Optical DNA read out for on-chip biocomputation

Domain topic

Nano-Bio Physics



There is a broad range of important multivariable, combinatorial problems such as electronic circuit optimisation, drug development, cryptography and route optimisation. These problems are very challenging to solve in a sequential manner, due to superpolynomial, and sometimes even exponential, time complexities. Developing powerful parallel computation techniques has therefore gained increasing attention in science and industry to overcome this fundamental limitation. One such approach is network-based biocomputation, where combinatorial problems are encoded into nanofabricated networks and solved by a large number of “agents”, such as molecular-motor-propelled protein filaments. Because of the highly parallel approach, combinatorial problems can be solved in polynomial time. To fully bring this method to fruition, it is highly desirable to encode information into the agents, such as fluorescent barcodes. This requires methods for automatized, single-molecule detection and analysis.

Project Description

Here, we will explore DNA labeling as a versatile method to encode the information of the travelling path of each molecular motor within the network. For this, the molecular motors will be functionalized and labelled with DNA molecules. Then, perpendicular fluidic channels will be used to flow small DNA probes, labelled with multi-color fluorophores, depending on their position within the network. The motor will incorporate these probes as it explores the network, as a unique barcode dependent on the travelling path. Furthermore, we will integrate a high sensitivity, high throughput laser assisted read out method to detect each molecule at the output of the device. Nano-optics can be used to improve the resolution of the readout method beyond diffraction.

Methodological keywords

Hydrodynamics, optical systems, detectors