Biomod/2011/Slovenia/BioNanoWizards/methgeneraldesignstrategy

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style="color: black; font-weight: bold;">General design strategy</span></big></big></big></big><br>

<br><br> <span style="font-family: Arial;"> We used DNA origami rectangle proposed by P. Rothemund with a seam in the middle. We used NanoEngineer-1 for 3D design of a selected shape and to determine short staple strand sequences. The resulting structure contained <a href="http://openwetware.org/images/4/4f/DnaOrder.xlsx">216 staple strands</a> folding M13 mp18 single stranded DNA into 24 parallel lines each 27 DNA turns long. DNA rectangles formed in such a way measured approx. 70 x 100 nm. To avoid hydrophobic interactions along short sides of the rectangle we included tetra-thymidine loops or d(pT)4 into marginal right and left staple strands (to view sequences click <a href="http://openwetware.org/images/0/0b/Robni_z_%28pT%294.xls">here</a>). <br> <br> </span>

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style="font-weight: bold;">Figure 43: Rectangular DNA origami design </span></td>
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<span style="font-family: Arial;"> We also devised a coordinate system for our DNA origami by which we unambiguously named each staple strand. We determined vertical (L, a-c, S, d-f and R) and horizontal (A-F) positional bands. The exact staple strand position within a cross section of a vertical and a horizontal band was specified with numbers (1 and 2 for L and R vertical bands, 1-4 for a-c and d-f vertical bands and 1-8 for S vertical band) and visualized with appropriate colors. This enabled us to easily follow the exact position of staple strands in the model only by their names. </span><br style="font-family: Arial;">

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style="font-weight: bold;">Figure 44:</span> Each staple strand in the model was named according to the system we devised. Marginal staples at the left and right edge of rectangle were numbered 1 or 2 from top to bottom after being assigned horizontal and vertical position. For example, lower left staple in the model is named FL2 and the upper right AR1. The core staples in vertical positions a-c and d-f were colored with 4 colors. They are numbered as represented in right close-up. For example, the blue staple is named Bf4. Staples positioned around the seam of the rectangle are numbered from 1-8 as depicted in the bottom close-up. For example, orange staple is named ES2.</td>
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