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Experimental CD spectra for capped hairpins with SA chromophores separated by 1–11 A:T base pairs (n = number of base pairs).
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Short DNA duplexes can be stabilized by the presence of organic chromophores, which serve as hairpin linkers or end-capping groups. Capped hairpins possessing one or more base pairs form stable folded structures in aqueous solution. Increasing the number of base pairs separating the two chromophores increases both the distance between the two chrom...
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... Till a decade ago, research in DNA has been associated with genetic engineering, medicine and microbiology. Fluorescence labelling based DNA sequencing (determining the order of nucleobases in a DNA strand) methods paved way for interaction between DNA and Photonics, which led to new field termed as 'DNA Photonics' [1][2][3] . Recently, DNA has been exploited in various fields of photonics, optoelectronics and nanotechnology. ...
... There has been numerous investigations on various fluorophore-doped DNA and reported its amplified spontaneous emission and lasing action [20][21][22]. Thus, the biopolymer with its renowned double helical structure has emerged to develop a new field 'DNA Photonics' [23][24][25][26], transforming itself into an exciting photonic material. ...
We have investigated the effect of DNA on nonlinear absorption of PicoGreen dye using single beam open aperture Z-scan technique in nanosecond regime. We observed reverse saturable absorption at 532 nm for PicoGreen without DNA. In the presence of DNA, the sample begins to behave like saturable absorbers and this effect increased as the concentration of DNA was increased. The dye-intercalated DNA showed SA characteristics near the focus but exhibited RSA characteristics at the focus. Theoretical analysis has been performed using a two-photon absorption model based on nonlinear absorption coefficient and saturation intensity. Such tailoring of optical nonlinear absorption in PicoGreen makes it a potential candidate for photonic application.
... The same and analogous hairpins have previously been used to study excitedstate properties and charge transfer experimentally. 52 3.1. Structural Dependence of the Site Energy. ...
... In this context, it is interesting that for hairpins containing a small number of base pairs (<4) a single bisignate curve appears in the experimental CD spectra, whereas a shoulder can clearly be identified on the positive peak for larger hairpins. 52 This can be attributed to the formation of a more rigid structure when the number of base pairs in the hairpin is increased. As discussed above for the absorption spectra, a more direct way to include the effect of disorder is by including it in the site energies in the exciton Hamiltonian. ...
... The bisignate feature in the CD spectrum strongly depends on the mutual orientation of the two stibenes. 52 The sign of this feature changes twice on increasing the number of AT base pairs from 2 to 6, and the amplitude decreases with increasing distance. Also, in the nucleobase region of the spectra, the CD spectrum is reasonably reproduced, although there is a slight shift toward high energy, as discussed above for the absorption spectrum. ...
In this article, a theoretical study of the electronic and spectroscopic properties of well-defined DNA hairpins is presented. The excited states in the hairpins are described in terms of an exciton Hamiltonan model, and the structural dynamics of the DNA model systems is explicitly taken into account by molecular dynamics simulations. The results show that the model reproduces the experimentally observed absorption and circular dichroism spectra accurately in most cases. It is shown that structural disorder leads to excited states that are largely localized on a single base pair, even for regular DNA sequences consisting only of AT base pairs. Variations in the base pair sequence have a significant effect on the appearance of the spectra but also on the degree of delocalization of the excited state.
Benzoperylene derivatives with two angularly attached dicarboxylic imide rings, which were prepared by the Diels-Alder-Reaction, exhibit strong fluorescence and their free peri positions allow either control of the UV/Vis spectra through their substituents or form anchor positions for the attachment of functional units. The angular chromophore 3 may be used both for fluorescent labeling such as for primary amines or enzymes or as building blocks for more complex assemblies where they may act as energy donors for FRET or electron acceptors in PET such as for photovoltaic solar cells.
Perylene and benzoperylene carboxylic imides were arranged to form a bichromophoric dye with orthogonal electronic transition moments. Thus, exciton interactions between the two chromophores could be excluded, in spite of their proximity. However, quantitative Förster-type energy transfer proceeds between the chromophores indicated by a fluorescence quantum yield close to unity even with hypsochromic excitation. Applications are discussed. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
An ongoing challenge in the construction of supramolecular systems is controlling the relative geometry of functional redox species for molecular electronics devices, including wires, switches, and gates. This review focuses on the use of artificial peptide strands to assemble inorganic complexes that are redox active. These approaches toward macromolecular assembly use varying oligoamide backbones and assembly motifs that grew from earlier reports of single oligolysine or proline chains containing pendant redox species that undergo photoinduced charge separation. Recently, peptide nucleic acid chains that form double-stranded duplexes analogous to DNA by hydrogen bonding of complementary base pairs have been modified to contain metal complexes. In these structures, hydrogen bonding and metal coordination combine to form crosslinks between the PNA strands. Finally, a family of structures is described that is based on an aminoethylglycine scaffold with pendant metal coordination sites, but without intervening nucleic acid base pairs. These structures form multimetallic complexes that are either single- or double-stranded, or that form hairpin loop structures. These motifs for using artificial peptide strands for self-assembly hold electron donors and acceptors in relative positions that provide structural connectivity and permit electron transfers between linked metal complexes. This is a new approach for creating polyfunctional redox architectures that could ultimately enable the construction of potentially large and complex molecular electronics devices.
