title: Analysis of the intrinsic bend in the M13 origin of replication by atomic force microscopy.
abstract: Atomic force microscopy (AFM) has been used to image a 471-bp bent DNA restriction fragment derived from the M13 origin of replication in plasmid LITMUS 28, and a 476-bp normal, unbent fragment from plasmid pUC19. The most probable angle of curvature of the 471-bp DNA fragment is 40-50 degrees, in reasonably good agreement with the bend angle determined by transient electric birefringence, 38 degrees +/- 7 degrees. The normal 476-bp DNA fragment exhibited a Gaussian distribution of bend angles centered at 0 degrees, indicating that this fragment does not contain an intrinsic bend. The persistence length, P, was estimated to be 60 +/- 8 and 62 +/- 8 nm for the 471- and 476-bp fragments, respectively, from the observed mean-square end-to-end distances in the AFM images. Since the P-values of the normal and bent fragments are close to each other, the overall flexibility of DNA fragments of this size is only marginally affected by the presence of a stable bend. The close agreement of AFM and transient electric birefringence results validates the suitability of both methods for characterizing DNA bending and flexibility.
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA.
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Lu
authors.forename: Brock D
authors.initials: BD
authors.lastname: Weers
authors.forename: Nancy C
authors.initials: NC
authors.lastname: Stellwagen
mesh_terms: D003461:Crystallography / Q000379:methods*; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D018625:Microscopy, Atomic Force / Q000379:methods*; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000737:chemistry*; D018741:Replication Origin