Nucleic acid structure and sequence probing using fluorescent base analogue tC^o

The fluorescent cytosine analog tC(o) is on average the brightest probe of its kind and, moreover, it introduces minimal perturbations to the normal secondary structure of DNA. Here several ways of how tC(o), with an advantage, can be used as a local fluorescent probe in nucleic acid systems are presented. Most importantly, we show that tCo is an excellent probe for the detection of individual melting processes of complex nucleic acid structures containing a large number of separate secondary structure motifs. Since conventional UV-melting investigations merely monitor the global melting process of the whole nucleic acid structure, e.g. multi-hairpin systems in RNA/DNA, and thus is incapable of estimating individual melting transitions of such systems, tC(o) represents a new method of characterization. Furthermore, we find that tCo may be used to detect bulges and loops in nucleic acids as well as to distinguish a matched base-pair from several of the mismatched

Photon upconversion facilitated molecular solar energy storage

Photon upconversion is used to facilitate the production of a solar fuel. This is done by collocating a triplet–triplet annihilation upconversion system in a microfluidic device with a molecular solar thermal energy storage system. Incoherent truncated white light is used to drive the reaction and the green part of the spectrum is upconverted to blue light, which in turn is absorbed by the solar fuel

Characterization of Nucleobase Analogue FRET Acceptor tC(nitro)

The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization Of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented similar to 27 degrees from the molecular long axis, This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum Of tC(nitro) is further characterized by density functional theory calculations

Tuning the photochemical properties of the fulvalene-tetracarbonyl-diruthenium system

In a Molecular Solar-Thermal Energy Storage (MOST) system, solar energy is converted to chemical energy using a compound that undergoes reversible endothermic photoisomerization. The high-energy photoisomer can later be converted back to the parent compound and the excess energy is released as heat. One of the most studied MOST systems is based on fulvalene-tetracarbonyl-diruthenium, and this paper demonstrates, for the first time, the possibility to tune the photochemical properties of this system by positive steric hindrance working on the fulvalene unit

Soft-Surface DNA Nanotechnology: DNA Constructs Anchored and Aligned to Lipid Membrane**

No strings attached: At least three attachment points are needed to align a two-dimensional DNA nanoconstruct to a soft lipid membrane surface with a porphyrin nucleoside as membrane anchor (see picture). The resulting freely diffusing DNA constructs can be reversibly assembled on the surface thus enabling the possibility of a self-repairing system. \ua9 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCO by Klenow fragment

Studies of the mechanisms by which DNA polymerases select the correct nucleotide frequently employ fluorescently labeled DNA to monitor conformational rearrangements of the polymerase–DNA complex in response to incoming nucleotides. For this purpose, fluorescent base analogs play an increasingly important role because they interfere less with the DNA–protein interaction than do tethered fluorophores. Here we report the incorporation of the 5′-triphosphates of two exceptionally bright cytosine analogs, 1,3-diaza-2-oxo-phenothiazine (tC) and its oxo-homolog, 1,3-diaza-2-oxo-phenoxazine (tCO), into DNA by the Klenow fragment. Both nucleotide analogs are polymerized with slightly higher efficiency opposite guanine than cytosine triphosphate and are shown to bind with nanomolar affinity to the DNA polymerase active site, according to fluorescence anisotropy measurements. Using this method, we perform competitive binding experiments and show that they can be used to determine the dissociation constant of any given natural or unnatural nucleotide. The results demonstrate that the active site of the Klenow fragment is flexible enough to tolerate base pairs that are size-expanded in the major groove. In addition, the possibility to enzymatically polymerize a fluorescent nucleotide with high efficiency complements the tool box of biophysical probes available to study DNA replication

Photoisomerization efficiency of a solar thermal fuel in the strong coupling regime

Strong exciton-photon coupling is achieved when the interaction between molecules and an electromagnetic field is increased to a level where they cannot be treated as separate systems. This leads to the formation of polaritonic states and an effective rearrangement of the potential energy surfaces, which opens the possibility to modify photochemical reactions. This work investigates how the strong coupling regime is affecting the photoisomerization efficiency and thermal backconversion of a norbornadiene–quadricyclane molecular photoswitch. The quantum yield of photoisomerization shows both an excitation wavelength and exciton/photon constitution dependence. The polariton-induced decay and energy transfer processes are discussed to be the reason for this finding. Furthermore, the thermal back conversion of the system is unperturbed and the lower polariton effectively shifts the absorption onset to lower energies. The reason for the unperturbed thermal backconversion is that it occurs on the ground state, which is unaffected. This work demonstrates how strong coupling can change material properties towards higher efficiencies in applications. Importantly, the experiments illustrate that strong coupling can be used to optimize the absorption onset of the molecular photoswitch norbonadiene without affecting the back reaction from the uncoupled quadricyclaneK.B. gratefully acknowledges financial support from the European Research council (ERC2017-StG-757733) and the Knut and Alice Wallenberg Foundation (KAW 2017.0192). J.F. and C.C. acknowledge financial support from the European Research Council through grant ERC-2016-StG-714870, and by the Spanish Ministry for Science, Innovation, and Universities—Agencia Estatal de Investigación through grants RTI2018-099737-B-I00, PCI2018-093145 (through the QuantERA program of the European Commission), and CEX2018-000805-M (through the María de Maeztu program for Units of Excellence in R&D

