b,B10,GAATCATTACCGCACCGACAAAAGGTe-5t8b,C10,TTTGTTTAACGTCGCCCAATAGCAAGet-rem1,D10,ACGCCAGAATCCTGAGAAGTGTTTTTet-rem2,E10,TTAAAGGGATTTTAGACAGGAACGGTet-rem3,F10,AGAGCGGGAGCTAAACAGGAGGCCGAet-rem4,G10,TATAACGTGCTTTCCTCGTTAGAATCet-rem5,H10,GTACTATGGTTGCTTTGACGAGCACGet-rem6,A11,GCGCTTAATGCGCCGCTACAGGGCGC

Supplementary Figure S31: Sequences for the equilateral composed of rectangular domains.

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For bridges between trapezoidal slant edgescontact type, name, and sequence1, t-5s2e-t6s23c-3T,A6, TTAATTAATTTTTTACCATATCAAA2, t-7s4e-t8s25c-2T,B6, TTAATTTCATCTTAGACTTTACAA3, t-9s6e-t10s27c-1T,C6, CTGTCCAGACGTATACCGAACGA4, t-11s8e-t12s29c-0T,D6, TCAAGATTAGTGTAGCAATACT

1, t-5s12e-t6s3c-3T,E6, TGTAGCATTCCTTTTATAAACAGTT2, t-7s14e-t8s5c-2T,F6, TTTAATTGTATTTCCACCAGAGCC3, t-9s16e-t10s7c-1T,G6, ACTACGAAGGCTTAGCACCATTA4, t-11s18e-t12s9c-0T,H6, ATAAGGCTTGCAACAAAGTTAC

1, t-5s22e-t6s13c-3T,A7, GTGGGAACAAATTTCTATTTTTGAG2, t-7s24e-t8s15c-2T,B7, CGGTGCGGGCCTTCCAAAAACATT3, t-9s26e-t10s17c-1T,C7, ATGAGTGAGCTTTTAAATATGCA4, t-11s28e-t12s19c-0T,D7, ACTATTAAAGAGGATAGCGTCC

1

2

3

4

1

2

3

4

1

2

3

4

00

0

a

b c

Supplementary Figure S 32: More details of sharp triangle design. a Block design for the sharp triangle composed of trapezoidal domains. Contacts between trapezoids on their slant faces are of type 0, 1, 2, 3, and 4. Contacts of type 0 arebridged by the scaffold strand as shown in the folding path ( b ). Other contacts are bridged by special staples ( c ) that eachreplace two of the staple strands in the staple sequences (Supplementary Fig. S34), identied by the composite names of thebridging staples. Assuming a 1 nm inter-helix gap and 32 bases/3 turns, I calculated that the contacts would have gaps of width of 1.5696 nm, 1.0822 nm, 0.5944 nm, 0.1070 nm for contact types 1,2,3, and 4. (The gap widths drawn in the block

diagram above are not accurate; contact type 4 has essentially no gap given an inter-helix gap of 1 nm.) Assuming that anunpaired thymine can bridge .43 nm (the length per base-pair of single stranded DNA 34 ), this would require adding 3.7, 2.5,1.4, or 0.25 Ts in the bridging staple for each contact point. In fact, 4T loops are often used to bridge 2 nm wide doublehelices to make them into hairpins assuming .5 nm per T. I used 3, 2, 1, and 0 Ts for contacts of type 1, 2, 3, and 4 as canbe seen inserted into the middle of the sequence in c . As in other block diagrams, in a , turns that occur between columns of red blocks and orange blocks have offset 0 with respect to the underlying crossover lattice. Other turns on the left and rightouter edges have +1 or -1 offsets depending on which side of the trapezoid they occur. Purple and green half-blocks show thatscaffold turns made at the central seams are an odd number of DNA 1 / 2 turns away from scaffold turns on the outer edges.

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Supplementary Figure S33: Crossover diagram for the sharp triangle composed of trapezoidal domains.

