title: Multimodal characterization of a linear DNA-based nanostructure.
abstract: Designer DNA structures have garnered much interest as a way of assembling novel nanoscale architectures with exquisite control over the positioning of discrete molecules or nanoparticles. Exploiting this potential for a variety of applications such as light-harvesting, molecular electronics, or biosensing is contingent on the degree to which various nanoarchitectures with desired molecular functionalizations can be realized, and this depends critically on characterization. Many techniques exist for analyzing DNA-organized nanostructures; however, these are almost never used in concert because of overlapping concerns about their differing character, measurement environments, and the disparity in DNA modification chemistries and probe structure or size. To assess these concerns and to see what might be gleaned from a multimodal characterization, we intensively study a single DNA nanostructure using a multiplicity of methods. Our test bed is a linear 100 base-pair double-stranded DNA that has been modified by a variety of chemical handles, dyes, semiconductor quantum dots, gold nanoparticles, and electroactive labels. To this we apply a combination of physical/optical characterization methods including electrophoresis, atomic force microscopy, transmission electron microscopy, dynamic light scattering, Förster resonance energy transfer, voltammetry, and structural modeling. In general, the results indicate that the differences among the techniques are not so large as to prevent their effective use in combination, that the data tend to be corroborative, and that differences observed among them can actually be quite informative.
authors.affiliation: Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States.
authors.forename: Susan
authors.initials: S
authors.lastname: Buckhout-White
authors.forename: Mario
authors.initials: M
authors.lastname: Ancona
authors.forename: Eunkeu
authors.initials: E
authors.lastname: Oh
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Deschamps
authors.forename: Michael H
authors.initials: MH
authors.lastname: Stewart
authors.forename: Juan B
authors.initials: JB
authors.lastname: Blanco-Canosa
authors.forename: Philip E
authors.initials: PE
authors.lastname: Dawson
authors.forename: Ellen R
authors.initials: ER
authors.lastname: Goldman
authors.forename: Igor L
authors.initials: IL
authors.lastname: Medintz
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004563:Electrochemistry; D031541:Fluorescence Resonance Energy Transfer; D008027:Light; D018625:Microscopy, Atomic Force; D046529:Microscopy, Electron, Transmission; D008958:Models, Molecular; D015335:Molecular Probes / Q000737:chemistry; D049329:Nanostructures; D009690:Nucleic Acid Conformation; D012542:Scattering, Radiation; D013194:Staining and Labeling
chemical_list: D015335:Molecular Probes; D004247:DNA