In Förster resonance energy transfer (FRET) experiments, the donor (D) and acceptor (A) fluorophores are usually attached to the macromolecule of interest via long flexible linkers of up to 15 Å in length. This causes significant uncertainties in quantitative distance measurements and prevents experiments with short distances between the attachment points of the dyes due to possible dye-dye interactions. We present two approaches to overcome the above problems as demonstrated by FRET measurements for a series of dsDNA and dsRNA internally labeled with Alexa488 and Cy5 as D and A dye, respectively. First, we characterize the influence of linker length and flexibility on FRET for different dye linker types (long, intermediate, short) by analyzing fluorescence lifetime and anisotropy decays. For long linkers, we describe a straightforward procedure that allows for very high accuracy of FRET-based structure determination through proper consideration of the position distribution of the dye and of linker dynamics. The position distribution can be quickly calculated with geometric accessible volume (AV) simulations, provided that the local structure of RNA or DNA in the proximity of the dye is known and that the dye diffuses freely in the sterically allowed space. The AV approach provides results similar to molecular dynamics simulations (MD) and is fully consistent with experimental FRET data. In a benchmark study for ds A-RNA, an rmsd value of 1.3 Å is achieved. Considering the case of undefined dye environments or very short DA distances, we introduce short linkers with a propargyl or alkenyl unit for internal labeling of nucleic acids to minimize position uncertainties. Studies by ensemble time correlated single photon counting and single-molecule detection show that the nature of the linker strongly affects the radius of the dye's accessible volume (6-16 Å). For short propargyl linkers, heterogeneous dye environments are observed on the millisecond time scale. A detailed analysis of possible orientation effects (κ(2) problem) indicates that, for short linkers and unknown local environments, additional κ(2)-related uncertainties are clearly outweighed by better defined dye positions.
We investigate the ultrafast resonant energy transfer of a perylene bisimide dyad by pump-probe spectroscopy, chemical variation, and calculations. This dyad undergoes transfer with near-unit quantum efficiency, although the transition dipole moments of the donor and acceptor are in a perfectly orthogonal arrangement to each other in the equilibrium geometry. According to the point dipole approximation used in Förster theory, no energy transfer should occur. Experimentally we do, however, find an ultrafast transfer time of 9.4 ps. With the transition density cube approach we show that in the orthogonal arrangement the Coulombic interactions do not contribute to the electronic coupling. Through the change of the spacer in both length and chemical character, we can clearly exclude any Dexter-type energy transfer. The temperature effects on the Förster resonant energy transfer rate demonstrate that energy transfer is enabled through low-frequency ground-state vibrations, which break the orthogonal arrangement of the transition dipole moments. The dyads presented here therefore are a first example that shows with extreme clarity the decisive role vibrational motion plays in energy transfer processes.
The synthesis and properties of three related families of alkane-linked DNA hairpins are reported. The first possesses a dodecane linker (C12) and 2-8 AT base pairs. The second possesses six AT base pairs and straight chain alkane linkers having 8-16 methylenes. The third has three alkane linkers of different length and a constant six base-pair stem with alternating A-T bases and a single TT step. The spectroscopic properties (UV, CD, and (1)H NMR) and molecular modeling are consistent with the formation of base-paired B-DNA structures for all hairpins having four or more AT base pairs. The thermal stability of hairpins having a C12 linker is greater than that of the commonly used hexa(ethylene glycol) linker but less than that of the stilbenediether linker having the same AT base-pair domain. Hairpin stability is related to both hydrophobic interactions between the linker and the adjacent base pair (stilbene > alkane > glycol) and the overall length of the linker. The stability of the alkane-linked hairpins having six AT base pairs is greater for a tetradecane linker than for either shorter or longer linkers. The good thermal stability of alkane-linked hairpins and absence of a chromophore which absorbs in the UV region makes them well-suited for studies of the electronic spectra and photochemistry of short hairpins having variable base-pair sequences.
Optimized synthetic strategies for the preparation of photoswitchable molecular scaffolds based on stilbene or on thioaurone chromophores and their conformationally directing properties, as studied by computations and by NMR spectroscopy, are addressed. For the stilbene peptidomimetics 1, 2 and 3, the length of connecting linkers between the chromophore and the peptide strands was varied, resulting in photochromic dipeptidomimetics with various flexibility. Building blocks of higher rigidity, based on para-substituted thioaurone (4 and 6) and meta-substituted thioaurone chromophores (5 and 7) are shown to have a stronger conformationally directing effect. Design, synthesis, theoretical and experimental conformational analyses are presented.
