ArticleProceedings of the National Academy of Sciences of the United States of America2001
Mapping the intrinsic curvature and flexibility along the DNA chain.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- DNA Wrapping by a tetrameric bacterial histone.Nature communications · 2025Article
- Systematic Targeting of GD2-Positive Neuroblastoma Tumors With a Photooncolytic Phage Nanovector Platform.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A modular phage vector platform for targeted photodynamic therapy of Gram-negative bacterial pathogens.iScience · 2023Article
- Enhanced nucleosome assembly at CpG sites containing an extended 5-methylcytosine analogue.Nucleic acids research · 2022Article
- Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.International journal of molecular sciences · 2020Article
- Environmentally Controlled Curvature of Single Collagen Proteins.Biophysical journal · 2018Article
- Tarantula myosin free head regulatory light chain phosphorylation stiffens N-terminal extension, releasing it and blocking its docking back.Molecular bioSystems · 2015Article
- Symmetric curvature descriptors for label-free analysis of DNA.Scientific reports · 2014Article
- Image analysis and length estimation of biomolecules using AFM.IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society · 2012Article
- Label-free, atomic force microscopy-based mapping of DNA intrinsic curvature for the nanoscale comparative analysis of bent duplexes.Nucleic acids research · 2012Article
- Modeling DNA-bending in the nucleosome: role of AA periodicity.The journal of physical chemistry. B · 2011Article
- Mechanics of the IL2RA gene activation revealed by modeling and atomic force microscopy.PloS one · 2011Article
- Sequence periodicity in nucleosomal DNA and intrinsic curvature.BMC structural biology · 2010Article
- Structural analysis of hyperperiodic DNA from Caenorhabditis elegans.Nucleic acids research · 2006Article
- Fine mapping of inherent flexibility variation along DNA molecules: validation by atomic force microscopy (AFM) in buffer.Molecular genetics and genomics : MGG · 2005Article
- Bending of adenovirus origin DNA by nuclear factor I as shown by scanning force microscopy is required for optimal DNA replication.Journal of virology · 2004Article
- Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion.Biophysical journal · 2003Article
- The coiled-coil of the human Rad50 DNA repair protein contains specific segments of increased flexibility.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Fluorescent heteroduplex assay for monitoring Bacillus anthracis and close relatives in environmental samples.Applied and environmental microbiology · 2003Article
- High-throughput approach for detection of DNA bending and flexibility based on cyclization.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The energy of DNA deformation plays a crucial and active role in its packaging and its function in the cell. Considerable effort has gone into developing methodologies capable of evaluating the local sequence-directed curvature and flexibility of a DNA chain. These studies thus far have focused on DNA constructs expressly tailored either with anomalous flexibility or curvature tracts. Here we demonstrate that these two structural properties can be mapped also along the chain of a "natural" DNA with any sequence on the basis of its scanning force microscope (SFM) images. To know the orientation of the sequence of the investigated DNA molecules in their SFM images, we prepared a palindromic dimer of the long DNA molecule under study. The palindromic symmetry also acted as an internal gauge of the statistical significance of the analysis carried out on the SFM images of the dimer molecules. It was found that although the curvature modulus is not efficient in separating static and dynamic contributions to the curvature of the population of molecules, the curvature taken with its direction (its sign in two dimensions) permits the direct separation of the intrinsic curvature from the flexibility contributions. The sequence-dependent flexibility seems to vary monotonically with the chain's intrinsic curvature; the chain rigidity was found to modulate as its local thermodynamic stability and does not correlate with the dinucleotide chain rigidities evaluation made from x-ray data by other authors.
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