title: Label-free, atomic force microscopy-based mapping of DNA intrinsic curvature for the nanoscale comparative analysis of bent duplexes.
abstract: We propose a method for the characterization of the local intrinsic curvature of adsorbed DNA molecules. It relies on a novel statistical chain descriptor, namely the ensemble averaged product of curvatures for two nanosized segments, symmetrically placed on the contour of atomic force microscopy imaged chains. We demonstrate by theoretical arguments and experimental investigation of representative samples that the fine mapping of the average product along the molecular backbone generates a characteristic pattern of variation that effectively highlights all pairs of DNA tracts with large intrinsic curvature. The centrosymmetric character of the chain descriptor enables targetting strands with unknown orientation. This overcomes a remarkable limitation of the current experimental strategies that estimate curvature maps solely from the trajectories of end-labeled molecules or palindromes. As a consequence our approach paves the way for a reliable, unbiased, label-free comparative analysis of bent duplexes, aimed to detect local conformational changes of physical or biological relevance in large sample numbers. Notably, such an assay is virtually inaccessible to the automated intrinsic curvature computation algorithms proposed so far. We foresee several challenging applications, including the validation of DNA adsorption and bending models by experiments and the discrimination of specimens for genetic screening purposes.
authors.affiliation: S.C. Nanobiotecnologie, National Institute for Cancer Research IST, Genova, Italy.
authors.forename: Renato
authors.initials: R
authors.lastname: Buzio
authors.forename: Luca
authors.initials: L
authors.lastname: Repetto
authors.forename: Francesca
authors.initials: F
authors.lastname: Giacopelli
authors.forename: Roberto
authors.initials: R
authors.lastname: Ravazzolo
authors.forename: Ugo
authors.initials: U
authors.lastname: Valbusa
mesh_terms: D004247:DNA / Q000737:chemistry / Q000648:ultrastructure*; D003627:Data Interpretation, Statistical; D006801:Humans; D018625:Microscopy, Atomic Force / Q000379:methods*; D049329:Nanostructures / Q000648:ultrastructure; D009690:Nucleic Acid Conformation; D053495:Osteopontin / Q000235:genetics; D017354:Point Mutation
chemical_list: D053495:Osteopontin; D004247:DNA