title: Duplex-selective ruthenium-based DNA intercalators.
abstract: We report the design and synthesis of small molecules that exhibit enhanced luminescence in the presence of duplex rather than single-stranded DNA. The local environment presented by a well-known [Ru(dipyrido[3,2-a:2',3'-c]phenazine)L2 ](2+) -based DNA intercalator was modified by functionalizing the bipyridine ligands with esters and carboxylic acids. By systematically varying the number and charge of the pendant groups, it was determined that decreasing the electrostatic interaction between the intercalator and the anionic DNA backbone reduced single-strand interactions and translated to better duplex specificity. In studying this class of complexes, a single Ru(II) complex emerged that selectively luminesces in the presence of duplex DNA with little to no background from interacting with single-stranded DNA. This complex shows promise as a new dye capable of selectively staining double- versus single-stranded DNA in gel electrophoresis, which cannot be done with conventional SYBR dyes.
authors.affiliation: Department of Chemistry, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA).
authors.forename: Chad M
authors.initials: CM
authors.lastname: Shade
authors.affiliation: Department of Chemistry, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA).
authors.forename: Robert D
authors.initials: RD
authors.lastname: Kennedy
authors.affiliation: Department of Chemistry, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA).
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Rouge
authors.affiliation: Department of Chemistry, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA).
authors.forename: Mari S
authors.initials: MS
authors.lastname: Rosen
authors.affiliation: Department of Chemical and Biological Engineering, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA).
authors.forename: Mary X
authors.initials: MX
authors.lastname: Wang
authors.affiliation: Department of Chemistry, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA).
authors.forename: Soyoung E
authors.initials: SE
authors.lastname: Seo
authors.affiliation: Department of Chemistry, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA).
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Clingerman
authors.affiliation: Department of Chemistry, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA). chadnano@northwestern.edu.|Department of Chemical and Biological Engineering, Northwestern University, 2190 Campus Drive, Evanston, IL 60208 (USA). chadnano@northwestern.edu.
authors.forename: Chad A
authors.initials: CA
authors.lastname: Mirkin
mesh_terms: D002264:Carboxylic Acids / Q000737:chemistry; D004247:DNA / Q000032:analysis*; D004277:DNA, Single-Stranded / Q000032:analysis; D004586:Electrophoresis; D007364:Intercalating Agents / Q000737:chemistry*; D049408:Luminescent Agents / Q000737:chemistry*; D009942:Organometallic Compounds / Q000737:chemistry*
chemical_list: D002264:Carboxylic Acids; D004277:DNA, Single-Stranded; D007364:Intercalating Agents; D049408:Luminescent Agents; D009942:Organometallic Compounds; C483523:ruthenium dipyridophenazine; D004247:DNA
keywords: DNA; bioinorganic chemistry; gels; luminescence; ruthenium