Biomod/2014/ASU/Design: Difference between revisions
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<p style = "color: #000000; font-size: 16px;"><b>Aptamer Evolution:</b></p> | <p style = "color: #000000; font-size: 16px;"><b>Aptamer Evolution:</b></p> | ||
<p style = "color: #000000; font-size: 16px;">1)We use systematic evolution of ligands by exponential enrichment (SELEX) to characterize the aptamers to the target site. </p> | <p style = "color: #000000; font-size: 16px;">1)We use systematic evolution of ligands by exponential enrichment (SELEX) to characterize the aptamers to the target site. </p> | ||
<p style = "color: #000000; font-size: 16px;font-weight: | <p style = "color: #000000; font-size: 16px;font-weight:1200;"><b>Base Structure (DNA Tile) variety:</b></p> | ||
<p style = "color: #000000; font-size: 16px;">1)Shape</p> | <p style = "color: #000000; font-size: 16px;">1)Shape</p> | ||
<p style = "color: #000000; font-size: 16px;">2)Size</p> | <p style = "color: #000000; font-size: 16px;">2)Size</p> | ||
Revision as of 07:55, 23 October 2014
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Biomod/2014/ASU
From OpenWetWare
< <a href="/wiki/Biomod" title="Biomod">Biomod</a> | <a href="/wiki/Biomod/2014" title="Biomod/2014">2014</a>
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Project Design
The overall design of this project is the construction of DNA antibodies that both simulate and outperform protein antibodies regarding structural and functional properties. We divided the aim of this project into two components: structure and function.
Traditional antibodies are comprised of several immunoglobulin domains. There are both light chains (green and yellow) and heavy chains (red and blue). In total, there are 7 constant domains and 9 variable domains within the light and heavy chains. Essentially, it is the variable domain that gives the antibody special properties to bind to foreign antigens.
<img src = "http://openwetware.org/images/f/f4/Screen_Shot_2014-10-23_at_12.17.38_AM.png">
Furthermore, protein antibodies undergo VDJ recombination in which Variable, Diverse, and Joining gene segments coding the antibody can recombine in order to create diversity among the antibody structure and target specificity regarding receptors and foreign pathogens.
Even though Antibodies are structurally and functionally sound, their overall potential is quite rigid with respect to structural DNA nanotechnology. Protein antibodies are quite difficult to incorporate into DNA structures because for one, they are protein based structures and two, the have structural limitations based on their overall shape and size limitations. DNA antibodies are composed of a base unit, which in this case is a DNA tile (shown in grey) and a characterizable portion which are the aptamers (shown in red, yellow, green, and blue). The tile can accommodate a variety of aptamers and orientations as shown below:
<img src = "http://openwetware.org/images/5/54/Screen_Shot_2014-10-23_at_12.24.13_AM.png">
Using the DNA tile and aptamers, we hope to mimic the antibody-antigen model.
<img src = "http://openwetware.org/images/1/1b/Screen_Shot_2014-10-23_at_12.32.48_AM.png">
DNA Must Solve Three Things
1)The aptamer secondary structures must be characterized to the target site to induce binding.
2)The combination/orientation of the aptamers relative to each other and the target site must be situated properly for optimal binding.
3)The number of aptamers used to bind the target site may have negative effects. .
Integrating Variability and Evolution
We construct Aptamer variety by setting the following:
1)Varying length
2)Random Body Sequence
3)Secondary Structures (Based on aptamer folding)
Aptamer Evolution:
1)We use systematic evolution of ligands by exponential enrichment (SELEX) to characterize the aptamers to the target site.
Base Structure (DNA Tile) variety:
1)Shape
2)Size
3)Aptamer Insert Orientation
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