title: Triangulating Nucleic Acid Conformations Using Multicolor Surface Energy Transfer.
abstract: Optical ruler methods employing multiple fluorescent labels offer great potential for correlating distances among several sites, but are generally limited to interlabel distances under 10 nm and suffer from complications due to spectral overlap. Here we demonstrate a multicolor surface energy transfer (McSET) technique able to triangulate multiple points on a biopolymer, allowing for analysis of global structure in complex biomolecules. McSET couples the competitive energy transfer pathways of Förster Resonance Energy Transfer (FRET) with gold-nanoparticle mediated Surface Energy Transfer (SET) in order to correlate systematically labeled points on the structure at distances greater than 10 nm and with reduced spectral overlap. To demonstrate the McSET method, the structures of a linear B-DNA and a more complex folded RNA ribozyme were analyzed within the McSET mathematical framework. The improved multicolor optical ruler method takes advantage of the broad spectral range and distances achievable when using a gold nanoparticle as the lowest energy acceptor. The ability to report distance information simultaneously across multiple length scales, short-range (10-50 Å), mid-range (50-150 Å), and long-range (150-350 Å), distinguishes this approach from other multicolor energy transfer methods.
authors.affiliation: Molecular Biophysics Program, Florida State University , Tallahassee, Florida 32306, United States.
authors.forename: Ryan A
authors.initials: RA
authors.lastname: Riskowski
authors.affiliation: Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States.
authors.forename: Rachel E
authors.initials: RE
authors.lastname: Armstrong
authors.affiliation: Department of Chemistry and Biochemistry, Hunter College and The Graduate Center of the City University of New York , New York, New York 10065, United States.
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Greenbaum
authors.affiliation: Molecular Biophysics Program, Florida State University , Tallahassee, Florida 32306, United States.|Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States.
authors.forename: Geoffrey F
authors.initials: GF
authors.lastname: Strouse
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D053768:Metal Nanoparticles / Q000737:chemistry; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA
keywords: Förster resonance energy transfer; long-range optical molecular ruler; noble metal nanoparticles; nucleic acid structure modeling; surface resonance energy transfer