title: Probing a label-free local bend in DNA by single molecule tethered particle motion.
abstract: Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of proteins. Developing a method to measure DNA bend angles that does not perturb the conformation of the DNA itself or the DNA-protein complex is a challenging task. Here, we propose a joint theory-experiment high-throughput approach to rigorously measure such bend angles using the Tethered Particle Motion (TPM) technique. By carefully modeling the TPM geometry, we propose a simple formula based on a kinked Worm-Like Chain model to extract the bend angle from TPM measurements. Using constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven 6A-tracts, we find that the sequence CA6CGG induces a bend angle of 19° ± 4°. Our method is successfully compared to more theoretically complex or experimentally invasive ones such as cyclization, NMR, FRET or AFM. We further apply our procedure to TPM measurements from the literature and demonstrate that the angles of bends induced by proteins, such as Integration Host Factor (IHF) can be reliably evaluated as well.
authors.affiliation: CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France.
authors.forename: Annaël
authors.initials: A
authors.lastname: Brunet
authors.affiliation: CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Chevalier
authors.affiliation: CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Destainville
authors.affiliation: CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France.
authors.forename: Manoel
authors.initials: M
authors.lastname: Manghi
authors.affiliation: CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Rousseau
authors.affiliation: CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France.
authors.forename: Maya
authors.initials: M
authors.lastname: Salhi
authors.affiliation: CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Salomé
authors.affiliation: CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France tardin@ipbs.fr.
authors.forename: Catherine
authors.initials: C
authors.lastname: Tardin
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D034982:Integration Host Factors / Q000378:metabolism; D008956:Models, Chemical; D009038:Motion; D009690:Nucleic Acid Conformation; D010825:Physics / Q000379:methods
chemical_list: D034982:Integration Host Factors; D004247:DNA