Ultra-sensitive analyte detection through kinetic proofreading

• Applicant: Dr. Fabian Schnitter
• Subject Area: Biological and Biomimetic Chemistry ; Biochemistry
• Term: from 2023 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 525991311

Current state of the art immunosorbent assays have poor detection limits which makes the early detection of a pathological state more difficult. In addition to low sensitivity, measuring proteins is hampered by low specificity due to unspecific antibody-antigen interactions. I propose to combine DNA nanotechnology with a kinetic proofreading approach for ultrasensitive, background free analyte detection. In such an essay, short oligonucleotides would polymerize and thereby transduce a record created by the analyte into detectable, microscopic structures. The polymerization would be initiated by single molecule DNA origami seeds. Thus, the assay’s sensitivity could be pushed towards the single molecule level. Besides the promising high degree in sensitivity, high specificity should be guaranteed by a kinetic proofreading step. I foresee to filter out false-positive signals by destroying the seeds over time. But, by stabilizing the seed in the presence of an analyte, only true-positives would survive a certain time of proofreading. I plan to test the concept starting with the detection of DNA. Especially short oligonucleotides like siRNA are currently difficult to detect because of its length. Then, I will expand the assay towards proteins by estimating a model protein’s limit of detection.

• DFG Programme: WBP Fellowship
• International Connection: USA
• Host: Professor William Shih, Ph.D.