title: Nucleotide-Independent Copper(II)-Based Distance Measurements in DNA by Pulsed ESR Spectroscopy.
abstract: A site-specific Cu2+binding motif within a DNA duplex for distance measurements by ESR spectroscopy is reported. This motif utilizes a commercially available 2,2'-dipicolylamine (DPA) phosphormadite easily incorporated into any DNA oligonucleotide during initial DNA synthesis. The method only requires the simple post-synthetic addition of Cu2+without the need for further chemical modification. Notably, the label is positioned within the DNA duplex, as opposed to outside the helical perimeter, for an accurate measurement of duplex distance. A distance of 2.7 nm was measured on a doubly Cu2+-labeled DNA sequence, which is in exact agreement with the expected distance from both DNA modeling and molecular dynamic simulations. This result suggests that with this labeling strategy the ESR measured distance directly reports on backbone DNA distance, without the need for further modeling. Furthermore, the labeling strategy is structure- and nucleotide-independent.
authors.affiliation: Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Lawless
authors.affiliation: Division of Biological, Chemical, and Environmental Sciences, Westminster College, 319 S Market St., New Wilmington, PA, 16172, USA.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Sarver
authors.affiliation: Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA.
authors.forename: Sunil
authors.identifier: 0000-0001-9098-6114
authors.initials: S
authors.lastname: Saxena
mesh_terms: D000588:Amines / Q000737:chemistry; D001665:Binding Sites; D003300:Copper / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D010848:Picolinic Acids / Q000737:chemistry; D013113:Spin Labels / Q000138:chemical synthesis
chemical_list: C501847:2,2'-dipicolylamine; D000588:Amines; D009711:Nucleotides; D010848:Picolinic Acids; D013113:Spin Labels; D003300:Copper; D004247:DNA
keywords: DEER; DNA; ESR spectroscopy; copper; spin labeling