Biomod/2011/Slovenia/BioNanoWizards/resultsdnatethers

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<big><big><big><big><span

style="color: black; font-weight: bold;">DNA tethers</span></big></big></big></big>

<br><br><br>

<span style="font-family: Arial;"> Potential applicability of vertical DNA origami stacks has been described in the Idea section (<a

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/ideaverticalstacks">vertical stacks</a>) as well as their potential applications for <a href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appnanoelectronics">nanoelectronics</a> in the Discussion. Stacking could be achieved either using DNA or protein tethers.

</span>

<br><br>

<span style="font-family: Arial;"> The idea behind DNA tethers is to use unique complementary single stranded sequences protruding perpendicularly from the DNA origami, where their positions on the opposing face of the other DNA origami stacking partner was decorated at the mirroring positions (<strong>Figure 1</strong>). Since we created a tube like structure in the initial attempt when we used only four tehters positioned at the four edges of the rectangle we decided to use tethering at 10 positions that are distributed asymmetrically throughout the surface of the DNA rectangle. We designed ten unique tethering sequences. We replaced the selected standard staples with the corresponding staples that were elongated with appropriate single stranded binding sequences. We separately annealed two types of rectangles that contained the first set and the second complementary set of binding sequences. Each type was ligated with T4 DNA ligase overnight at 16 °C to increase the DNA origami stability. After ligation we removed the excess staple strands with filtration. Then we measured the absorbance at 260 nm and mixed the two DNA rectangles as depicted in <strong>Figure 1</strong> at the 1:1 ratio. </span>

<br><br>

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     <td style="text-align: justify;"><span
style="font-weight: bold;">Figure 1: Schematic representation of the idea and implementation of using DNA tethers for vertical DNA origami stacks. </span> a. creation of two complementary DNA origami rectangles decorated with complementary single-stranded tethers; b. asymmetric arrangement of 10 tethering positions on two DNA origami rectangles.</td>
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<span style="font-family: Arial;"> We designed 10 unique binding sequences for DNA rectangle stacking. Set 1 comprises standard staples that were elongated with appropriate binding sequences according to their position. Each staple was added a binding sequence at their 3'-terminus except staples CS4 and ES4. Set 2 comprises binding staples composed of 10 pairs of half staples. First half staple contains the first half of the sequence from original staple and is elongated with appropriate complementary binding sequence according to its position at its 3'-terminus. The second half staple contains the rest of the original sequence. This cutting was performed so that binding sequences would protrude from the rectangle at the opposite direction while preserving rectangle orientation. </span> <br><br> <span style="font-family: Arial;"> We divided the mix into aliquots and heated them to 75, 65, 55 and 45 °C respectively. The mixtures were then allowed to cool with the rate of -1 °C/min. Measuring samples with AFM revealed total DNA origami degradation of samples heated to 75 and 65 °C. DNA rectangles were present in the sample heated up to 55 °C, but their structure was severely damaged, however, no double rectangle stacks were observed. </span>

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style="font-weight: bold;">Figure 2: a) AFM imaging of DNA origami rectangles annealed at different temperatures.</span> Complementary DNA rectangles were mixed and reannealed at 55 (a), 65 (b) and 75°C (c) to anneal DNA tethers. Although DNA rectangle structures are easily discernible, heating the sample to 55 °C already visibly damages the fold. b) and c) demonstrate the complete collapse of DNA origami structures when heated up to 65 and 75 °C respectively.</td>
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<br>

<span style="font-family: Arial;">We then tested the same approach using non-ligated DNA rectangles with an excess of the remaining staple strands. We reasoned that during the heating process some staple strands might detach from long M13 single stranded DNA and destabilize the fold. Presence of the excess staples allows them to replace the detached staples. We separately annealed two different sets of DNA origami as before, mixed them at 1:1 ratio and divided into aliquots. We then heated the aliquots to 50, 55, 60, 65 and 70 °C. Although yields were not very high, we found origami stacks in all of the samples. Origami stacks are recognizable as brighter rectangles that showed two times the height of the majority of rectangles which is clearly seen on the height profile.</span>

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style="font-weight: bold;">Figure 3: Formation of DNA origami stacks with the expected height visualized by the AFM.</span> The upper left sample was annealed from 70 °C and the lower from 60 °C. Both samples contained  perfectly arranged double layer stacks. Red arrows indicate the zigzag path of the profile extraction made with PicoImage software (Agilent). Profile clearly depicts that the height of stacks is double in size of the non-stacked DNA origami rectangles.</td>
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<br>

<span style="font-family: Arial;">Our results demonstrate that vertical DNA stacks can be made using DNA tethers and that we can produce a perfect superposition of the two DNA rectangles. Length of the DNA tether used was 20 nucleotides, which means that the maximal distance between the stacks could be around 7 nm. However in our samples the DNA was dehydrated and the DNA origami stack height collapsed to the double of the single DNA rectangle. Presumably in aqueous solution the distance should depend on the ionic strength and presence of ions, however for the fixed separation of the stacks protein tethers /spacers clearly represent a better choice.</span>

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