ArticleJournal of molecular biology2009
Crystallographic analysis of a sex-specific enhancer element: sequence-dependent DNA structure, hydration, and dynamics.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 48 citations in OpenAlex.
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- Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective.Frontiers in bioengineering and biotechnology · 2021Review
- Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA.Communications chemistry · 2020Article
- Forces maintaining the DNA double helix.European biophysics journal : EBJ · 2020Article
- Thermodynamics of DNA: heat capacity changes on duplex unfolding.European biophysics journal : EBJ · 2019Article
- Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: artificial analogues of DNA mimic proteins.Nucleic acids research · 2019Article
- Hydration differences between the major and minor grooves of DNA revealed from heat capacity measurements.European biophysics journal : EBJ · 2019Article
- Development of a Molecular Marker Linked to theMycobiology · 2019Article
- K63-linked polyubiquitin chains bind to DNA to facilitate DNA damage repair.Science signaling · 2018Article
- Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy.Structural dynamics (Melville, N.Y.) · 2016Article
- The structural diversity of artificial genetic polymers.Nucleic acids research · 2016Review
- An ancient protein-DNA interaction underlying metazoan sex determination.Nature structural & molecular biology · 2015Article
- A parallel quadruplex DNA is bound tightly but unfolded slowly by pif1 helicase.The Journal of biological chemistry · 2015Article
- All-atom polarizable force field for DNA based on the classical Drude oscillator model.Journal of computational chemistry · 2014Article
- Two glycosylase families diffusively scan DNA using a wedge residue to probe for and identify oxidatively damaged bases.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Euler buckling and nonlinear kinking of double-stranded DNA.Nucleic acids research · 2013Article
- [Fe₂L₃]⁴⁺ cylinders derived from bis(bidentate) 2-pyridyl-1,2,3-triazole "click" ligands: synthesis, structures and exploration of biological activity.Molecules (Basel, Switzerland) · 2013Article
- Crystallization of a self-assembled three-dimensional DNA nanostructure.Acta crystallographica. Section F, Structural biology and crystallization communications · 2013Article
- Hydration changes upon DNA folding studied by osmotic stress experiments.Biophysical journal · 2012Article
- Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.Journal of chemical theory and computation · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The crystal structure of a sex-specific enhancer element is described at a resolution of 1.6 A. This 16-bp site, designated Dsx(A), functions in the regulation of a genetic switch between male and female patterns of gene expression in Drosophila melanogaster. Related sites are broadly conserved in metazoans, including in the human genome. This enhancer element is unusually rich in general regulatory sequences related to DNA recognition by multiple classes of eukaryotic transcription factors, including the DM motifs, homeodomain, and high mobility group box. Whereas free DNA is often crystallized as an A-form double helix, Dsx(A) was crystallized as B-DNA and thus provides a model for the prebound conformation of diverse regulatory DNA complexes. Sequence-dependent conformational properties that extend features of shorter B-DNA fragments with respect to double helical parameters, groove widths, hydration, and binding of divalent metal ions are observed. The structure also exhibits a sequence-dependent pattern of isotropic thermal B-factors, suggesting possible variation in the local flexibility of the DNA backbone. Such fluctuations are in accord with structural variability observed in prior B-DNA structures. We speculate that sites of intrinsic flexibility within a DNA control element provide hinges for its protein-directed reorganization in a transcriptional preinitiation complex.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.