Long-term effects of no-take zones in Swedish waters

Marine protected areas (MPAs) are increasingly established worldwide to protect and restore degraded ecosystems. However, the level of protection varies among MPAs and has been found to affect the outcome of the closure. In no-take zones (NTZs), no fishing or extraction of marine organisms is allowed. The EU Commission recently committed to protect 30% of European waters by 2030 through the updated Biodiversity Strategy. Importantly, one third of these 30% should be of strict protection. Exactly what is meant by strict protection is not entirely clear, but fishing would likely have to be fully or largely prohibited in these areas. This new target for strictly protected areas highlights the need to evaluate the ecological effects of NTZs, particularly in regions like northern Europe where such evaluations are scarce. The Swedish NTZs made up approximately two thirds of the total areal extent of NTZs in Europe a decade ago. Given that these areas have been closed for at least 10 years and can provide insights into long-term effects of NTZs on fish and ecosystems, they are of broad interest in light of the new 10% strict protection by 2030 commitment by EU member states.In total, eight NTZs in Swedish coastal and offshore waters were evaluated in the current report, with respect to primarily the responses of focal species for the conservation measure, but in some of the areas also ecosystem responses. Five of the NTZs were established in 2009-2011, as part of a government commission, while the other three had been established earlier. The results of the evaluations are presented in a synthesis and also in separate, more detailed chapters for each of the eight NTZs. Overall, the results suggest that NTZs can increase abundances and biomasses of fish and decapod crustaceans, given that the closed areas are strategically placed and of an appropriate size in relation to the life cycle of the focal species. A meta-regression of the effects on focal species of the NTZs showed that CPUE was on average 2.6 times higher after three years of protection, and 3.8 times higher than in the fished reference areas after six years of protection. The proportion of old and large individuals increased in most NTZs, and thereby also the reproductive potential of populations. The increase in abundance of large predatory fish also likely contributed to restoring ecosystem functions, such as top-down control. These effects appeared after a 5-year period and in many cases remained and continued to increase in the longer term (>10 years). In the two areas where cod was the focal species of the NTZs, positive responses were weak, likely as an effect of long-term past, and in the Kattegat still present, recruitment overfishing. In the Baltic Sea, predation by grey seal and cormorant was in some cases so high that it likely counteracted the positive effects of removing fisheries and led to stock declines in the NTZs. In most cases, the introduction of the NTZs has likely decreased the total fishing effort rather than displacing it to adjacent areas. In the Kattegat NTZ, however, the purpose was explicitly to displace an unselective coastal mixed bottom-trawl fishery targeting Norway lobster and flatfish to areas where the bycatches of mature cod were smaller. In two areas that were reopened to fishing after 5 years, the positive effects of the NTZs on fish stocks eroded quickly to pre-closure levels despite that the areas remained closed during the spawning period, highlighting that permanent closures may be necessary to maintain positive effects.We conclude from the Swedish case studies that NTZs may well function as a complement to other fisheries management measures, such as catch, effort and gear regulations. The experiences from the current evaluation show that NTZs can be an important tool for fisheries management especially for local coastal fish populations and areas with mixed fisheries, as well as in cases where there is a need to counteract adverse ecosystem effects of fishing. NTZs are also needed as reference for marine environmental management, and for understanding the effects of fishing on fish populations and other ecosystem components in relation to other pressures. MPAs where the protection of both fish and their habitats is combined may be an important instrument for ecosystembased management, where the recovery of large predatory fish may lead to a restoration of important ecosystem functions and contribute to improving decayed habitats.With the new Biodiversity Strategy, EUs level of ambition for marine conservation increases significantly, with the goal of 30% of coastal and marine waters protected by 2030, and, importantly, one third of these areas being strictly protected. From a conservation perspective, rare, sensitive and/or charismatic species or habitats are often in focus when designating MPAs, and displacement of fisheries is then considered an unwanted side effect. However, if the establishment of strictly protected areas also aims to rebuild fish stocks, these MPAs should be placed in heavily fished areas and designed to protect depleted populations by accounting for their home ranges to generate positive outcomes. Thus, extensive displacement of fisheries is required to reach benefits for depleted populations, and need to be accounted for e.g. by specific regulations outside the strictly protected areas. These new extensive EU goals for MPA establishment pose a challenge for management, but at the same time offer an opportunity to bridge the current gap between conservation and fisheries management

Optical cavity-mediated exciton dynamics in photosynthetic light harvesting 2 complexes

Strong light-matter interaction leads to the formation of hybrid polariton states and alters the photophysical dynamics of organic materials and biological systems without modifying their chemical structure. Here, we experimentally investigated a well-known photosynthetic protein, light harvesting 2 complexes (LH2) from purple bacteria under strong coupling with the light mode of a Fabry-Perot optical microcavity. Using femtosecond pump probe spectroscopy, we analyzed the polariton dynamics of the strongly coupled system and observed a significant prolongation of the excited state lifetime compared with the bare exciton, which can be explained in terms of the exciton reservoir model. Our findings indicate the potential of tuning the dynamic of the whole photosynthetic unit, which contains several light harvesting complexes and reaction centers, with the help of strong exciton-photon coupling, and opening the discussion about possible design strategies of artificial photosynthetic devices