Dissecting and reducing the heterogeneity of excited-state energy transport in DNA-based photonic wires

Molecular photonic wires are one-dimensional representatives of a family of nanoscale molecular devices that transport excited-state energy over considerable distances in analogy to optical waveguides in the far-field. In particular, the design and synthesis of such complex supramolecular devices is challenging concerning the desired homogeneity of energy transport. On the other hand, novel optical techniques are available that permit direct investigation of heterogeneity by studying one device at a time. In this article, we describe our efforts to synthesize and study DNA-based molecular photonic wires that carry several chromophores arranged in an energetic downhill cascade and exploit fluorescence resonance energy transfer to convey excited-state energy. The focus of this work is to understand and control the heterogeneity of such complex systems, applying single-molecule fluorescence spectroscopy (SMFS) to dissect the different sources of heterogeneity, i.e., chemical heterogeneity and inhomogeneous broadening induced by the nanoenvironment. We demonstrate that the homogeneity of excited-state energy transport in DNA-based photonic wires is dramatically improved by immobilizing photonic wires in aqueous solution without perturbation by the surface. In addition, our study shows that the in situ construction of wire molecules, i.e., the stepwise hybridization of differently labeled oligonucleotides on glass cover slides, further decreases the observed heterogeneity in overall energy-transfer efficiency. The developed strategy enables efficient energy transfer between up to five chromophores in the majority of molecules investigated along a distance of approximately 14 nm. Finally, we used multiparameter SMFS to analyze the energy flow in photonic wires in more detail and to assign residual heterogeneity under optimized conditions in solution to different leakages and competing energy-transfer processes.     

Genome projects and the functional-genomic era

The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.     

FTIR spectra and normal-mode analysis of a tetranuclear manganese adamantane-like complex in two electrochemically prepared oxidation states: relevance to the oxygen-evolving complex of photosystem II

The IR spectra and normal-mode analysis of the adamantane-like compound [Mn(4)O(6)(bpea)(4)](n+) (bpea = N,N-bis(2-pyridylmethyl)ethylamine) in two oxidation states, Mn(IV)(4) and Mn(III)Mn(IV)(3), that are relevant to the oxygen-evolving complex of photosystem II are presented. Mn-O vibrational modes are identified with isotopic exchange, (16)O-->(18)O, of the mono-micro-oxo bridging atoms in the complex. IR spectra of the Mn(III)Mn(IV)(3) species are obtained by electrochemical reduction of the Mn(IV)(4) species using a spectroelectrochemical cell, based on attenuated total reflection [Visser, H.; et al. Anal. Chem. 2001, 73, 4374-4378]. A novel method of subtraction is used to reduce background contributions from solvent and ligand modes, and the difference and double-difference spectra are used in identifying Mn-O bridging modes that are sensitive to oxidation state change. Two strong IR bands are observed for the Mn(IV)(4) species at 745 and 707 cm(-1), and a weaker band is observed at 510 cm(-1). Upon reduction, the Mn(III)Mn(IV)(3) species exhibits two strong IR bands at 745 and 680 cm(-1), and several weaker bands are observed in the 510-425 cm(-1) range. A normal-mode analysis is performed to assign all the relevant bridging modes in the oxidized Mn(IV)(4) and reduced Mn(III)Mn(IV)(3) species. The calculated force constants for the Mn(IV)(4) species are f(r)(IV)= 3.15 mdyn/A, f(rOr) = 0.55 mdyn/A, and f(rMnr) = 0.20 mdyn/A. The force constants for the Mn(III)Mn(IV)(3) species are f(r)(IV)= 3.10 mdyn/A, f(r)(III)= 2.45 mdyn/A, f(rOr) = 0.40 mdyn/A, and f(rMnr) = 0.15 mdyn/A. This study provides insights for the identification of Mn-O modes in the IR spectra of the photosynthetic oxygen-evolving complex during its catalytic cycle.     

Homomorphisms of Products of Graphs into Graphs Without Four Cycles

Given two graphs A and G, we write if there is a homomorphism of A to G and if there is no such homomorphism. The graph G is -free if, whenever both a and c are adjacent to b and d, then a = c or b = d. We will prove that if A and B are connected graphs, each containing a triangle and if G is a -free graph with and , then (here " denotes the categorical product). Received August 31, 1998/Revised April 19, 2000 RID="†" ID="†" Supported by NSERC of Canada Grant #691325.     

Measurement of the electron electric dipole moment using YbF molecules

The most sensitive measurements of the electron electric dipole moment d(e) have previously been made using heavy atoms. Heavy polar molecules offer a greater sensitivity to d(e) because the interaction energy to be measured is typically 10(3) times larger than in a heavy atom. We have used YbF to make the first measurement of this kind. Together, the large interaction energy and the strong tensor polarizability of the molecule make our experiment essentially free of the systematic errors that currently limit d(e) measurements in atoms. Our first result d(e) = (-0.2+/-3.2)x10(-26)e cm is less sensitive than the best atom measurement but is limited only by counting statistics and demonstrates the power of the method.     

Δ-isobar contributions to the charge asymmetry of the three-nucleon bound states

Mechanisms of isospin violation in the nuclear force due to the Δ-isobar are studied. They arise from the coupling of the Δ to the photon and from the charge splitting of the Δ-mass. The charge-asymmetry contribution of the Δ to the ³He-³H binding-energy difference is calculated. Cancellations between different mechanisms are found yielding a small total result. The effect of the photon-induced Δ-excitation, traditionally considered, is negligible. The uncertainty in the Δ-mass splitting shows up in a sizeable theoretical uncertainty for the total result.