Designer DNA-based materials for DNA and virus sensing

Chauhan, Neha
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Lewis, Daniel
Shi, Yunfeng
Ullal, Chaitanya
Wang, Xing
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Materials engineering
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This electronic version is a licensed copy owned by Rensselaer Polytechnic Institute (RPI), Troy, NY. Copyright of original work retained by author.
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Over the past few decades, the use of DNA has expanded from its well-known role as a carrier of genetic information to being exploited as a nanomaterial in its own right. Central to this exciting development is the programmable nature of Watson-Crick base pairing combined with its well-characterized and predictable nanoscale structure. Nano- and micron-scale structures built out of DNA can be combined with other functional materials like inorganic nanoparticles, biomolecules, and organic molecules to form unique hybrid structures with the combined functionality of both, the DNA and the functional materials. In this thesis, two novel functional hybrid DNA-based materials are investigated. First, the important and insufficiently understood biological phenomenon of Homologous Pairing (herein, HP) is implicated in the formation of phase-separated colloidal crystals upon annealing of binary mixtures of certain short DNA grafted polystyrene particles. The effect of DNA sequence and structure on the size of the colloidal crystals and the particle fraction that forms colloidal crystals is studied. DNA with higher GC content and isotropic bendability are found to be correlated with a greater extent of crystallization and therefore predicted to have a higher incidence of HP over their counterparts. The second DNA nanomaterial platform addresses a pressing societal need in the sensing of SARS-CoV-2, the virus that causes COVID-19. A tile-based 2-dimensional DNA nanostructure that spatially organizes multiple aptamers to target the spike receptor-binding domains (RBD) of SARS-CoV-2 was designed and synthesized. The DNA net-aptamer complex superimposes both the intra- and inter-cluster spatial patterns of the receptor-binding domains for maximum binding avidity. The SARS-CoV-2 spike RBD-specific aptamer was tagged with a fluorescent reporter, along with a quencher-labeled “lock” DNA that forms a partial duplex with the aptamer. The result is a highly sensitive and highly specific optical sensor that generates a fluorescence signal upon virus binding, with a limit of detection of 10^5 viral genome copies / mL in buffer and 10^3 viral genome copies /mL in the saliva matrix, and no cross-reactivity with related coronaviruses.
August 2021
School of Engineering
Dept. of Materials Science and Engineering
Rensselaer Polytechnic Institute, Troy, NY
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