title: Symmetric curvature descriptors for label-free analysis of DNA.
abstract: High-resolution microscopy techniques such as electron microscopy, scanning tunnelling microscopy and atomic force microscopy represent well-established, powerful tools for the structural characterization of adsorbed DNA molecules at the nanoscale. Notably, the analysis of DNA contours allows mapping intrinsic curvature and flexibility along the molecular backbone. This is particularly suited to address the impact of the base-pairs sequence on the local conformation of the strands and plays a pivotal role for investigations relating the inherent DNA shape and flexibility to other functional properties. Here, we introduce novel chain descriptors aimed to characterize the local intrinsic curvature and flexibility of adsorbed DNA molecules with unknown orientation. They consist of stochastic functions that couple the curvatures of two nanosized segments, symmetrically placed on the DNA contour. We show that the fine mapping of the ensemble-averaged functions along the molecular backbone generates characteristic patterns of variation that highlight all pairs of tracts with large intrinsic curvature or enhanced flexibility. We demonstrate the practical applicability of the method for DNA chains imaged by atomic force microscopy. Our approach paves the way for the label-free comparative analysis of duplexes, aimed to detect nanoscale conformational changes of physical or biological relevance in large sample numbers.
authors.affiliation: CNR-SPIN Institute for Superconductors, Innovative Materials and Devices, Genova, Italy.
authors.forename: Renato
authors.initials: R
authors.lastname: Buzio
authors.affiliation: Department of Physics, University of Genova, Genova, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Repetto
authors.affiliation: 1] Department of Pediatrics and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy [2] Laboratory of Molecular Genetics, G. Gaslini Institute, Genova, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Giacopelli
authors.affiliation: 1] Department of Pediatrics and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy [2] Laboratory of Molecular Genetics, G. Gaslini Institute, Genova, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Ravazzolo
authors.affiliation: Department of Physics, University of Genova, Genova, Italy.
authors.forename: Ugo
authors.initials: U
authors.lastname: Valbusa
mesh_terms: D004247:DNA / Q000032:analysis* / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D018625:Microscopy, Atomic Force; D008854:Microscopy, Electron; D009690:Nucleic Acid Conformation; D053495:Osteopontin / Q000737:chemistry* / Q000235:genetics*
chemical_list: D053495:Osteopontin; D004247:DNA