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Amy Whitaker, PhD

About

Assistant Professor

Research Program

Lab Overview

Projects in the Whitaker lab aim to elucidate the molecular mechanisms coupling two key biological responses to oxidative DNA damage within G-quadruplex forming sequences. Specifically, base excision repair (BER) and the epigenic-like transcriptional regulation of key tumor suppressors and oncogenes. The long-term goal is to identify molecular targets that can be exploited to improve cancer therapies.

The primary techniques utilized in the lab include structural biology (X-ray crystallography, Cryo-EM), nucleic acid enzymology, single-molecule fluorescence microscopy, as well as human cell-based assays.

 
Education and Training

Educational Background

  • PhD, Biochemistry and Biophysics, Texas A&M University, College Station, TX, 2015
  • BS, Chemistry, University of St. Thomas, Houston, TX, 2008

Memberships

  • American Society for Biochemistry and Molecular Biology (ASBMB)
  • American Cancer Society Cancer Action Network (ACSCAN), 2018 - Present
  • Environmental Mutagenesis and Genomics Society (EMGS), 2016 - Present
  • American Association for the Advancement of Science (AAAS), 2015 - Present

Honors & Awards

  • 2nd Place Oral Presentation by a New Investigator, EMGS 52nd Annual Meeting, 2021
  • Karen and Kelly Gregg Trainee Award, 2021
  • NIH Pathway to Independence Award (K99/R00), 2020
  • American Cancer Society Postdoctoral Fellowship, 2019
  • 1st Place Oral Presentation by a New Investigator, EMGS 50th Annual Meeting, 2019
  • 1st Place Oral Presentation by a New Investigator, EMGS 48th Annual Meeting, 2017
  • 2nd Place Oral Presentation at Resident, Postdoc, and Fellow (RPF) Research Forum, 2017
Research Profile

Research Program

Research Interests

  • The epigenetic-like role of oxidative DNA lesions as transcriptional regulators of cancer-associated genes through DNA repair
  • DNA repair strategies used to complete oxidative lesion repair in G-quadruplex forming DNA sequences
  • DNA structural dynamics in response to DNA damage and repair in G-quadruplexes and other non-canonical DNA secondary structures
Lab Staff

Haley Kravitz, BS

Scientific Technician

Room: P2017
215-214-1499

Shanae Franklin, BS

Scientific Technician

Room: P2017
215-214-1499
Publications

Selected Publications

Deposited and published 30 X-ray crystal structures in the PDB (Protein Data Bank).

Xun Lu*, Sarah L. Lucas*, Amy M. Whitaker, Brittany Ripley, Todd M. Washington, Christopher B. Stanley, Bret D. Frequential, Samuel H. Wilson, and Matthew J. Cuneo. Deconvolution of complex molecular DNA repair assemblies into individual components using small-angle neutron scattering. *Co-first authors (In preparation)

Amy M. Whitaker, Wesley J. Stark, Bret. D. Freudenthal. AP-Endonuclease 1 (APE1) cleansing of DNA dirty ends. (under review at Nucleic Acids Research)

Max S. Fairlamb, Amy M. Whitaker, Fletcher E. Bain, Maria Spies, Bret D. Freudenthal. 2021. Construction of a Three-Color Prism-Based TIRF Microscope to study the Interactions and Dynamics of Macromolecules. Biology (Basel). PMID: 34201434.

Amy M. Whitaker, Bret D. Freudenthal. 2020. History of DNA polymerase β X-ray crystallography. DNA Repair (Amst). PMID: 33087265.

Amy M. Whitaker, Wesley J. Stark, Tony S. Flynn, Bret D. Freudenthal. 2020. Molecular and structural characterization of disease-associated APE1 polymorphisms. DNA Repair (Amst). Jul-Aug:91-92. PMID: 32454397.

Nicole M. Hoitsma, Amy M. Whitaker, Emily C. Beckwitt, S. Jang, P. Agarwal, Bennett Van Houten, Bret D. Freudenthal. 2020. AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop. Nucleic Acid Res. Online ahead of print. PMID: 32542366.

Daniel R. McNeill, Amy M. Whitaker, Wesley J. Stark, Jennifer L. Illuzzi, Peter J. McKinnon, Bret D. Freudenthal, David M. Wilson III. 2020. Functions of APE1 that are critical to cell viability and genotoxin resistance. Mutagenesis. 35:27-38. PMID: 31816044.

Note: This paper was awarded paper of the year by Mutagenesis

Nicole M. Hoitsma*, Amy M. Whitaker*, Matthew A. Schaich, Mallory R. Smith, Max S. Fairlamb, and Bret D. Freudenthal. 2020. Structure and function relationships in mammalian DNA polymerases. Cell Mol Life Sci. 77:35-59. PMID: 31722068. *Co-first authors

Amy M. Whitaker, Rockann E. Mosser, Mandar, T. Naik, and Gregory D. Reinhart. 2019. Propagation of the Allosteric Signal in Bacillus stearothermophilus Phosphofructokinase Examined by Methyl-TROSY NMR. Biochemistry. PMID: 31478644.

Amy M. Whitaker, Bret D. Freudenthal. 2018. APE1: A skilled nucleic acid surgeon. DNA Repair (Amst). 71:93-100. PMID: 30170830.

Max S. Fairlamb*, Amy M. Whitaker*, Bret D. Freudenthal. 2018. Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches. Acta Crystallogr D Struct Biol. 74(Pt 8):760-768. PMID: 30082511. *Co-first authors

Amy M. Whitaker, Tony S. Flynn, Bret D. Freudenthal. 2018. Molecular snapshots of APE1 proofreading mismatches and removing DNA damage. Nature Communications. 9:399. PMID: 9374164.

Amy M. Whitaker*, Mallory S. Smith*, Matthew A. Schaich, Bret D. Freudenthal. 2017. Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res. PMID: 28449123. *Co-first Authors

Amy M. Whitaker*, Matthew A. Schaich*, Mallory S. Smith, Tony S. Flynn, Bret D. Freudenthal. 2017. Base excision repair of oxidative DNA damage: from mechanism to disease. Front Biosci (Landmark Ed). 22:1493-1522. PMID: 28199214. *Co-first authors

Amy M. Whitaker, Gregory D. Reinhart. 2016. The effect of introducing small cavities on the allosteric inhibition of phosphofructokinase from Bacillus stearothermophilus. Arch Biochem Biophys. 607:1-6. PMID: 27477958.

Additional Publications

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