title: Sequence-dependent DNA curvature and flexibility from scanning force microscopy images.
abstract: This paper reports a study of the sequence-dependent DNA curvature and flexibility based on scanning force microscopy (SFM) images. We used a palindromic dimer of a 1878-bp pBR322 fragment and collected a large pool of SFM images. The curvature of each imaged chain was measured in modulus and direction. It was found that the ensemble curvature modulus does not allow the separation of static and dynamic contributions to the curvature, whereas the curvature, when its direction in the two dimensions is taken into account, permits the direct separation of the intrinsic curvature contributions static and dynamic contributions. The palindromic symmetry also acted as an internal gauge of the validity of the SFM images statistical analysis. DNA static curvature resulted in good agreement with the predicted sequence-dependent intrinsic curvature. Furthermore, DNA sequence-dependent flexibility was found to correlate with the occurrence of A.T-rich dinucleotide steps along the chain and, in general, with the normalized basepair stacking energy distribution.
authors.affiliation: Dipartimento di Chimica, Università La Sapienza, P. le A. Moro 5, Rome I-00185, Italy.
authors.forename: Anita
authors.initials: A
authors.lastname: Scipioni
authors.forename: Claudio
authors.initials: C
authors.lastname: Anselmi
authors.forename: Giampaolo
authors.initials: G
authors.lastname: Zuccheri
authors.forename: Bruno
authors.initials: B
authors.lastname: Samori
authors.forename: Pasquale
authors.initials: P
authors.lastname: De Santis
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D018625:Microscopy, Atomic Force / Q000379:methods*; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004247:DNA