title: Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes.
abstract: A broad series of homochiral perylene bisimide (PBI) dyes were synthesized that are appended with amino acids and cationic side chains at the imide positions. Self-assembly behavior of these ionic PBIs has been studied in aqueous media by UV/Vis spectroscopy, revealing formation of excitonically coupled H-type aggregates. The interactions of these ionic PBIs with different ds-DNA and ds-RNA have been explored by thermal denaturation, fluorimetric titration and circular dichroism (CD) experiments. These PBIs strongly stabilized ds-DNA/RNA against thermal denaturation as revealed by high melting temperatures of the formed PBI/polynucleotide complexes. Fluorimetric titrations showed that these PBIs bind to ds-DNA/RNA with high binding constants depending on the number of the positive charges in the side chains. Thus, spermine-containing PBIs with six positive charges each showed higher binding constants (logKs =9.2-9.8) than their dioxa analogues (logKs =6.5-7.9) having two positive charges each. Induced circular dichroism (ICD) of PBI assemblies created within DNA/RNA grooves was observed. These ICD profiles are strongly dependent on the steric demand of the chiral substituents of the amino acid units and the secondary structure of the DNA or RNA. The observed ICD effects can be explained by non-covalent binding of excitonically coupled PBI dimer aggregates into the minor groove of DNA and major groove of RNA which is further supported by molecular modeling studies.
authors.affiliation: Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry, Am Hubland, 97074 Würzburg (Germany), Fax: (+49) 931-31-84756.
authors.forename: Jana
authors.initials: J
authors.lastname: Gershberg
authors.forename: Marijana
authors.initials: M
authors.lastname: Radić Stojković
authors.forename: Marko
authors.initials: M
authors.lastname: Škugor
authors.forename: Sanja
authors.initials: S
authors.lastname: Tomić
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Rehm
authors.forename: Stefanie
authors.initials: S
authors.lastname: Rehm
authors.forename: Chantu R
authors.initials: CR
authors.lastname: Saha-Möller
authors.forename: Ivo
authors.initials: I
authors.lastname: Piantanida
authors.forename: Frank
authors.initials: F
authors.lastname: Würthner
mesh_terms: D001665:Binding Sites; D002942:Circular Dichroism; D004396:Coloring Agents / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D005470:Fluorometry; D007094:Imides / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010569:Perylene / Q000031:analogs & derivatives* / Q000737:chemistry; D012330:RNA, Double-Stranded / Q000737:chemistry*; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D004396:Coloring Agents; D007094:Imides; D012330:RNA, Double-Stranded; C510697:perylene bisimide; D014867:Water; D010569:Perylene; D004247:DNA
keywords: DNA/RNA recognition; chiral perylene bisimide; groove binding; induced circular dichroism; self-assembly