A Solution Phase Platform to Characterize Chemical Reaction Compatibility with DNA-Encoded Chemical Library Synthesis

Abstract

DNA-encoded chemical library (DECL) synthesis must occur in aqueous media under conditions that preserve the integrity of the DNA encoding tag. While the identification of “DNA-compatible” reaction conditions is critical for the development of DECL designs that explore previously inaccessible chemical space, reports measuring such compatibility have been largely restricted to methods that do not faithfully capture the impact of reaction conditions on DNA fidelity in solution phase. Here we report a comprehensive methodology that uses soluble DNA substrates that exactly recapitulate DNA’s exposure to the chemically reactive species of DECL synthesis. This approach includes the assessment of chemical fidelity (reaction yield and purity), encoding fidelity (ligation efficiency), and readability (DNA compatibility), revealing the fate of the DNA tag during DECL chemistry from a single platform.

Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries

“…However, the compatible chemistries for DEL builds are more restricted since they are performed in water and must not significantly damage the DNA tag. 50 The largest libraries are typically formed by the combination of monomers in three or four cycles of chemistry, which tends to lead to high-MW molecules that can be unattractive starting points for chemistry teams, and it is our experience that the follow-up of hits off DNA requires first a confirmation of true binder identification and then resynthesis that (depending on available resources) can be an activation hurdle for chemistry engagement. In the experimental part of this article, we describe how we have built our internal DEL process to overcome some of these challenges and make our DEL platform a more appealing primary strategy for project teams.…”

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

“…Importantly, the integrity of the tethered DNA barcode was not impacted significantly by the employed photocatalytic manifold. This was confirmed by a bioanalytical assay, [42] which we developed specifically for evaluating potential DNA damage caused during chemical transformations. Thereby, both the encodability and the detectability of the DNA tag, before and after exposure to the respective reaction conditions, are considered to gauge the “DNA compatibility” of a new reaction.…”

“…By sequestering the DNA substrate on a quaternary ammonium ion‐based solid support, chemical transformations could be achieved under largely anhydrous conditions. Another requirement for DNA‐encoded chemistry is that the reagents and reaction conditions must not lead to the degradation or modification of the oligonucleotide as this would negatively affect the final decoding of a libary [41,42] . Lastly, reactions usually have to proceed at a rather low concentration of the DNA substrate ( c ≈1 mM).…”

DNA Encoded Libraries: A Visitor's Guide

“…[27] Another confounding issue is that reactions commonly accepted as "DNA-compatible" are in fact less compatible than previously thought. [62,64] Recently, a new method for the evaluation of reaction induced DNA degradation has shed new light on the extent of DNA damage that occurs during commonly utilized DEL reactions (Boc deprotections and Pd-mediated cross couplings). [64] Such side-reactions can affect both ligation and PCR efficiency.…”

“…Also, it is common for each library member to be purified after the first cycle of diversification . Another confounding issue is that reactions commonly accepted as “DNA‐compatible” are in fact less compatible than previously thought . Recently, a new method for the evaluation of reaction induced DNA degradation has shed new light on the extent of DNA damage that occurs during commonly utilized DEL reactions (Boc deprotections and Pd‐mediated cross couplings) .…”