Photophysics of DFHBI bound to RNA aptamer Baby Spinach.

The discovery of the GFP-type dye DFHBI that becomes fluorescent upon binding to an RNA aptamer, termed Spinach, led to the development of a variety of fluorogenic RNA systems that enable genetic encoding of living cells. In view of increasing interest in small RNA aptamers and the scarcity of their photophysical characterisation, this paper is a model study on Baby Spinach, a truncated Spinach aptamer with half its sequence. Fluorescence and fluorescence excitation spectra of DFHBI complexes of Spinach and Baby Spinach are known to be similar. Surprisingly, a significant divergence between absorption and fluorescence excitation spectra of the DFHBI/RNA complex was observed on conditions of saturation at large excess of RNA over DFHBI. Since absorption spectra were not reported for any Spinach-type aptamer, this effect is new. Quantitative modelling of the absorption spectrum based on competing dark and fluorescent binding sites could explain it. However, following reasoning of fluorescence lifetimes of bound DFHBI, femtosecond-fluorescence lifetime profiles would be more supportive of the notion that the abnormal absorption spectrum is largely caused by trans-isomers formed  within the cis-bound DFHBI/RNA complex. Independent of the origin, the unexpected discrepancy between absorption and fluorescence excitation spectra allows for easily accessed screening and insight into the efficiency of a fluorogenic dye/RNA system.

Perturbation-Induced Seeding and Crystallization of Hybrid Perovskites over Surface-Modified Substrates for Optoelectronic Devices.

Growing a monocrystalline layer of lead halide perovskites directly over substrates is necessary to completely harness their stellar properties in optoelectronic devices, as the single crystals of these materials are extremely brittle. We study the crystallization mechanism of perovskites by antisolvent vapor diffusion to its precursor solution and find that heterogeneous nucleation prevails in the process, with the crystallization dish walls providing the energy to overcome the nucleation barrier. By perturbing the system using sonication, we are able to introduce homogeneously nucleated seed crystals in the precursor solution. These seeds lead to the growth of closely packed crystals over surface-modified substrates kept in the precursor solution. This crystallization process is substrate independent and scalable and can be utilized to fabricate planar optoelectronic devices. We demonstrate a methylammonium lead iodide planar crystal photoconductor with a colossal detectivity of 1.48 × 1013 Jones.

Monitoring Electron-Phonon Interactions in Lead Halide Perovskites Using Time-Resolved THz Spectroscopy.

Lead halide perovskite semiconductors have low-frequency phonon modes within the lead halide sublattice and thus are considered to be soft. The soft lattice is considered to be important in defining their interesting optoelectronic properties. Electron-phonon coupling governs hot-carrier relaxation, carrier mobilities, carrier lifetimes, among other important electronic characteristics. Directly observing the interplay between free charge carriers and phonons can provide details on how phonons impact these properties (e.g., exciton populations and other collective modes). Here, we observe a delicate interplay among carriers, phonons, and excitons in mixed-cation and mixed-halide perovskite films by simultaneously resolving the contribution of charge carriers and phonons in time-resolved terahertz photoconductivity spectra. We are able to observe directly the increase in phonon population during carrier cooling and discuss how thermal equilibrium populations of carriers and phonons modulate the carrier transport properties, as well as reduce the population of carriers within band tails. We are also able to observe directly the formation of free charge carriers when excitons interact with phonons and dissociate and to describe how free carriers and exciton populations exchange through phonon interactions. Finally, we also time-resolve how the carriers are screened via the Coulomb interaction at low and room temperatures. Our studies shed light on how charge carriers interact with the low-energy phonons and discuss implications.

Elucidating the role of disorder and free-carrier recombination kinetics in CH3NH3PbI3 perovskite films.

Apart from broadband absorption of solar radiation, the performance of photovoltaic devices is governed by the density and mobility of photogenerated charge carriers. The latter parameters indicate how many free carriers move away from their origin, and how fast, before loss mechanisms such as carrier recombination occur. However, only lower bounds of these parameters are usually obtained. Here we independently determine both density and mobility of charge carriers in a perovskite film by the use of time-resolved terahertz spectroscopy. Our data reveal the modification of the free carrier response by strong backscattering expected from these heavily disordered perovskite films. The results for different phases and different temperatures show a change of kinetics from two-body recombination at room temperature to three-body recombination at low temperatures. Our results suggest that perovskite-based solar cells can perform well even at low temperatures as long as the three-body recombination has not become predominant.

Structural and evolutionary aspects of antenna chromophore usage by class II photolyases.

Light-harvesting and resonance energy transfer to the catalytic FAD cofactor are key roles for the antenna chromophores of light-driven DNA photolyases, which remove UV-induced DNA lesions. So far, five chemically diverse chromophores have been described for several photolyases and related cryptochromes, but no correlation between phylogeny and used antenna has been found. Despite a common protein topology, structural analysis of the distantly related class II photolyase from the archaeon Methanosarcina mazei (MmCPDII) as well as plantal orthologues indicated several differences in terms of DNA and FAD binding and electron transfer pathways. For MmCPDII we identify 8-hydroxydeazaflavin (8-HDF) as cognate antenna by in vitro and in vivo reconstitution, whereas the higher plant class II photolyase from Arabidopsis thaliana fails to bind any of the known chromophores. According to the 1.9 Å structure of the MmCPDII·8-HDF complex, its antenna binding site differs from other members of the photolyase-cryptochrome superfamily by an antenna loop that changes its conformation by 12 Å upon 8-HDF binding. Additionally, so-called N- and C-motifs contribute as conserved elements to the binding of deprotonated 8-HDF and allow predicting 8-HDF binding for most of the class II photolyases in the whole phylome. The 8-HDF antenna is used throughout the viridiplantae ranging from green microalgae to bryophyta and pteridophyta, i.e. mosses and ferns, but interestingly not in higher plants. Overall, we suggest that 8-hydroxydeazaflavin is a crucial factor for the survival of most higher eukaryotes which depend on class II photolyases to struggle with the genotoxic effects of solar UV exposure.