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Plate number: 1t10s17c,A1,TTAAATATGCAt10s27c,B1,ATACCGAACGAt10s7c,C1,TAGCACCATTAt11s18h,D1,AATACTGCGGAATCGTAGGGGGTAATAGTAAAATGTTTAGACTt11s28h,E1,TCTTTGATTAGTAATAGTCTGTCCATCACGCAAATTAACCGTTt11s8h,F1,CAGAAGGAAACCGAGGTTTTTAAGAAAAGTAAGCAGATAGCCGt12s19c,G1,GGATAGCGTCCt12s29c,H1,GTAGCAATACTt12s9c,A2,AACAAAGTTACt1s10g,B2,GACGGGAGAATTAACTCGGAATAAGTTTATTTCCAGCGCCt1s12i,C2,TCATATGTGTAATCGTAAAACTAGTCATTTTCt1s14i,D2,GTGAGAAAATGTGTAGGTAAAGATACAACTTT

t1s16i,E2,GGCATCAAATTTGGGGCGCGAGCTAGTTAAAGt1s18i,F2,TTCGAGCTAAGACTTCAAATATCGGGAACGAGt1s20g,G2,GAATACCACATTCAACTTAAGAGGAAGCCCGATCAAAGCGt1s22i,H2,TCGGGAGATATACAGTAACAGTACAAATAATTt1s24i,A3,CCTGATTAAAGGAGCGGAATTATCTCGGCCTCt1s26i,B3,GCAAATCACCTCAATCAATATCTGCAGGTCGAt1s28i,C3,CGACCAGTACATTGGCAGATTCACCTGATTGCt1s2i,D3,CGGGGTTTCCTCAAGAGAAGGATTTTGAATTAt1s30g,E3,TTGACGAGCACGTATACTGAAATGGATTATTTAATAAAAGt1s4i,F3,AGCGTCATGTCTCTGAATTTACCGACTACCTTt1s6i,G3,TTCATAATCCCCTTATTAGCGTTTTTCTTACCt1s8i,H3,ATGGTTTATGTCACAATCAATAGATATTAAACt2s11g,A4,AGAAAAGCCCCAAAAAGAGTCTGGAGCAAACAATCACCATt2s13g,B4,ACAGTCAAAGAGAATCGATGAACGACCCCGGTTGATAATCt2s15f,C4,ATAGTAGTATGCAATGCCTGAGTAGGCCGGAGt2s17f,D4,AACCAGACGTTTAGCTATATTTTCTTCTACTAt2s1g,E4,GATAAGTGCCGTCGAGCTGAAACATGAAAGTATACAGGAGt2s21g,F4,CCTGATTGCTTTGAATTGCGTAGATTTTCAGGCATCAATAt2s23g,G4,TGGCAATTTTTAACGTCAGATGAAAACAATAACGGATTCGt2s25f,H4,AAGGAATTACAAAGAAACCACCAGTCAGATGAt2s27f,A5,GGACATTCACCTCAAATATCAAACACAGTTGAt2s3g,B5,TTTGATGATTAAGAGGCTGAGACTTGCTCAGTACCAGGCGt2s5f,C5,CCGGAACCCAGAATGGAAAGCGCAACATGGCTt2s7f,D5,AAAGACAACATTTTCGGTCATAGCCAAAATCAt3s10g,E5,GTCAGAGGGTAATTGATGGCAACATATAAAAGCGATTGAGt3s14e,F5,CAATATGACCCTCATATATTTTAAAGCATTAAt3s16e,G5,CATCCAATAAATGGTCAATAACCTCGGAAGCAt3s18g,H5,AACTCCAAGATTGCATCAAAAAGATAATGCAGATACATAAt3s20g,A6,CGCCAAAAGGAATTACAGTCAGAAGCAAAGCGCAGGTCAGt3s24e,B6,TAATCCTGATTATCATTTTGCGGAGAGGAAGGt3s26e,C6,TTATCTAAAGCATCACCTTGCTGATGGCCAACt3s28g,D6,AGAGATAGTTTGACGCTCAATCGTACGTGCTTTCCTCGTTt3s30g,E6,AGAATCAGAGCGGGAGATGGAAATACCTACATAACCCTTCt3s4e,F6,TGTACTGGAAATCCTCATTAAAGCAGAGCCACt3s6e,G6,CACCGGAAAGCGCGTTTTCATCGGAAGGGCGAt3s8g,H6,CATTCAACAAACGCAAAGACACCAGAACACCCTGAACAAAt4s11g,A7,GCAAATATTTAAATTGAGATCTACAAAGGCTACTGATAAAt4s13g,B7,CGTTCTAGTCAGGTCATTGCCTGACAGGAAGATTGTATAAt4s15f,C7,CAGGCAAGATAAAAATTTTTAGAATATTCAACt4s17f,D7,GATTAGAGATTAGATACATTTCGCAAATCATAt4s1g,E7,TAGCCCGGAATAGGTGAATGCCCCCTGCCTATGGTCAGTGt4s21g,F7,GCGCAGAGGCGAATTAATTATTTGCACGTAAATTCTGAATt4s23g,G7,GATTATACACAGAAATAAAGAAATACCAAGTTACAAAATCt4s25f,H7,TAGGAGCATAAAAGTTTGAGTAACATTGTTTGt4s27f,A8,TGACCTGACAAATGAAAAATCTAAAATATCTTt4s3g,B8,TTTAACGGTTCGGAACCTATTATTAGGGTTGATATAAGTAt4s5f,C8,CTCAGAGCATATTCACAAACAAATTAATAAGTt4s7f,D8,GGAGGGAATTTAGCGTCAGACTGTCCGCCTCCt5s10g,E8,GATAACCCACAAGAATGTTAGCAAACGTAGAAAATTATTCt5s14e,F8,TTAATGCCTTATTTCAACGCAAGGGCAAAGAAt5s16e,G8,TTAGCAAATAGATTTAGTTTGACCAGTACCTT

