Browsing by Author "Natarajan, Ashwin"
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- Design and synthesis of a custom ssDNA scaffold for functional DNA origami devices
Kemian tekniikan korkeakoulu | Master's thesis(2024-06-17) Hakala, ElinaDNA is an intriguing biomaterial in addition to its role as a genetic carrier. DNA can be used as a construction material to form nanoscale structures. In DNA origami technique, DNA is folded into almost arbitrary shapes from a long single-stranded scaffold strand and hundreds of shorter staple strands. The scaffold plays an important role in DNA origami design, as it is the largest component of the origami structure, and its length and sequence define the size of the origami and binding of other molecules. Hence, to expand the size and to incorporate a custom sequence to the origami, the aim of this thesis is to design and synthesize a functional scaffold with tailored size and sequence. Different scaffold production methods are analyzed and compared in the literature part to select the most suitable synthesis method for the experiments. In brief, bacteriophage-based scaffold production methods typically have higher yields, whereas enzymatic and PCR-based methods help manipulate the scaffold sequences with greater ease. In this thesis, PCR-based methods were used to create a functional DNA origami scaffold with a defined sequence. Scaffold production was optimized using two promising enzymatic production methods: asymmetric PCR and T7 exonuclease based enzymatic digestion. Asymmetric PCR production worked with all the PCR templates used, whereas enzymatic digestion failed to produce expected single-stranded scaffold DNA. A custom DNA sequence was inserted into the scaffold and successful incorporation was verified by Sanger DNA sequencing. The synthesized scaffold DNA was folded into 24-helix bundle DNA origami structures and the folding was verified with transmission electron microscopy. Custom DNA origami scaffolds provide an opportunity to functionalize various molecules and overcome the size limitations of DNA origami structures. Although the production methods still need to be improved to produce scaffolds at a larger scale, custom scaffolds will greatly expand utility and applicability of DNA origami technique. - A DNA Origami-Based Chiral Plasmonic Sensing Device
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2018-12-26) Huang, Yike; Nguyen, Kha; Natarajan, Ashwin; Kuzyk, AntonAccurate and reliable biosensing is crucial for environmental monitoring, food safety, and diagnostics. Spatially reconfigurable DNA origami nanostructures are excellent candidates for the generation of custom sensing probes. Here we present a nanoscale biosensing device that combines the accuracy and precision of the DNA origami nanofabrication technique, unique optical responses of chiral plasmonic assemblies, and high affinity and selectivity of aptamers. This combination enables selective and sensitive detection of targets even in strongly absorbing fluids. We expect that the presented sensing scheme can be adapted to a wide range of analytes and tailored to specific needs.