# Project 3 Structural Biology of Complex DNA Damage

> **NIH NIH P01** · VANDERBILT UNIVERSITY · 2021 · $371,008

## Abstract

DNA alkylating agents, including nitrogen mustards (NM) such as cyclophosphamide, are mainstays in the
treatment of a variety of cancers, including breast cancers. A central theme of our project is that initially
formed DNA alkylation products undergo chemical transformations into complex DNA damage, involving
formamidopyrimidine (Fapy-dG) chemistry, interstrand cross-linking (ICL) and apurinic (AP) site formation,
and this unmasks chemical functionalities that modulate repair or replication or serve as obligate
intermediates to facilitate secondary reactions. These secondary reactions can be exploited to design and
implement therapeutic modalities designed to enhance treatment outcomes. Specifically, the mechanistic
basis of combination anthracycline-cyclophosphamide and anthracycline-cyclophosphamide-taxane (AC or
AC-T) treatments, used clinically in breast cancer chemotherapy is of interest. Two secondary products
arise following N7-dG alkylation and are key players in forming complex damage sites: formamidopyrimidine
(alkyl-Fapy-dG) adducts resulting from the imidazole ring-opening of guanine, and AP sites resulting from
depurination of N7-dG alkylation products. We will utilize both NMR and crystallographic approaches to
rigorously characterize the structural biology of these complex damage sites, including the potential for
anthracyclines and other small molecules to form conjugates at AP sites that are generated following
nitrogen mustard alkylation in DNA; these sites may be complex and clustered in the DNA. Project 1 and
the DNA Synthesis Resource Core will prepare samples for structural analyses. A fundamental knowledge
of the structural biology of complex DNA damage that is formed during AC or AC-T treatments is essential
to explaining the cellular processing of this damage by genome surveillance, replication, repair and
tolerance proteins, which is the goal of Project 2. Indeed, Project 3 lies at the crucial intersection between
complex DNA damage induced by specific agents or combination chemotherapies, and the cellular
processing of this damage, which influences the ultimate fate of the cell. We will utilize NMR to determine
the structures of these lesions in DNA, which are related to their recognition by repair enzymes, and we will
utilize crystallography to determine there structures in complex with repair and replication proteins involved
in their processing, in an effort to understand the molecular origins of genotoxicity and cytotoxicity. With
Project 1, we will use NMR and crystallography to delineate the structural biology of AP-site conjugates
involving anthracyline antibiotics, new analogs of these antibiotics prepared by Project 1, and small
molecule AP-lyase inhibitors identified by Project 2. Ultimately our goal is to leverage a more complete
understanding of the chemistry and biology of DNA alkylating agents to discover new therapeutic strategies
in clinical oncology.!
!

## Key facts

- **NIH application ID:** 10220864
- **Project number:** 5P01CA160032-29
- **Recipient organization:** VANDERBILT UNIVERSITY
- **Principal Investigator:** Michael P Stone
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $371,008
- **Award type:** 5
- **Project period:** 1997-08-01 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10220864

## Citation

> US National Institutes of Health, RePORTER application 10220864, Project 3 Structural Biology of Complex DNA Damage (5P01CA160032-29). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10220864. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*