Synthesis and Assembly of xDNA: Toward Unnatural DNA Nanostructures (Chemical Sciences)
Technical Report,01 Jul 2015,31 Oct 2018
Stanford University Stanford United States
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DNA-based self-assembling nanotechnology is a highly promising approach to making programmable structures and devices on the nanometer to micron scale. Many laboratories have made impressive progress on designing large static structures e.g. origami, tubes and structures with moving features e.g. capsules, robots. However, some limits of DNA place constraints on this technology namely, low hybridization affinity, and mishybridization due to low sequence complexity. This project in the long term was aimed at addressing these issues by testing xDNA as an alternative genetic polymer to replace DNA. xDNA forms hydrogen-bonded base pairs similar to DNA, but the bases are larger, rendering the helix wider by 2.4. xDNA hybridizes much more stably than DNA, and it contains 8 nucleotides rather than 4, increasing sequence complexity greatly. Our initial specific aims for this project included the following 1 identifying the helical repeat, rigidity, and optimal loop residues as basic structural features of xDNA 2 studying chemical and enzymatic ligation-based methods for constructing larger xDNAs, and incorporating them into DNA nanostructures 3 testing the assembly and structure of an even larger proposed new genetic form, xxDNA. As described in our early progress reports, our early work revealed that synthesis of the xDNA nucleosidecomponents was highly rate limiting the compounds require many steps, and this places a constraint on what sequences could be made, since they would need to be assembled on a DNA synthesizer. To address this issue first, we focused on 4 synthesizing monomers on larger scale esp. dxG, the most difficult monomer 5 testing whether DNA polymerases might be used to synthesize xDNA on very small scales, thus conserving monomers.
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