Chemical Biology of                       Base Excision Repair   

Welcome to the David Lab! We use chemical approaches to investigate the fascinating area of DNA repair.  Damage to DNA can result in deleterious outcomes, such as cancer and aging; fortunately, most DNA damage is repaired by DNA repair enzymes.  Our laboratory focuses on the repair of damaged DNA bases which is mediated by the process of base excision repair.  The key enzymes in this pathway are the damage-specific DNA glycosylases that search through the vast amount of normal DNA to find subtle potentially mutagenic base modifications.  Our goals are to understand the molecular details associated with the recognition and repair of DNA damage, and how these features impact mutagenesis and carcinogenesis.  As chemical biologists interested in DNA repair, we use a variety of approaches, including enzymology, synthesis of modified substrates, spectroscopy, and cell biology.  Importantly, putting these approaches together in unique ways allows connections to be made between the molecular insight derived from our in vitro studies, and how these features impact repair in cells.  Ultimately this will reveal the critical features of the DNA repair process that prevents deleterious mutations leading to cancer, and how these processes may be manipulated for beneficial therapeutic purposes.

 

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Publication of Interest

Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. Here we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge–dipole and CH–π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism5. Hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.

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News From the David LaB

  • January 2016
    The David Lab is now Green Lab Certified! Congratulations to all who made this certification possible.
  • December 2015
    The David lab welcomes Kori Lay as a new grad student!
  • January 2015
    The David lab welcomes Chandrima Majumdar as a new grad student!
  • December 2014
    The Beal Lab was crushed by the David Lab competition at the annual Christmas party
  • September 2014
    The David lab welcomes Dr. Jonathan Ashby as a new postdoc! Good luck to Jongchan Yeo with starting his Postdoc. We will miss you!
  • June 2014
    Congratulations to Dr. Ryan Woods on his new job, Dr. JongChan Yeo on his new Postdoc and Dr. Patrick Rogers on his internship!
  • May 2014
    All three of the second years have made it through their QEs! Congratulations to Nicole Chaffee, Doug Banda, and Brittany Anderson on overcoming this huge milestone!

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