Contents

The road to design completion of the QR code

· Setting of folding patterns and number of bases
· Design a simplified figure with ChemDraw
· Adjustment of seam
· Adjust seam positions not to overlap
· Calculate the number of bases (32 units) between transfer points

· Using M13 of 7560 bases (Eurofin)
· Design Y sequence by Adobe Illustrator CC 2018

· When creating in units of 32 bases, it exceeds 7560 bases. So we reduce each one base in the area surrounded by red and adjust them.
· Fill in the sequence of 7560 bases (Eurofin)

· Fill in matched strand using matched strand script
· Design a staple pattern

· It was corrected since the transfer position of the scaffold and the staple is shifted by a half pitch. As a result, we obtained a position where seam overlapped, so the shape of the staple pattern was modified not to be continuous
· Attach staple number
· Insert a sequence of hairpin between QR code position detection pattern and timing pattern (to emerge)

· Prepare staple DNA mix to design DNA QR code and mix it with M13mp18 ssDNA and 10 × TAE / Mg2+buffer. Mess up with sterile water so that M13mp18 ssDNA becomes 4 nM and staple DNA mix becomes 20 nM, and annealing (90 ˚ C for 10 min, 90 ˚ C → 25 ˚ C, -1 ˚ C / min) and DNA QR make a sample of the code. Thereafter, do ultrafiltration (50 k Amicon 15 ° C., 10000 rpm 10 min × 3 times) Then, drop 1 μl of sample and 30 μl of 1 × TAE / Mg2+buffer on mica and observe with AFM.

· This is the result of observing by AFM.

· As the shape of the QR code became a parallelogram instead of a square, we need to change the design of the QR code.
· We were able to observe that the height of the part which the dumbbell hairpin was inserted turned white.

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