Photoinduced charge and energy transfer involving fullerene derivatives.

In this feature article, a brief overview over the photoinduced energy and charge transfer mechanisms involving fullerenes will be presented. The photoinduced charge separation between organic donor and acceptor molecules is the basic photophysical mechanism for natural photosynthesis and nearly all organic solar cell concepts. We will give a short introduction to the mechanisms of excited state charge transfer and resonant energy transfer and present examples of relevant applications in organic optoelectronics and photodynamic tumor therapy.     

Electronic interactions and energy transfer in oligothiophene-linked bis-porphyrins.

The photophysical and spectroscopic properties of a series of bis-porphyrin compounds meso-meso-linked via oligothiophene bridges are reported. In particular the effects of the different bridges on the porphyrin properties as well as their ability to enhance energy transfer is investigated. The main findings are: a splitting of the degeneracy of the porphyrin Soret band transition with a lower energy transition aligned along the bridge, a dramatic decrease in triplet lifetime and the occurrence of "superexchange" as the main mechanism for mediating singlet-singlet energy transfer in the case where the bridge is a quaterthiophene. Our results show significant perturbations of the intrinsic porphyrin properties induced by the bridge, which are important for the function of porphyrin assemblies.     

Dynamics of transfer of charge carriers in DNA molecule

An equivalent electrical circuit of DNA molecule is suggested and used to model the charge transfer dynamics in the molecule. Its switching time is shown to be in the femtosecond time range and to depend on the frequency of input electric signal. Raising the input signal frequency from 1 GHz to 4 THz and lowering the temperature decrease the current through DNA. The switching rate of DNA molecule is determined by the processes of delocalization and localization of holes, which is achieved by variation in the base sequence and length.     

Excitation energy transfer and charge separation in photosystem II membranes revisited

We have performed time-resolved fluorescence measurements on photosystem II (PSII) containing membranes (BBY particles) from spinach with open reaction centers. The decay kinetics can be fitted with two main decay components with an average decay time of 150 ps. Comparison with recent kinetic exciton annihilation data on the major light-harvesting complex of PSII (LHCII) suggests that excitation diffusion within the antenna contributes significantly to the overall charge separation time in PSII, which disagrees with previously proposed trap-limited models. To establish to which extent excitation diffusion contributes to the overall charge separation time, we propose a simple coarse-grained method, based on the supramolecular organization of PSII and LHCII in grana membranes, to model the energy migration and charge separation processes in PSII simultaneously in a transparent way. All simulations have in common that the charge separation is fast and nearly irreversible, corresponding to a significant drop in free energy upon primary charge separation, and that in PSII membranes energy migration imposes a larger kinetic barrier for the overall process than primary charge separation.     

Dynamics of charge carrier transfer in a DNA molecule

An equivalent electric circuit has been developed which describes the charge transfer in DNA molecule. A computer simulation of the charge carrier transfer dynamics in the molecule has been performed based on this circuit. It was found that the switching time of a molecular junction lies in the femtosecond range and depends on the frequency of the input electric signal. An increase in the frequency of the input signal in the range from 1 GHz to 4 THz and a reduction of temperature lead to a decrease in the current passing through the DNA molecule. It has been shown that the sequence of the DNA base pairs defines the rate of localization and delocalization of holes and controls the signal propagation rate in the DNA molecule.     

Kinetics of charge transfer in DNA containing a mismatch

Charge transfer (CT) in DNA offers a unique approach for the detection of a single-base mismatch in a DNA molecule. While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear. Recently, we determined the rate constants of the CT through the fully matched DNA, and we can now estimate the CT rate constant for a certain fully matched sequence. We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics. In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.     

Conformational coupling in DNA polymerase information transfer.

The extraordinary fidelity of DNA replication during forward polymerization and exonuclease error correction is largely a function of a conformational change that occurs in response to a correct dNTP binding to properly base-paired duplex DNA. The conformational change serves as a kinetic barrier to effect the rapid incorporation of correct bases while minimizing the rate of polymerization with incorrect bases and allowing for selective removal of mismatches. However, in spite of the number of attractive features to the conformational change model, the evidence in support of such a rate-limiting step is still subject to significant uncertainty. It is the challenge of further work on DNA polymerases as well as many other enzyme systems to devise new methods to define the transient state of the enzyme during catalysis and to relate the kinetic and thermodynamic parameters to the enzyme structure.     

Combined hopping-superexchange mechanism of charge transfer in DNA: Consideration of nearest interactions

Within the framework of a previously developed combined hopping-superexchange mechanism, a model of charge transfer in DNA is proposed that takes into account all nearest interactions. The charge transfer rate constants calculated using this model for a number of nucleotide sequences agree well with the experimentally measured values.     

Lipid radicals--possible mediators of charge transfer and energy transformation (a hypothesis)

A number of enzymatic reactions with the participation of lipid radicals is discussed in the article. It is supposed that NADPH- and NADH-dependent formation of the lipid radicals has a functional importance. The uptake of oxygen by free radicals is considered as one of the reactions of radicals utilization. It is proposed that other reactions with participation of lipid radicals can take place in the membranes of microsomes and mitochondria: the reaction of electron transfer from flavoprotein to cytochrome P448 and the reaction of energy transfer which provide the coupling of oxidation and phosphorylation.     

