ArticleBiochemistry2012
Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.
Article in Biochemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 53 citations in OpenAlex.
- Long-Range Allosteric Modulation of DNA Duplex Dynamics Induced by Pyrrole-Imidazole Polyamide Binding.The journal of physical chemistry letters · 2025Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Mechanical codes of chemical-scale specificity in DNA motifs.Chemical science · 2023Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE iminoMagnetic resonance (Gottingen, Germany) · 2021Article
- Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.The Journal of biological chemistry · 2020Article
- A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.Biochemistry · 2020Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].Living journal of computational molecular science · 2019Article
- Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles.Biophysical journal · 2018Article
- cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA.Nucleic acids research · 2018Article
- The intrinsic mechanics of B-DNA in solution characterized by NMR.Nucleic acids research · 2016Article
- Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics.PLoS computational biology · 2015Article
- On the Possibility of Facilitated Diffusion of Dendrimers Along DNA.The journal of physical chemistry. B · 2015Article
- Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes.Nucleic acids research · 2015Article
- Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo.Genome biology · 2015Article
- Free-energy landscape and characteristic forces for the initiation of DNA unzipping.Biophysical journal · 2015Article
- Single-Walled Carbon Nanotubes Modulate the B- to A-DNA Transition.The journal of physical chemistry. C, Nanomaterials and interfaces · 2014Article
- On the absence of intrahelical DNA dynamics on the μs to ms timescale.Nature communications · 2014Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Sequence-specific DNA flexibility plays a key role in a variety of cellular interactions that are critical for gene packaging, expression, and regulation, yet few studies have experimentally explored the sequence dependence of DNA dynamics that occur on biologically relevant time scales. Here, we use nuclear magnetic resonance (NMR) carbon spin relaxation combined with molecular dynamics (MD) simulations to examine the picosecond to nanosecond dynamics in a variety of dinucleotide steps as well as in varying length homopolymeric A(n)·T(n) repeats (A(n)-tracts, where n = 2, 4, or 6) that exhibit unusual structural and mechanical properties. We extend the NMR spin relaxation time scale sensitivity deeper into the nanosecond regime by using glycerol and a longer DNA duplex to slow overall tumbling. Our studies reveal a structurally unique A-tract core (for n > 3) that is uniformly rigid, flanked by junction steps that show increasing sugar flexibility with A-tract length. High sugar mobility is observed at pyrimidine residues at the A-tract junctions, which is encoded at the dinucleotide level (CA, TG, and CG steps) and increases with A-tract length. The MD simulations reproduce many of these trends, particularly the overall rigidity of A-tract base and sugar sites, and suggest that the sugar-backbone dynamics could involve transitions in sugar pucker and phosphate backbone BI ↔ BII equilibria. Our results reinforce an emerging view that sequence-specific DNA flexibility can be imprinted in dynamics occurring deep within the nanosecond time regime that is difficult to characterize experimentally at the atomic level. Such large-amplitude sequence-dependent backbone fluctuations might flag the genome for specific DNA recognition.
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