Simple and Practical DNA Quantification Method for DNA-Encoded Library Synthesis

Abstract

Over the past three decades, DNA-encoded library (DEL) technologies have become one of the most relevant strategies for hit-finding. Recent advances in synthetic methodologies for DNA-encoded libraries rendered the increased chemical space available, but it is unknown how every variety of chemistry affects DNA’s integrity. Available assays to quantify DNA damage are restricted to electrophoresis, ligation efficiency, and mostly qPCR quantification and sequencing, which may contain predisposition and inconsistency. We developed an external standard method through LC-MS analysis to accurately quantify DNA damage throughout the chemical transformations. An assessment was conducted on on-DNA chemical reactions that are frequently employed in DEL synthesis, and these results were compared to traditional qPCR measurements. Our study provides a simple, practicable, and accurate measurement for DNA degradation during DEL synthesis. Our finding reveals substantial disagreement among the usual DNA-damaging assessment methods, which have been largely neglected so far.

Innovative On-DNA Synthesis of Sulfides and Sulfoximines: Enriching the DEL Synthesis Toolbox

“…The results indicated that only negligible DNA damage under the standard reaction conditions could be observed for both sulfide and sulfoximine formation (see section 8.1 and 8.2 of the Supporting Information for details). In parallel, we subjected a capped substrate with no predicted reactivity to the standard reaction conditions as a control experiment, and the results clearly indicated that the DNA conjugate remained intact throughout the entire synthetic route, hereby further validating the integrity of encoding DNA tags (see section 8.7 of the Supporting Information for details).…”

Development of on-DNA Formation of Benzofuran for DNA-Encoded Library Synthesis

“…To our delight, the results indicated that the reaction conditions did not cause any evident DNA damage. As well, a capped substrate with no expected reactivity was subjected to the typical coupling conditions as a control experiment, and the results demonstrated that the DNA oligo conjugate remained intact throughout the reaction process, thereby further verifying the DNA oligos’ integrity (see SI S212–S223 for details) …”

Light-induced β-hydroxy sulfone synthesis in DNA-encoded libraries

“…Moreover, a capped substrate with no predicted reactivity was exposed to the standard reaction conditions as a control experiment, and the results demonstrated that the DNA oligo conjugate remained intact throughout the reaction process, thereby further confirming the integrity of encoding DNA tags (see ESI† for details). 29…”