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DNA-encoded library (DEL) synthesis involves chemical reactions that can damage DNA. This study introduces a new LC-MS method to accurately quantify DNA damage, revealing significant discrepancies with traditional methods like qPCR.

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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.