Following G-quadruplex formation by its intrinsic fluorescence.

We characterized and compared the fluorescence properties of various well-defined G-quadruplex structures. The increase of intrinsic fluorescence of G-rich DNA sequences when they form G-quadruplexes can be used to monitor the folding and unfolding of G-quadruplexes as a function of cations and temperature. The temperature-dependent fluorescence spectra of different G-quadruplexes also exhibit characteristic patterns. Thus, the stability and possibly also the structure of G-quadruplexes can be characterized and distinguished by their intrinsic fluorescence spectra.

Chromophore/DNA interactions: femto- to nanosecond spectroscopy, NMR structure, and electron transfer theory.

The mechanism of photoinduced hole injection into DNA has been studied using an integrated approach that combines NMR structural analysis, time-resolved spectroscopy, and quantum-chemical calculations. A covalently linked acridinium derivative, the protonated 9-amino-6-chloro-2-methoxyacridine (X+), is replacing a thymine and separated from either guanine (G) or the easier to oxidize 7-deazaguanine (Z) by one adenine.thymine (A.T) base pair. The key features of this donor/acceptor system are the following: (i) In more than 95% of the duplexes, X+ is located in a central, coplanar position between the neighboring A.T base pairs with its long axis in parallel showing minimal twist and tilt angles (<15 degrees). The complementary adenine base is turned out into the extrahelical space. In a minority of less than 5%, X+ is found to be still attached to the duplex. X+ is most probably associated with one of the phosphates, since it is neither intercalated between more remote base pairs nor bound to sugars or grooves. This minority characterized by an excited state lifetime >10 ns gives rise to a small background signal in time-resolved measurements and contributes predominantly to steady-state fluorescence spectra. (ii) Although the intercalation mode of X+ is well defined, the NMR structure reveals that there are two conformations of X+ with respect to the arrangement of its methoxy substituent. In one conformation, the methoxy group is in the plane of the chromophore, while, in the other extraplanar conformation, the methoxy group forms an angle of 70 degrees with the acridinium ring. The fluorescence decay of 5'-ZAX and 5'-GAX tracts can be fitted to a biexponential function with similar amplitudes, reflecting the oxidation dynamics of G and Z, with the slower rate being determined by larger thermal activation energy. The attribution of biexponential electron transfer (ET) dynamics to the bimodal orientation of the methoxy group at the acridinium is supported by quantum-chemical calculations. These predict a larger free energy change for hole transfer in the nonplanar conformation as compared to the planar one, whereas the difference in the electronic couplings is negligible. (iii) Kinetic studies of the directionality of the 1(X+)* induced hole injection reveal similarly fast decay components in both directions of the duplex, that is, in 5'-ZAX and 5'-XAZ, with the amplitude of the fast component being significantly reduced in 5'-XAZ. The NMR structure shows that local structural deviations from B-DNA are much more pronounced in the 3'-5' direction than in the 5'-3' direction. According to quantum-chemical calculations, the directionality of charge injection is not a universal feature of the DNA duplex but depends critically on the rotation angle of the aromatic plane of the acridinium within the pi stack. The arrangement of X+ in 5'-ZAX and 5'-XAZ corresponds to a conformation with weak directionality of the electronic couplings. The increased disorder in the 3'-5'direction favors slow hole transfer components at the expense of the fast ones. (iv) A comparison of the hole transfer in 5'-GAX and 5'-ZAG shows that classical Marcus theory can explain the ratio of the charge shift rates of more than 2 orders of magnitude on the basis of a free energy difference between G and Z of 0.3 eV. Both NMR structures and quantum-chemical calculations justify the appreciable neglect of differences of electronic couplings as well as in the reorganization energy in 5'-GAX and 5'-ZAG. Despite the attractive concept for the behavior of floppy DNA oligonucleotides, in this acridinium/DNA system, there is no evidence for conformational gating, that is, for fluctuations in the electronic couplings that permit the ET to occur.

Distance-dependent activation energies for hole injection from protonated 9-amino-6-chloro-2-methoxyacridine into duplex DNA.

The recent investigation of the apparently anomalous attenuation factor (beta > 1.5 A(-1)) for photoinduced hole injection into DNA duplexes modified by protonated 9-amino-6-chloro-2-methoxyacridine (X+) led to the conclusion that in addition to the electronic couplings, the activation energy must also be distance-dependent. In this communication we report the verification of this postulate by direct measurements of the activation energies for a series of (X+)-modified DNA duplexes which sample an appreciable range of donor-acceptor distances (approximately 4-11 A). The resulting changes in thermal activation energy can be explained within the framework of a distance-dependent reorganization energy.