[R01] Role of DNA structural dynamics in mutagenesis and oncogenesis
Ente: National Institute of General Medical Sciences
Scadenza: 2029-05-31
Importo max: 444.908 EUR
Paese: US
Descrizione
Project Summary
Mutations are fundamental to evolution, yet they can also cause cancer and various genetic disorders. Despite
their significance, our understanding of processes which generate or defend against mutations is incomplete.
We don’t understand why the probability of a base substitution mutation varies by many orders of magnitude
depending on the type of substitution and sequence context or why the efficiency of DNA damage repair differs
significantly depending on the kind of damage and sequence. Neither the sequence of the DNA nor its three-
dimensional structure can explain most mutational signatures and the biochemical origins of most signatures
remain unknown. The central hypothesis in this project is that DNA dynamics, which leads to changes in the
mode of base pairing, is a significant driver of mutational processes and mechanisms maintaining genomic
stability. The project will develop and apply techniques for predicting and quantitatively measuring the
propensities to form alternative conformational states of DNA base pairs in high throughput and in large protein-
DNA assemblies and for mapping alternative base pair conformations at single nucleotide resolution genome-
wide in vivo. Aim 1 will advance a thermodynamic ensemble model and determine the propensities of all
mismatches to form mutagenic Watson-Crick-like conformations across sixteen trinucleotide sequence contexts,
comprehensively measure replicative errors by proofreading-deficient human polymerase ε and b and use the
results to test and refine a quantitative and predictive model for nucleotide misincorporation. Aim 2 will develop
biophysical approaches to measure the propensities for base-opening, intra- and extra-helical flipping for A-8OG,
A-G, and G-T in sixteen trinucleotide sequence contexts and use the results to test and refine a quantitative and
predictive model for sequence-specific damage repair by MUTYH and Thymine DNA Glycosylase (TDG). Aim 3
will demonstrate that many DNA-binding proteins employ Hoogsteen base pairs to recognize DNA, determine
the role of Hoogsteen base pairs in p53-DNA interactions in vitro and in vivo, and demonstrate the existence of
Hoogsteen base pairs in nucleosomes across the yeast genome. If successful, the project will illuminate the role
of DNA dynamics in mutation and genomic stability maintenance; deliver the first comprehensive database of
DNA conformational propensities, which can aid the discovery of other mutational processes; advance
quantitative and predictive models for fundamental processes driving oncogenesis; and potentially append the
Watson-Crick paradigm by revealing Hoogsteen base pairs as an alternative building block of DNA in vivo.
Istituzione: COLUMBIA UNIVERSITY HEALTH SCIENCES
PI: Hashim M Al-Hashimi
Progetto: 5R01GM089846-16
Settori: National Institute of General Medical Sciences
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