DNA is a highly dynamic biopolymer that undergoes sequence-specific structural changes in response to cellular trigger factors that are essential for fundamental processes such as replication, transcription, recombination, and DNA repair. The mechanism by which DNA undergoes functionally optimized conformational changes remains poorly understood. There is growing evidence that intrinsic sequence-specific flexibility guides DNA structural transitions along functional pathways;however, a direct test of this hypothesis has been hindered by lack of techniques that can be used to visualize DNA deformability at the atomic scale. Intrinsic flexibility also guides the DNA dynamic response to cellular supercoiling and bending forces. Despite growing evidence that such forces can dramatically affect DNA structure and function, the current DNA structure-function paradigm is based almost exclusively on studies of DNA in the more experimentally accessible relaxed duplex form. The goal of this proposal is to develop NMR methods, complemented by molecular dynamics simulations and biochemical assays, to visualize sequence and damage-specific DNA flexibility at the atomic scale in the presence and absence of supercoiling.
Specific Aim 1 will test the hypothesis that DNA undergoes sequence-specific and spatially non-random thermally-induced fluctuations and that trigger factors, such as proteins, take advantage of this flexibility and induce specific changes in DNA structure by """"""""capturing"""""""" distinct conformations from a pre-existing dynamical ensemble. These studies will focus on variable length A-tracts, dinucleotide CpA steps, their combination, and will explore the biological significance of sequence-specific flexibility in adaptive recognition.
Specific Aim 2 will test the hypothesis that DNA damage induction is correlated to sequence-specific flexibility and that repair enzymes exploit the modified flexibility of damaged DNA and """"""""capture"""""""" transient states from a dynamical ensemble rather than induce new ones by """"""""induced fit"""""""". These studies will focus on damaged DNA substrates of the base pair excision pathway enzyme human alkyladenine DNA glycosylase.
Specific Aim 3 will develop minicircles as a model NMR system for experimentally characterizing DNA structural dynamics at atomic resolution in the presence of supercoiling. We will test the hypothesis that supercoiling dramatically affects the basic structural and dynamical properties of DNA, causing an increase in motional correlations between residues, promoting B-to-Z transitions, and enhancing the conformational deformability of A-tracts and damaged DNA, thus providing a mechanism for long-range signaling and communication.

Public Health Relevance

There is growing evidence that sequence-specific DNA flexibility plays a fundamental role in key genetic transactions such as replication, transcription, recombination, and DNA repair that lead to pathology when improperly functioning. Understanding sequence-specific DNA flexibility is also of key importance for rationally designing small molecules that specifically bind to DNA and thus act as therapeutics or chemical tools for investigating diverse biological questions.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
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Preusch, Peter C
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University of Michigan Ann Arbor
Schools of Arts and Sciences
Ann Arbor
United States
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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
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
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 108:1727-38
Zhou, Huiqing; Hintze, Bradley J; Kimsey, Isaac J et al. (2015) New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Res 43:3420-33
Alvey, Heidi S; Gottardo, Federico L; Nikolova, Evgenia N et al. (2014) Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics. Nat Commun 5:4786
Bothe, Jameson R; Stein, Zachary W; Al-Hashimi, Hashim M (2014) Evaluating the uncertainty in exchange parameters determined from off-resonance R1? relaxation dispersion for systems in fast exchange. J Magn Reson 244:18-29

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