title: Mapping of surface-immobilized DNA with force-based atomic force microscopy.
abstract: Single-stranded 50-mer, 100-mer, and 150-mer DNAs were immobilized on a surface, and force-based atomic force microscopy (AFM) was employed to examine their behavior. A complementary 20-mer probe DNA on an AFM tip was used for the measurements. High-resolution maps were generated, and relevant parameters, including the force, stretching distance, unbinding probability, cluster size, and degree of distortion, were analyzed. Due to thermal drift, the cluster shape became increasingly distorted as the scan speed was decreased and as the map area was reduced. The cluster radius increased with the number of base (N), and the radius was proportional to N(0.6) (r = 0.977) and N(0.53) (r = 0.991). Due to the effect of the pulling angle, the apparent values of the stretching distance and the unbinding force decreased as the AFM probe was moved away from the center position; these values can be described as a function of sin θ.
authors.affiliation: Department of Chemistry, Pohang University of Science and Technology, San 31 Hyoja-dong, Pohang, 790-784, South Korea.
authors.forename: Yoonhee
authors.initials: Y
authors.lastname: Lee
authors.forename: Sung Hong
authors.initials: SH
authors.lastname: Kwon
authors.forename: Youngkyu
authors.initials: Y
authors.lastname: Kim
authors.forename: Jong-Bong
authors.initials: JB
authors.lastname: Lee
authors.forename: Joon Won
authors.initials: JW
authors.lastname: Park
mesh_terms: D015342:DNA Probes / Q000032:analysis*; D004277:DNA, Single-Stranded / Q000032:analysis*; D005898:Glass; D057446:Hydrodynamics; D061925:Immobilized Nucleic Acids / Q000032:analysis*; D018625:Microscopy, Atomic Force; D012821:Silanes
chemical_list: D015342:DNA Probes; D004277:DNA, Single-Stranded; D061925:Immobilized Nucleic Acids; D012821:Silanes