title: Binding of hairpin polyamides to DNA studied by fluorescence correlation spectroscopy for DNA nanoarchitectures.
abstract: We have recently constructed a "DNA strut" consisting of two DNA-binding hairpin polyamides of Dervan-type connected via a long flexible linker and were able to show that this strut can be used to sequence-selectively connect DNA helices. This approach provides a second structural element (besides the Watson-Crick base pairing) for the assembly of higher-order DNA nanoarchitectures from smaller DNA building blocks. Since none of the existing analytical techniques for studying this kind of system were found suitable for detection and quantification of the formation of the resulting complexes, we chose fluorescence correlation spectroscopy (FCS). In the present study we show that FCS allowed us in a versatile and fast way to investigate the binding of Dervan polyamides to DNA. In particular it also shows its power in the quantitative detection of the formation of multimeric complexes and the in investigation of binding under nonphysiological conditions.
authors.affiliation: Institute for Physical and Theoretical Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
authors.forename: Chayan K
authors.initials: CK
authors.lastname: Nandi
authors.forename: Partha P
authors.initials: PP
authors.lastname: Parui
authors.forename: Thorsten L
authors.initials: TL
authors.lastname: Schmidt
authors.forename: Alexander
authors.initials: A
authors.lastname: Heckel
authors.forename: Bernhard
authors.initials: B
authors.lastname: Brutschy
mesh_terms: D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D049329:Nanostructures / Q000737:chemistry*; D009757:Nylons / Q000032:analysis* / Q000737:chemistry*; D013050:Spectrometry, Fluorescence / Q000379:methods*
chemical_list: D009757:Nylons; D004247:DNA