Biomod/2014/ASU/Project

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Biomod/2014/ASU

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Introduction


In our project we investigated the creation of a DNA antibody which is able to select and specifically bind to the 3-dimensional surface of a targeted protein of interest. We created this antibody using a flat DNA tile to which 4 aptamers, comprised of random DNA sequences, were attached (see Figure P1).



Inspiration


Our inspiration is the antibody, the body’s natural means for binding to specific surfaces on the outside of pathogens. The high selectivity and specificity of antibodies that allows them to bind to foreign invaders in vivo also makes them very useful in the lab. Many assays rely on this same selectivity and specificity to identify or target certain proteins.

We hope to create a new form of antibody made from DNA which is composed of a variable region from which extend strands that cooperatively bind a protein target and a base that orders the orientation of these strands in space.


Goals


Our goal is to use the power and flexibility of DNA nanotechnology to develop a multivalent binding surface that would mimic natural antibodies. We used alpha-thrombin as our target protein since positive control aptamers are already known (Rinker 2008). We will then move to incorporating random oligonucleotide sequences into the DNA antibody to test the selection process. After showing that DNA antibodies bind a target protein we plan to recover the DNA antibody to sequence the oligonucleotides. We aim to develop a method for creating a DNA structure and a selection method that can be applicable for use for a diverse range of proteins.

In order to prove the concept for this project we propose a few key targets:

        1. To create a DNA structure suitable for binding a target protein.

        2. To demonstrate DNA antibody binding to protein using positive control DNA strands known to

             bind alpha-thrombin.

        3. To demonstrate DNA antibody binding to protein using randomized DNA oligonucleotides.

        4. To demonstrate the recovery of the DNA antibody after binding and the amplification of the randomized

             oligonucleotide strands for confirmation by sequencing.

        5. To create a molecular dynamics simulation as a visualization tool for the project.


References


1) Rinker, S., Ke, Y., Liu, Y. Chhabra, R., Yan, H. Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. Nature Nanotechnology 3, 418-422 (2008).

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