# How Damaged DNA Forms, and its Subsequent Chemistry: Fundamental Studies and Applications

> **NIH NIH R35** · JOHNS HOPKINS UNIVERSITY · 2021 · $656,845

## Abstract

Our research group addresses fundamental questions concerning how nucleic acids are damaged and what the
biochemical consequences of damage are. We also capitalize on the fundamental discoveries made in these
investigations to create enzyme inhibitors, radiosensitizing agents, and tools that are useful in biotechnology. To
bring these research projects to fruition, we utilize organic chemistry, biochemistry, as well as molecular and cell
biology. Over more than two decades, this research approach has enabled us to uncover novel pathways of
DNA damage, adjudicate mechanistic controversies, and reveal biochemical effects of damaged DNA that
illustrate that nucleic acid damage itself is not always the end of the story. We request support to continue all 3
aspects of this research program. We will utilize our ability to independently generate reactive intermediates to
elucidate questions concerning oxidative damage in free and nucleosomal DNA. For instance, we will examine
the reactivity of nitrogen radicals, which we demonstrated are capable of initiating tandem lesion formation via
hydrogen atom abstraction, unlike most carbon radicals. Tandem lesions are a deleterious form of DNA damage
that are a hallmark of g-radiolysis. Some of the nitrogen radicals are also chameleon-like in that their pKa's are
sufficiently high that reasonable quantities of the respective radical cations are present at neutral pH. Radical
cations are important species produced from the direct effect of ionizing radiation and initiate hole transfer in
DNA. We will study hole transfer in nucleosomal DNA by independently generating radical cations in nucleosome
core particles (NCPs) at defined sites. This will enable us to determine the effects of NCP structure on hole
migration, a topic that is of increasing interest due to the realization that hole transfer is important in signaling
between proteins and DNA. Efforts on understanding the effects of DNA damage will focus on chemistry in NCPs
and the consequences of DNA damage-induced histone modification. We will build upon our discoveries that
alkylated DNA forms DNA-protein cross-links (DPCs) with histones and that histone catalyzed chemistry of
oxidized abasic sites results in modification of lysine residues. These studies will range from experiments in test
tubes to cells to determine the prevalence of histone modifications formed in cells and to identify their biochemical
("downstream") effects. We will also determine whether DPC formation occurs in NCPs when DNA is alkylated
in the minor groove. Finally, we will utilize halogenated purines to potentiate the effects of DNA alkylation by
stabilizing the DPCs formed. This research will contribute to our fundamental understanding of DNA damage
and its connection to the etiology and treatment of disease.

## Key facts

- **NIH application ID:** 10161792
- **Project number:** 5R35GM131736-03
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** MARC M GREENBERG
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $656,845
- **Award type:** 5
- **Project period:** 2019-06-01 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10161792

## Citation

> US National Institutes of Health, RePORTER application 10161792, How Damaged DNA Forms, and its Subsequent Chemistry: Fundamental Studies and Applications (5R35GM131736-03). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10161792. Licensed CC0.

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