SEEKER: CRISPR-powered keyword search engine in DNA data storage Shortened version: A search engine for DNA archives

The global demand for data storage will continue to skyrocket in the next few decades. Traditional electro-mechanical storage devices, such as hard drives, are facing challenges in recording such an unprecedented amount of data due to their limited storage density and capacity. DNA, the life’s native information storage medium, has emerged as a promising alternative to conventional storage medium to meet the era of information explosion. Polymerase chain reaction (PCR) enables selective retrieval of DNA-encoded files sharing the same primer set. However, random access is typically based on unique file identifications (IDs) rather than the actual content, preventing access to files of interest without prior knowledge of the link between the content and IDs. Therefore, it is of great importance to develop a simple yet effective method to allow content-based searching directly conducted in the storage medium, with a highly accurate and easily comprehensible return of results. 
In CRISPR systems, sequence complementarity between the guide RNA and its target enables highly specific identification of a DNA sequence, even in the presence of numerous interfering sequences. This mechanism is analogous to keyword search in a huge database. In this seminar, we will demonstrate this idea using CRISPR-Cas12a, since the hybridization between guide RNA queries and DNA target keywords triggers massive indiscriminate degradation of single-stranded DNA fluorophore-quencher (ssDNA-FQ) reporters, producing a visible search result. This method is named Search Enabled by Enzymatic Keyword Recognition (SEEKER). Using four queries, we correctly identify keywords in 40 files with a background of ~8000 irrelevant terms. Overall, SEEKER provides simple implementation of quantitative and parallel searching over the complete content stored in DNA with real-time readout. 

Learning Objectives:

1. Describe the limitations of conventional electro-mechanical storage devices in meeting future global data demands.

2. Explain how CRISPR-Cas12a enables content-based searching in DNA data storage systems through guide RNA–DNA complementarity.

3. Discuss how the SEEKER method achieves accurate, real-time keyword recognition in DNA-encoded files.