Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex

Abstract

The preparation of homo- and heterocomplexes composed of the parent perylene diimide (PH) and pyrrolidine-substituted perylene diimide (PN) in DNA and rapid electron transfer in these complexes, which has been analyzed by steady-state fluorescence and femtosecond transient absorption measurements, have been demonstrated. The DNA molecules possessing PH and PN were prepared through a recently developed method that involved the reaction of enzymatically generated abasic sites with the amino groups of the perylene diimide molecules, through which these molecules can be incorporated as base surrogates within the DNA base stack. Melting temperature analysis showed that the PH and PN monomers, and their homo- and heterodimers, contribute to the stabilization of the DNA duplex, and is comparable to that of natural base pairs. Fluorescence measurements showed that PH in a single-stranded oligopyrimidine showed a strong fluorescence, whereas the fluorescence of PH was completely quenched upon pairing with PN (PH/PN) through duplex formation. The transient absorption measurements showed that a rapid electron-transfer reaction in the stacked PH/PN heterodimer occurred on a sub-picosecond timescale, which allowed highly efficient fluorescence quenching. The PH/PN pair, which served as a fluorophore and quencher, were utilized to design molecular beacon probes with a high signal/noise ratio. The PH/PN pair was also capable of forming a stable, stacked dimer structure and induced rapid electron transfer that could serve as a good signal reporter for fluorescent nucleic acid detection.

Effects of pendant side groups on the properties of the silicon-containing arylacetylene resins with 2,5-diphenyl-[1,3,4]-oxadiazole moieties

“…3). 25 The morphologies of the resins. The difference of crystallinity of PODSA-MM resins before and aer introducing side group were investigated by X-ray diffraction (XRD) analysis at the range of 5 -50 .…”

Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions

“…The covalent incorporation of TO molecules into DNA was achieved through the reductive amination at abasic sites generated by an enzymatic reaction based on our previous method (Figure 1, Table 1). [59,60] We have demonstrated that the abasic sites can work as both binding pockets for the hydrophobic dyes and reactive sites for the conjugation, allowing DNA modification at a specific site and efficient multiple incorporation of functional molecules. [59,60] We utilized our strategy for the preparation of the TO-conjugated DNA.…”

“…[59,60] We have demonstrated that the abasic sites can work as both binding pockets for the hydrophobic dyes and reactive sites for the conjugation, allowing DNA modification at a specific site and efficient multiple incorporation of functional molecules. [59,60] We utilized our strategy for the preparation of the TO-conjugated DNA. The modification of TO was carried out according to the scheme shown in Figure 1b.…”

“…[20,57,58] We have recently developed a useful method for the multiple incorporation of functional chromophores at specific locations of DNA by utilizing abasic sites generated by an enzymatic reaction. [59,60] In this study, based on our previously developed method, we prepared DNA modified with multiple TO dyes and investigated their fluorescence properties. We show that the fluorescent response and wavelength of the helically arranged TO dyes in DNA can be changed through the configuration of the TO dyes and adjacent nucleobases.…”

One- to Two-Exciton Transitions in Perylene Bisimide Dimer Revealed by Two-Dimensional Electronic Spectroscopy

“…Molecular structures based on the perylene bisimide (PBI) chromophore have been the object of extensive studies both from the perspective of fundamental photophysical properties, for instance, high emission yield 1,2 , energy transfer 3,4,5 , electron transfer 6,7 and singlet fission 8,9 , as well as from the perspective of potential application in optoelectronic devices, such as optical sensors 10,11 , solar light collectors 12,13 and optical power limiters 14 . Recently, properties of PBI aggregates have begun to be explored 15,16,17 .…”