title: Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules.
abstract: Direct imaging with the atomic force microscope has been used to identify specific nucleotide sequences in plasmid DNA molecules. This was accomplished using EcoRI (Gln-111), a mutant of the restriction enzyme that has a 1000-fold greater binding affinity than the wild-type enzyme but with cleavage rate constants reduced by a factor of 10(4). ScaI-linearized plasmids with single (pBS+) and double (pGEM-luc and pSV-beta-galactosidase) EcoRI recognition sites were imaged, and the bound enzyme was localized to a 50- to 100-nt resolution. The high affinity for the EcoRI binding site exhibited by this mutant endonuclease, coupled with an observed low level of nonspecific binding, should prove valuable for physically mapping large DNA clones by direct atomic force microscope imaging.
authors.affiliation: Health Sciences Research Division, Oak Ridge National Laboratory, TN 37831-6123, USA.
authors.forename: D P
authors.initials: DP
authors.lastname: Allison
authors.forename: P S
authors.initials: PS
authors.lastname: Kerper
authors.forename: M J
authors.initials: MJ
authors.lastname: Doktycz
authors.forename: J A
authors.initials: JA
authors.lastname: Spain
authors.forename: P
authors.initials: P
authors.lastname: Modrich
authors.forename: F W
authors.initials: FW
authors.lastname: Larimer
authors.forename: T
authors.initials: T
authors.lastname: Thundat
authors.forename: R J
authors.initials: RJ
authors.lastname: Warmack
mesh_terms: D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D015246:Deoxyribonuclease EcoRI / Q000235:genetics / Q000648:ultrastructure*; D018625:Microscopy, Atomic Force / Q000379:methods*; D009154:Mutation; D010957:Plasmids / Q000648:ultrastructure*; D017421:Sequence Analysis / Q000379:methods*
chemical_list: D015246:Deoxyribonuclease EcoRI