A DNA-based mechanical loop for molecular geometric footprint magnification allows ultra-sensitive detection

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Mette Galsgaard Malle


Aarhus University


DKK 1,095,654




Internationalisation Fellowships


This project aims to develop a molecular loop constructed of self-assembling DNA to study the geometrical arrangement of protein aggregations and seeds in an ultra-sensitive manner. Specifically, the early aggregation of alpha-synuclein protein will be studied, a pathogenic hallmark of Parkinson's disease. Aggregation of alpha-synuclein in selective arrangements will, using the proposed methodology, result in a rapidly growing DNA polymerization magnifying the nanoscopic structure. This offers a platform for both sensitively detecting the presence of early aggregation and seeding along with a DNA magnification of the initial patterns from the aggregation of alpha-synuclein proteins.


Sensitive detection and deconvolution of molecular patterns will convert the detection of toxic microscopic structures from a needle-in-a-haystack-search to a conspicuous detectable platform. This is particularly important for two reasons: 1) Amplification of initial molecular aggregation will provide a mechanistic understanding of aggregations seeding macroscopic structures. 2) Developing a methodology for detecting ultra-low concentrations of protein aggregation and pattern recognition is important in early-stage detection and identification of diseases such as Parkinson's disease.


Alpha-synuclein oligomers will be targeted using specific aptamer tags. This will create a nucleation fundament for rapid DNA amplification. Single-stranded DNA strings will in a highly programmable and self-assembled fashion arrange and grow into large micrometer elongated ribbon structures from the targeted protein nucleation. This offers thousands of times of mechanical magnification of the initial nucleation and thereby an easy-to-detect structure that reveals the geometrical arrangement and heterogeneity of the nucleation event. The initial nucleation will also be studied using state-of-the-art microscopy techniques such as DNA-PAINT to resolve each individual molecule arrangement to design the rapid programmable growing DNA structure for amplification.

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