Our basic understanding of how DNA carries out its biological function has been based on the Watson-Crick double helix as the dominant functional form of duplex DNA. However, Watson-Crick base-pairs cannot explain many fundamental biochemical aspects of duplex DNA, including how proteins recognize DNA with high sequence-specificity; how Watson-Crick faces of nucleotide base-pairs can become appreciably solvent exposed and prone to chemical damage; how damaged base-pairs can be stably accommodated in DNA and recognized by repair enzymes; and how errors arise during replication, transcription, and translation. The main hypothesis in this proposal is that canonical Watson-Crick base-pairs and non-canonical mispairs can transiently adopt alternative, higher energy, and sparsely populated conformations that are difficult to detect and characterize by biophysical methods, and that these transient alternative base-pairs provide a new layer of structural and dynamic complexity that is employed to drive many important DNA functions.
Aim 1 will develop methods for identifying and experimentally characterizing Hoogsteen base-pairs in X-ray structures of DNA that may have been improperly modeled as Watson-Crick base-pairs.
This Aim will also test the hypothesis that Hoogsteen base-pairs play important roles in maintaining genome stability in structurally stressed environments and in sequence-specific DNA recognition by proteins.
Aim 2 will test the hypothesis that Hoogsteen base-pairs provide a basis for exposing Watson-Crick faces of nucleotide bases for sequence-specific alkylation damage. It will also test the hypothesis that damaged bases can be stably accommodated in DNA as Hoogsteen base-pairs that induce DNA bending and play functional roles in recognition by repair enzymes.
Aim 3 will develop methods to characterize transient Watson-Crick-like mispairs that are stabilized by rare tautomeric and anionic bases. We will test the hypothesis that anionic Watson-Crick-like G-T mispairs provide the basic mechanisms for spontaneous and damaged-induced G-T misincorporation during DNA replication. The proposed fundamental studies of DNA structure and dynamics will redefine our view of the iconic DNA double helix, and uncover a rich layer of mechanistic complexity hidden in unconventional base-pairs that have so far proven difficult to capture and characterize at atomic resolution.

Public Health Relevance

This project will characterize dynamic DNA base-pairs that play essential roles in sequence-specific DNA-protein recognition, genome stability, damage induction, accommodation and repair, and spontaneous and damaged-induced mutations. The research is expected to significantly improve our understanding of the mechanisms that lead to diseases such as cancer as well as expose new structural forms of DNA for targeting with the use of small molecule therapeutics.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM089846-08
Application #
9324247
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter
Project Start
2010-09-15
Project End
2019-07-31
Budget Start
2017-08-01
Budget End
2018-07-31
Support Year
8
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Duke University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705
Xu, Yu; McSally, James; Andricioaei, Ioan et al. (2018) Modulation of Hoogsteen dynamics on DNA recognition. Nat Commun 9:1473
Shi, Honglue; Clay, Mary C; Rangadurai, Atul et al. (2018) Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. J Biomol NMR 70:229-244
Kimsey, Isaac J; Szymanski, Eric S; Zahurancik, Walter J et al. (2018) Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature 554:195-201
Stelling, Allison L; Xu, Yu; Zhou, Huiqing et al. (2017) Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA. FEBS Lett 591:1770-1784
Szymanski, Eric S; Kimsey, Isaac J; Al-Hashimi, Hashim M (2017) Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs. J Am Chem Soc 139:4326-4329
Zhou, Huiqing; Kimsey, Isaac J; Nikolova, Evgenia N et al. (2016) m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat Struct Mol Biol 23:803-10
Kimsey, Isaac J; Petzold, Katja; Sathyamoorthy, Bharathwaj et al. (2015) Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes. Nature 519:315-20
Salmon, Loïc; Giamba?u, George M; Nikolova, Evgenia N et al. (2015) Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. J Am Chem Soc 137:12954-65
Ficici, Emel; Andricioaei, Ioan (2015) On the Possibility of Facilitated Diffusion of Dendrimers Along DNA. J Phys Chem B 119:6894-904
Mentes, Ahmet; Florescu, Ana Maria; Brunk, Elizabeth et al. (2015) Free-energy landscape and characteristic forces for the initiation of DNA unzipping. Biophys J 108:1727-1738

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