Towards faster super-resolution DNA optical mapping using plasmon-enhanced fluorescence

Human microbiome science is advancing, showing promise of having important impacts on human health with new insights into disease etiology and general human biology. Accordingly, DNA sequencing platforms have been developed rapidly, expanding the scope in microbiome research.

Among others, optical mapping technique, capable of imaging single DNA molecules provides access to genetic information on single molecules up to ~1 Mbp in length.

It uses fluorescence imaging of linearly stretched DNA molecules labelled at specific sites to probe information patterns along the molecules.

The precision of the method is further improved by resolving single molecules below the diffraction limit through super-resolution imaging.

However, requirement of large photon budget slows down the speed of imaging, as long acquisitions are required to build up sufficient photons for precise localization.

This affects the throughput of DNA optical mapping which involves imaging large areas, thereby limiting its capabilities in providing real-time information of the microbiome on daily basis. Enhancing the emission rates from single molecules can overcome this limitation to permit faster image acquisition.

Here we propose to use plasmon-enhanced fluorescence by employing substrate made out of wet-chemically synthesized gold nanotriangles for optical mapping of human gut microbiome.

Plasmonic nanostructures can confine incident electromagnetic field into small area near their surface leading to strong light absorption and higher emission rates from fluorophores in their vicinity.

The use of wet-chemical plasmonic substrate exhibiting strong plasmon resonance can significantly increase the number of photons released from the labelled DNA, allowing faster image acquisition.

With the improved speed, the time required for optical mapping analysis can be significantly shortened, enabling longitudinal metagenomic analysis with practical implications for quicker diagnosis and personalized health care.