ABSTRACT
The synthesis and characterization of intramolecular triple-helical DNA structures containing polyaromatic pyrene and perylene (perylenetetracarboxylic acid diimide, PDI) building blocks are presented. Two 1,8-dialkynylpyrene units are located in the Watson-Crick stem of the construct, while a PDI or a natural thymidine is present in the Hoogsteen strand. The triple helical structures were investigated by UV/VIS absorbance, fluorescence spectroscopy, and circular dichroism (CD) measurements. The folding of the intramolecular triple helix can be monitored by changes in the vibronic transition ratios, as well as by a change in the alkynylpyrene fluorescence (monomer vs. excimer). It is shown that thymine in the third strand has a pronounced influence on the interaction and, thus, on the fluorescence properties of two pyrene building blocks.
Subject(s)
DNA/chemistry , Perylene/chemistry , Pyrenes/chemistry , Base Sequence , Circular Dichroism , DNA/chemical synthesis , Fluorescence , Nucleic Acid Conformation , Perylene/chemical synthesis , Pyrenes/chemical synthesis , Spectrometry, Fluorescence , Spectrophotometry, UltravioletABSTRACT
A light-harvesting system based on a DNA-organized oligopyrene-cyanine complex is described. Energy transfer from the pyrene units to the cyanine dye was found to proceed via FRET from locally confined excimers to the acceptor.
Subject(s)
Carbocyanines/chemistry , DNA/chemistry , Fluorescent Dyes/chemistry , Light-Harvesting Protein Complexes/chemistry , Pyrenes/chemistry , Carbocyanines/metabolism , DNA/metabolism , Energy Transfer , Fluorescence Resonance Energy Transfer , Fluorescent Dyes/metabolism , Light-Harvesting Protein Complexes/metabolism , Models, Molecular , Molecular Structure , Pyrenes/metabolismABSTRACT
The DNA three-way junction serves as a scaffold for the molecular organization of non-nucleosidic alkynylpyrene and perylenediimide chromophores located at the branch point of the structure. Depending on the composition of the tripartite assembly, the constructs possess distinct spectroscopic properties, ranging from monomer or excimer fluorescence to completely quenched tripartite aggregates.
Subject(s)
DNA/chemistry , Fluorescent Dyes/chemistry , Imides/chemistry , Perylene/analogs & derivatives , Pyrenes/chemistry , Base Sequence , Models, Molecular , Nucleic Acid Conformation , Perylene/chemistry , Spectrometry, Fluorescence , SpectrophotometryABSTRACT
Control yourself! A two-color molecular beacon with non-nucleosidic chromophores in a triplex stem is presented. Pyrene and PDI fluorophores act as mutual quenchers by formation of a donor-acceptor complex in the closed form. Hybridization with the target results in two independent fluorescence signals. The two-color read-out provides a "self-control" feature, which helps to eliminate false positive signals in imaging and screening applications.
Subject(s)
DNA/genetics , RNA/genetics , Base Sequence , DNA/chemistry , Fluorescent Dyes/chemistry , Nucleic Acid Conformation , RNA/chemistryABSTRACT
Pyrene excimer fluorescence is efficiently regulated through formation of π-stacked aggregates between dialkynylpyrene (Y) and perylenediimide (E) residues located in the stem region of a molecular beacon (MB). The building blocks form organized, multichromophoric complexes in the native form. Hybridization to the target results in a conformational reorganization of the chromophores. The nature of the aggregates was investigated by changing the number of chromophores and natural base pairs in the beacon stem. The formation of different types of complexes (EYEYâYEYâEY) is revealed by characteristic spectroscopic changes. The data show that signal control is an intrinsic property of the interacting chromophores. The directed assembly of non-nucleosidic chromophores can be used for the generation of an on/off switch of a fluorescence signal. The concept may find applications in various types of light-based input/output systems.