t5s18g,H8,TAATTGCTTTACCCTGACTATTATGAGGCATAGTAAGAGCt5s20g,A9,AACACTATCATAACCCATCAAAAATCAGGTCTCCTTTTGAt5s24e,B9,AATGGAAGCGAACGTTATTAATTTCTAACAACt5s26e,C9,TAATAGATCGCTGAGAGCCAGCAGAAGCGTAAt5s28g,D9,GAATACGTAACAGGAAAAACGCTCCTAAACAGGAGGCCGAt5s30g,E9,TTAAAGGGATTTTAGATACCGCCAGCCATTGCGGCACAGAt5s4e,F9,CCTTGAGTCAGACGATTGGCCTTGCGCCACCCt5s6e,G9,TCAGAACCCAGAATCAAGTTTGCCGGTAAATAt5s8g,H9,TTGACGGAAATACATACATAAAGGGCGCTAATATCAGAGAt6s13c,A10,CTATTTTTGAGt6s15g,B10,ATAAAGCCTTTGCGGGAGAAGCCTGGAGAGGGTAGt6s17f,C10,TAAGAGGTCAATTCTGCGAACGAGATTAAGCAt6s23c,D10,ACCATATCAAAt6s25g,E10,TCAATAGATATTAAATCCTTTGCCGGTTAGAACCTt6s27f,F10,CAATATTTGCCTGCAACAGTGCCATAGAGCCGt6s3c,G10,TATAAACAGTTt6s5g,H10,CAGAGCCAGGAGGTTGAGGCAGGTAACAGTGCCCGt6s7f,A11,ATTAAAGGCCGTAATCAGTAGCGAGCCACCCTt7s10g,B11,ATAAGAGCAAGAAACATGGCATGATTAAGACTCCGACTTGt7s14e,C11,ATGACCCTGTAATACTTCAGAGCAt7s16e,D11,TAAAGCTATATAACAGTTGATTCCCATTTTTGt7s18g,E11,CGGATGGCACGAGAATGACCATAATCGTTTACCAGACGACt7s20g,F11,GATAAAAACCAAAATATTAAACAGTTCAGAAATTAGAGCTt7s24e,G11,ACAATTCGACAACTCGTAATACATt7s26e,H11,TTGAGGATGGTCAGTATTAACACCTTGAATGGt7s28g,A12,CTATTAGTATATCCAGAACAATATCAGGAACGGTACGCCAt7s30g,B12,GAATCCTGAGAAGTGTATCGGCCTTGCTGGTACTTTAATGt7s4e,C12,GCCGCCAGCATTGACACCACCCTCt7s6e,D12,AGAGCCGCACCATCGATAGCAGCATGAATTATt7s8g,E12,CACCGTCACCTTATTACGCAGTATTGAGTTAAGCCCAATAt8s15c,F12,CCAAAAACATTt8s17g,G12,TAATTGCTTGGAAGTTTCATTCCAAATCGGTTGTAt8s25c,H12,AGACTTTACAA

Plate number: 2t8s27g,A1,CGCGAACTAAAACAGAGGTGAGGCTTAGAAGTATTt8s5c,B1,CCACCAGAGCCt8s7g,C1,AGCCATTTAAACGTCACCAATGAACACCAGAACCAt9s10h,D1,TATCTTACCGAAGCCCAAACGCAATAATAACGAAAATCACCAGt9s16e,E1,ACTAAAGTACGGTGTCGAATATAAt9s18g,F1,TGCTGTAGATCCCCCTCAAATGCTGCGAGAGGCTTTTGCAt9s20h,G1,AAAGAAGTTTTGCCAGCATAAATATTCATTGACTCAACATGTTt9s26e,H1,ACCACCAGCAGAAGATGATAGCCCt9s28g,A2,TAAAACATTAGAAGAACTCAAACTTTTTATAATCAGTGAGt9s30h,B2,GCCACCGAGTAAAAGAACATCACTTGCCTGAGCGCCATTAAAAt9s6e,C2,CCATTAGCAAGGCCGGGGGAATTAt9s8g,D2,GAGCCAGCGAATACCCAAAAGAACATGAAATAGCAATAGC

