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A form of nanoscale steganography exists described as DNA origami cryptography which is a technique of secure information encryption through scaffold, staple, and varying docking strand self- assembling mixtures. The all-DNA steganography based origami was imaged through high-speed DNA-PAINT super-resolution imaging which uses periodic docking sequences to eliminate the need

A form of nanoscale steganography exists described as DNA origami cryptography which is a technique of secure information encryption through scaffold, staple, and varying docking strand self- assembling mixtures. The all-DNA steganography based origami was imaged through high-speed DNA-PAINT super-resolution imaging which uses periodic docking sequences to eliminate the need for protein binding. The purpose of this research was to improve upon the DNA origami cryptography protocol by encrypting information in 2D Rothemund Rectangular DNA Origami (RRO) and 3D cuboctahedron DNA origami as a platform of self-assembling DNA nanostructures to increase the routing possibilities of the scaffold. The initial focus of the work was increasing the incorporation efficiency of all individual docking spots for full 20nm grid RRO pattern readout. Due to this procedural optimization was pursued by altering annealing cycle length, centrifugal spin rates for purification, and lengthening docking strands vs. imager poly T linkers. A 14nm grid was explored as an intermediate prior to the 10nm grid for comparison of optimized experimental procedure for a higher density encryption pattern option. Imager concentration was discovered to be a vital determining factor in effectively resolving the 10nm grids due to high concentrations of imager strands inducing simultaneous blinking of adjacent docking strands to be more likely causing the 10nm grids to not be resolved. A 2 redundancy and 3 redundancy encryption scheme was developed for the 10nm grid RRO to be encrypted with. Further experimentation was completed to resolve full 10nm DNA-origami grids and encrypt with the message ”ASU”. The message was successfully encrypted and resolved through the high density 10nm grid with 2 and 3 redundancy patterns. A cuboctahedron 3D origami was explored with DNA-PAINT techniques as well resulting in successful resolution of the z-axis through variation of biotin linker length and calibration file. Positive results for short message ”0407” encryption of the cuboctahedron were achieved. Data encryption in DNA origami is further being explored and could be an optimal solution for higher density data storage with greater longevity of media.

ContributorsSukhareva, Daria (Author) / Hariadi, Rizal (Thesis director) / Sulc, Petr (Committee member) / Matthies, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2023-05
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Mycobacterium tuberculosis is the primary bacteria responsible for tuberculosis, one of the most dangerous diseases, and top causes of death worldwide, as identified by the World Health Organization in a 2018 report. Diagnostic tools currently exist for identifying those who carry active or latent versions of the infection including chest

Mycobacterium tuberculosis is the primary bacteria responsible for tuberculosis, one of the most dangerous diseases, and top causes of death worldwide, as identified by the World Health Organization in a 2018 report. Diagnostic tools currently exist for identifying those who carry active or latent versions of the infection including chest radiographs, a Mantoux tuberculin skin test, or an acid-fast bacilli smear of sputum samples. These methods are standard in the medical community of high income countries, but pose challenges for lower-income regions of the world as well as vulnerable populations. The need for a rapid, inexpensive, and non-invasive method of tuberculosis detection is evident by the ten million that contracted and 1.6 million that died from TB in 2017 alone. In our study, we used a previously developed nanoplasmon-enhanced scattering technology combined with dark field microscopy in order to investigate the potential for a blood-based TB detection assay. Twenty-eight capture antibodies were screened using cell culture exosomes and human serum samples to identify candidates for a TB-derived exosome biomarker. Four antibodies demonstrated potential for distinguishing negative controls from positive controls in this study: anti-AG85, anti-AG85B, anti-SodA, anti-Ald. These capture antibodies displayed significant differences (p<0.05) for both cell culture exosomes and human serum samples on more than one occasion. The work is significant in its ability to distinguish potential capture antibody targets, and future experimentation may yield a technology ready for clinical settings to address the gap in current TB detection methods.
ContributorsWalls, Robert (Author) / Hu, Tony (Thesis director) / Fan, Jia (Committee member) / School of Molecular Sciences (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05