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

Area of Science:

• Medicinal Chemistry
• Biotechnology
• Analytical Chemistry

Background:

• DNA-encoded libraries (DELs) are crucial for hit-finding in drug discovery.
• Advances in DEL synthesis have expanded chemical space but raised concerns about DNA integrity.
• Existing DNA damage assays (qPCR, sequencing) have limitations in accuracy and consistency.

Purpose of the Study:

• To develop and validate a precise method for quantifying DNA damage during DEL synthesis.
• To assess the impact of common on-DNA chemical reactions on DNA integrity.
• To compare the new method's results with traditional DNA damage assessment techniques.

Main Methods:

• Development of an external standard method using Liquid Chromatography-Mass Spectrometry (LC-MS).
• Application of the LC-MS method to evaluate DNA damage from various on-DNA chemical reactions.
• Comparative analysis of LC-MS data against conventional quantitative PCR (qPCR) measurements.

Main Results:

• The LC-MS method provides accurate and practical quantification of DNA degradation during DEL synthesis.
• Significant disagreements were observed between the LC-MS method and traditional qPCR assessments.
• Certain chemical transformations commonly used in DEL synthesis can cause substantial DNA damage.

Conclusions:

• The developed LC-MS method offers a reliable approach for monitoring DNA integrity in DEL workflows.
• Traditional methods for assessing DNA damage in DELs may yield inconsistent or misleading results.
• Accurate DNA damage assessment is critical for optimizing DEL synthesis and ensuring data reliability.