t-10s17h,E2,ACCAACCTAAAAAATCAACGTAACAAATAAATTGGGCTTGAGAt-10s27h,F2,AACTCACATTATTGAGTGTTGTTCCAGAAACCGTCTATCAGGGt-10s7h,G2,ACGACAATAAATCCCGACTTGCGGGAGATCCTGAATCTTACCAt-11s18e,H2,ATAAGGCTTGCt-11s28e,A3,ACTATTAAAGAt-11s8e,B3,TCAAGATTAGTt-12s19h,C3,CCTGACGAGAAACACCAGAACGAGTAGGCTGCTCATTCAGTGAt-12s29h,D3,ACGTGGACTCCAACGTCAAAGGGCGAATTTGGAACAAGAGTCCt-12s9h,E3,TGCTATTTTGCACCCAGCTACAATTTTGTTTTGAAGCCTTAAAt-1s10e,F3,AGAGAATAACATAAAAACAGGGAAGCGCATTAt-1s12i,G3,AGGGATAGCTCAGAGCCACCACCCCATGTCAAt-1s14e,H3,ATTTTCTGTCAGCGGAGTGAGAATACCGATATt-1s14i,A4,CAACAGTTTATGGGATTTTGCTAATCAAAAGGt-1s16e,B4,ATTCGGTCTGCGGGATCGTCACCCGAAATCCGt-1s16i,C4,GCCGCTTTGCTGAGGCTTGCAGGGGAAAAGGTt-1s18g,D4,CGACCTGCGGTCAATCATAAGGGAACGGAACAACATTATTt-1s18i,E4,GCGCAGACTCCATGTTACTTAGCCCGTTTTAAt-1s20e,F4,ACAGGTAGAAAGATTCATCAGTTGAGATTTAGt-1s22i,G4,CGCGTCTGATAGGAACGCCATCAACTTTTACAt-1s24e,H4,CAGTTTGACGCACTCCAGCCAGCTAAACGACGt-1s24i,A5,AGGAAGATGGGGACGACGACAGTAATCATATTt-1s26e,B5,GCCAGTGCGATCCCCGGGTACCGAGTTTTTCTt-1s26i,C5,CTCTAGAGCAAGCTTGCATGCCTGGTCAGTTGt-1s28g,D5,TTTCACCAGCCTGGCCCTGAGAGAAAGCCGGCGAACGTGGt-1s28i,E5,CCTTCACCGTGAGACGGGCAACAGCAGTCACAt-1s2i,F5,CCTTTTTTCATTTAACAATTTCATAGGATTAGt-1s30e,G5,CGAGAAAGGAAGGGAAGCGTACTATGGTTGCTt-1s4e,H5,TTATCAAACCGGCTTAGGTTGGGTAAGCCTGTt-1s4i,A6,TTTAACCTATCATAGGTCTGAGAGTTCCAGTAt-1s6e,B6,TTAGTATCGCCAACGCTCAACAGTCGGCTGTCt-1s6i,C6,AGTATAAAATATGCGTTATACAAAGCCATCTTt-1s8g,D6,TTTCCTTAGCACTCATCGAGAACAATAGCAGCCTTTACAGt-1s8i,E6,CAAGTACCTCATTCCAAGAACGGGAAATTCATt-2s11g,F6,CCTCAGAACCGCCACCCAAGCCCAATAGGAACGTAAATGAt-2s13g,G6,AGACGTTACCATGTACCGTAACACCCCTCAGAACCGCCACt-2s15f,H6,CACGCATAAGAAAGGAACAACTAAGTCTTTCCt-2s17f,A7,ATTGTGTCTCAGCAGCGAAAGACACCATCGCCt-2s1g,B7,AAAACAAAATTAATTAAATGGAAACAGTACATTAGTGAATt-2s21g,C7,GCTCATTTTTTAACCAGCCTTCCTGTAGCCAGGCATCTGCt-2s23g,D7,GTAACCGTCTTTCATCAACATTAAAATTTTTGTTAAATCAt-2s25f,E7,ACGTTGTATTCCGGCACCGCTTCTGGCGCATCt-2s27f,F7,CCAGGGTGGCTCGAATTCGTAAT

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Paul W. K. Rothemund- Folding DNA to create nanoscale shapes and patterns: Supplementary Notes 1-11