Sequence dependence of energy transfer in DNA oligonucleotides

The sequence, temperature, concentration, and solvent dependence of singlet energy transfer from normal DNA bases to the 2-aminopurine base in synthesized DNA oligomers were investigated by optical spectroscopy. Transfer was shown directly by a variable fluorescence excitation band at 260-280 nm. Adenine (A) is the most efficient energy donor by an order of magnitude. Stacks of A adjacent to 2AP act as an antenna for 2AP excitation. An interposed G, C, or T base between A and 2AP effectively blocks transfer from A to 2AP. Base stacking facilitates transfer, while base pairing reduces energy transfer slightly. The efficiency is differentially temperature dependent in single- and double-stranded oligomers and is highest below 0 degrees C in samples measured. An efficiency transition occurs well below the melting transition of a double-stranded decamer. The transfer efficiency in the duplex decamer d(CTGA[2AP]TTCAG)(2) is moderately dependent on the sample and salt concentration and is solvent dependent. Transfer at physiological temperature over more than a few bases is improbable, except along consecutive A's, indicating that singlet energy transfer is not a major factor in the localization of UV damage in DNA. These results have features in common with recently observed electron transfer from 2AP to G in oligonucleotides.     

The medium reorganization energy for the charge transfer reactions in proteins

A low static dielectric permittivity of proteins causes the low reorganization energies for the charge transfer reactions inside them. This reorganization energy does not depend on the pre-existing intraprotein electric field. The charge transferred inside the protein interacts with its aqueous surroundings; for many globular proteins, the effect of this surroundings on the reorganization energy is comparable with the effect of reorganization of the protein itself while for the charge transfer in the middle of membrane the aqueous phase plays a minor role. Reorganization energy depends strongly on the system considered, and hence there is no sense to speak on the "protein reorganization energy" as some permanent characteristic parameter. We employed a simple algorithm for calculation of the medium reorganization energy using the numerical solution of the Poisson-Boltzmann equation. Namely, the reaction field energy was computed in two versions - all media having optical dielectric permittivity, and all the media with the static one; the difference of these two quantities gives the reorganization energy. We have calculated reorganization energies for electron transfer in cytochrome c, various ammine-ruthenated cytochromes c, azurin, ferredoxin, cytochrome c oxidase, complex of methylamine dehydrogenase with amicyanin, and for proton transfer in α-chymotrypsin. It is shown that calculation of the medium reorganization energy can be a useful tool in analysis of the mechanisms of the charge transfer reactions in proteins.     

DNA sequencing with solid-phase-capturable dideoxynucleotides and energy transfer primers

False terminations occurring in fluorescent dye-primer DNA sequencing, and nonsequencing primer extension DNA fragments generated in dye-terminator sequencing cause background noise in fluorescent electropherograms, leading to errors in sequence determination. We describe here a DNA sequencing chemistry that produces accurate and clean sequencing data on a fluorescent DNA sequencer, eliminating the false terminations and background noise. The procedure involves coupling fluorescence energy transfer (ET) primers that produce high fluorescent signals with solid-phase-capturable biotinylated dideoxynucleotides to generate Sanger DNA sequencing fragments. After the sequencing reaction,the DNA extension fragments that carry a biotin at the 3' end are captured with streptavidin-coated magnetic beads, while the other components in the sequencing reaction are washed away. Only pure DNA extension products terminated by the biotinylated dideoxynucleotides are released from the magnetic beads and are loaded onto a sequencing gel to produce accurate sequencing data.     

Excitation energy transfer and charge separation in the isolated Photosystem II reaction center

The nature of excitation energy transfer and charge separation in isolated Photosystem II reaction centers is an area of considerable interest and controversy. Excitation energy transfer from accessory chlorophyll a to the primary electron donor P680 takes place in tens of picoseconds, although there is some evidence that thermal equilibration of the excitation between P680 and a subset of the accessory chlorophyll a occurs on a 100-fs timescale. The intrinsic rate for charge separation at low temperature is accepted to be ca. (2 ps)^–1, and is based on several measurements using different experimental techniques. This rate is in good agreement with estimates based on larger sized particles, and is similar to the rate observed with bacterial reaction centers. However, near room temperature there is considerable disagreement as to the observed rate for charge separation, with several experiments pointing to a ca. (3 ps)^–1 rate, and others to a ca. (20 ps)^-1 rate. These processes and the experiments used to measure them will be reviewed.Abbreviations Chl chlorophyll - FWHM full-width at half-maximum - Pheo pheophytin - PS II Photosystem II - P680 primary electron donor of the Photosystem II reaction center - RC reaction center The US Government right to retain a non-exclusive, royalty free licence in and to any copyright is acknowledged.     

New energy transfer dyes for DNA sequencing.

We have synthesized a set of four energy transfer dyes and demonstrated their use in automated DNA sequencing. The donor dyes are the 5- or 6-carboxy isomers of 4'-aminomethylfluorescein and the acceptor dyes are a novel set of four 4,7-dichloro-substituted rhodamine dyes which have narrower emission spectra than the standard, unsubstituted rhodamines. A rigid amino acid linker, 4-aminomethylbenzoic acid, was used to separate the dyes. The brightness of each dye in an automated sequencing instrument equipped with a dual line argon ion laser (488 and 514 nm excitation) was 2-2.5 times greater than the standard dye-primers with a 2 times reduction in multicomponent noise. The overall improvement in signal-to-noise was 4- to 5-fold. The utility of the new dye set was demonstrated by sequencing of a BAC DNA with an 80 kb insert. Measurement of the extinction coefficients and the relative quantum yields of the dichlororhodamine components of the energy transfer dyes showed their values were reduced by 20-25% compared with the dichlororhodamine dyes alone.