Nucleic Acid‐Barcoding Technologies: Converting DNA Sequencing into a Broad‐Spectrum Molecular Counter

Abstract

The emergence of high-throughput DNA sequencing technologies sparked an immediate revolution in the field of genomics that has rippled into many branches of the life and physical sciences. The remarkable sensitivity, specificity, throughput, and multiplexing capacity that are inherent to massively parallel DNA sequencing have since motivated its use as a broad-spectrum molecular counter in small molecule and peptide-based inhibitor discovery, high-throughput biochemistry, protein and cellular detection and diagnostics, and even materials science. A key aspect of extrapolating DNA sequencing to 'non-traditional' applications is the underlying need to append nucleic acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled facile nucleic acid barcoding of proteinaceous and non-proteinaceous materials, and provide exciting examples of downstream technologies that have been made possible by DNA-encoded molecules. Considering that commercially available high-throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature for years to come, and close by proposing potential new frontiers to support this assertion.

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering

“…Understanding the molecular basis of DNA recognition by HUH-endonucleases could provide much needed solutions for bacterial antibiotic resistance resulting from HUH-endonuclease mediated horizontal gene transfer ( 17 ), as well as in the prevention or treatment of HUH-endonuclease mediated viral infections, such as geminivirus infections of plants that ravage the agricultural crop industry ( 18 , 19 ) and parvovirus B19 infections of humans ( 20 ) that are associated with a range of autoimmune diseases ( 21 , 22 ). Moreover, the ability to rationally engineer HUH-endonucleases to recognize a desired DNA sequence has huge potential in genome engineering ( 23 ) and DNA delivery applications as well as in expanding the multiplexibility of HUH-tagging to meet the demand of the recent explosion of DNA-barcoding applications ( 24–27 ).…”

Navigating the Biological‐Material Interface with the Guide of Chemical Biology

“…Considerations in experimental design, including control compounds [24,25] and biochemical validation, will be needed to fully dissect the pathways involved. Moreover, the rapidly declining cost of DNA sequencing technologies has led to a renaissance of new high‐throughput tools to characterize biological processes [26] . Approaches to adapt the readout of a binding interaction to DNA sequencing, analogous to DNA‐encoded libraries for small‐molecule screening, [27] will accelerate the characterization of in vivo material behavior and aid in the discovery of new bioactive materials [28,29] …”

Employing Photocatalysis for the Design and Preparation of DNA‐Encoded Libraries: A Case Study

“…The latter compound screening technology was conceptually introduced by Brenner and Lerner in 1992 [16] . The central idea of this innovative technology is that the synthesis of each member of an expansive compound library can be encoded by a unique, DNA‐based barcode [17] . Library members, enriched during a selection campaign, [12,18] can then be easily identified through amplification of the DNA tag by polymerase chain reaction (PCR) [19] followed by decoding via conventional DNA sequencing.…”