Digital Nucleic Acid Memory Folding Condition Optimization

Digital Nucleic Acid Memory (dNAM) is an emerging form of DNA-based computer storage, utilizing single-stranded DNA scaffolding to store data. This scaffolding is folded into a breadboard-like structure, which is tagged with fluorescent probes that can be read through super-resolution microscopy. The current folding protocol used shows a band of supercoiled excess scaffold at the top of an agarose gel run through gel electrophoresis. We hypothesize a different concentration of buffer will help to stop the scaffold from binding with itself, instead of folding. Five different concentrations of TAE will be used in the folding process, then the origami will be imaged to identify if the supercoiled scaffold band is still present. We have found a higher volume of TAE does assist the folding process, leading to a decreased volume of the present supercoiled scaffold band. Our results signify that a higher concentration of TAE could be beneficial in the folding process of the scaffold. However, further research and imaging should be done to ensure the scaffold is still folding properly.