Abstract Title
DNA Origami FRET Ruler for Nucleic Acid Memory
Additional Funding Sources
This work was funded by the National Science Foundation (ECCS 1807809), the Semiconductor Research Corporation, and the State of Idaho through the Idaho Global Entrepreneurial Mission and Higher Education Research Council.
Abstract
Due to its non-volatile nature, high information density, durability, and energy efficiency, DNA is a promising material to address the growing demands for data storage. Recently our lab developed an innovative DNA data storage system: digital Nucleic Acid Memory (dNAM). dNAM uses DNA origami breadboards that encode data by using different patterns of protruding strands. These patterns are then revealed by fluorescence signals using DNA-PAINT super resolution microscopy. This technique uses dye-labelled DNA strands that transiently hybridize to the protruding ones providing a blinking signal. In this way, the data patterns are read with sub-10nm optical resolution. The dNAM prototype has introduced a completely new way for data to be stored in a two-dimensional fashion. As a future perspective, we aim to encode information on a three-dimensional plane. One possibility is to utilize fluorescence resonance energy transfer (FRET) to expand imaging to multiple dimensions and to this end, we are currently working to create a DNA origami FRET ruler. This structure carries a Cy3-Cy5 FRET fluorophore couple that will allow us to quantify distance measurements on a nanometer scale. By developing a FRET ruler of known donor-acceptor distances we can use it to calibrate fluorescence signal efficiency in 3D, utilizing it to measure FRET efficiencies between data strands. This could ultimately lead to improved data capacity and furthering innovations in three-dimensional dNAM.
DNA Origami FRET Ruler for Nucleic Acid Memory
Due to its non-volatile nature, high information density, durability, and energy efficiency, DNA is a promising material to address the growing demands for data storage. Recently our lab developed an innovative DNA data storage system: digital Nucleic Acid Memory (dNAM). dNAM uses DNA origami breadboards that encode data by using different patterns of protruding strands. These patterns are then revealed by fluorescence signals using DNA-PAINT super resolution microscopy. This technique uses dye-labelled DNA strands that transiently hybridize to the protruding ones providing a blinking signal. In this way, the data patterns are read with sub-10nm optical resolution. The dNAM prototype has introduced a completely new way for data to be stored in a two-dimensional fashion. As a future perspective, we aim to encode information on a three-dimensional plane. One possibility is to utilize fluorescence resonance energy transfer (FRET) to expand imaging to multiple dimensions and to this end, we are currently working to create a DNA origami FRET ruler. This structure carries a Cy3-Cy5 FRET fluorophore couple that will allow us to quantify distance measurements on a nanometer scale. By developing a FRET ruler of known donor-acceptor distances we can use it to calibrate fluorescence signal efficiency in 3D, utilizing it to measure FRET efficiencies between data strands. This could ultimately lead to improved data capacity and furthering innovations in three-dimensional dNAM.