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=='''Introduction to DNA origami'''==
=='''Introduction to DNA origami'''==


==='''introduction to DNA origami'''===
==='''Introduction to DNA origami'''===
The over-all design was made using the DNA origami principle first described by Rothemund in 2006.. The design was based on a plate with active components attached to it, and a dome was designed to function as a lid to protect the functional components and to make sure that the system is only active upon activition where the lid is removed.  
The over-all design was made using the DNA origami principle first described by Rothemund in 2006.. The design was based on a plate with active components attached to it, and a dome was designed to function as a lid to protect the functional components and to make sure that the system is only active upon activition where the lid is removed.  
The origamis were made by folding the ~ 7249 base long,  single stranded M13mp18 plasmid DNA with staple strands in a self-assembly reaction. Several staple strands with the 3’ facing the desired side of the plate origami were modified with functional components before assembly.
The origamis were made by folding the ~ 7249 base long,  single stranded M13mp18 plasmid DNA with staple strands in a self-assembly reaction. Several staple strands with the 3’ facing the desired side of the plate origami were modified with functional components before assembly.

Revision as of 12:56, 19 October 2013

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Introduction to DNA origami

Introduction to DNA origami

The over-all design was made using the DNA origami principle first described by Rothemund in 2006.. The design was based on a plate with active components attached to it, and a dome was designed to function as a lid to protect the functional components and to make sure that the system is only active upon activition where the lid is removed. The origamis were made by folding the ~ 7249 base long, single stranded M13mp18 plasmid DNA with staple strands in a self-assembly reaction. Several staple strands with the 3’ facing the desired side of the plate origami were modified with functional components before assembly.

Origami plate

The design of the origami plate was inspired by Hao Yan’s work with a multilayered DNA origami. The plate was designed with a double layer to increase its stability. The goal was to design the plate so that it would be very flat and have a minimal overall twist to the structure. This was done to ensure that the plate could attach to the cell surface properly through cholesterol modifications, thereby bringing the photosensitizers close enough to the cell to be able to induce apoptosis. Furthermore, a flat, rigid structure would also allow the dome to be attached to the surface of the plate.

One side was chosen to be the ‘up-side’, which would be the side that carried the functional modifications. Several staple strands that faced the up-side were 3’ end modified with different functional groups (cholesterol, photosensitizer, peptide lock, sisiRNA).

Two different versions of the overall system were made. In the first version the plate was modified with cholesterol, to ensure attachment to the cell surface, and photosensitizers that produce cytotoxic singlet oxygen once radiated with 635 nm light.

The second version features a plate modified with sisiRNAs that are conjugated to a cell penetrating peptide and are attached to the plate with a peptide lock. This lock was designed to be cleaved by matrix metallo protease II that is overexpressed by some metastasizing cancer cells.

The staple strands used to assemble the plate was divided into several different modules, depending on their function, so that it was possible to take out one module and replace it with another if unsuccessful,. Using the different modules of modified and unmodified staple strands along with M13 DNA, the plate was assembled in a self-assembly reaction . Different plates were folded with sisiRNA-CPP conjugates annealed to the up-facing staples, and with cholesterol and photosensitizer-modified staples. Furthermore, attempts were made to connect the plate and dome to each other through the peptide lock, so that the dome could serve as the lid as intended.

Origami dome

The dome origami was designed as a lid for the plate origami. It is based on the hemisphere origami design created by Hao Yans group (as this structure allows for a cavity inside the whole origami structure where the dome is placed on top of the plate. This cavity was large enough to close in our functional modifications (cholesterol, photosensitizer, sisiRNA and peptide lock).

The dome was assembled in a self-assembly reaction. The reaction was optimized with regards to the concentration of magnesium in the self-assembly buffer and the time ramp.

After successful assembly of the dome we attempted to attach the dome to the plate an attempt was made to connect the dome and plate through the peptide lock.

Results and discussion

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</style> </head> <body> <div id="indexing"> <div id="sitemap"> <p id="sitemapTitle">SITEMAP | BIOMOD 2013 NANO CREATORS | Aarhus University</p> <div id="footer-contents"> <div class="footer-section"> <p class="footer-section-title">INTRODUCTION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus">Home, abstract, animation and video</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Introduction">Introduction</a></li </ul> </div> <div class="footer-section"> <p class="footer-section-title">RESULTS AND DISCUSSION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/System_In_Action">System in action</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">MATERIALS AND METHODS</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/System_In_Action">System in action</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Methods">Methods</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">SUPPLEMENTARY</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Team_And_Acknowledgments">Team and acknowledgments</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Optimizations">Optimizations</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Data">Supplementary data</a></li> 

                                               <li><a

href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Informations">Supplementary informations</a> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/References">References</a></li> </ul> </div> </div> <div> <p id="copyright">Copyright (C) 2013 | BIOMOD Team Nano Creators @ Aarhus University | Programming by: <a href="mailto:pvskaarup@gmail.com?Subject=BIOMOD 2013:">Peter Vium Skaarup</a>.</p> </div> </div>

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