Two-dimensional spectroscopy for non-specialists.

Detailed studies of the excitation dynamics in photosynthetic pigment-proteins require an application of a wide range of spectroscopic methods. From the later part of the previous century, pump-probe and time-resolved fluorescence spectroscopy provided an impressive amount of information. Being simple to grasp, these methods are well-understood and widely used by the photosynthesis research community.

Discrimination of Diverse Coherences Allows Identification of Electronic Transitions of a Molecular Nanoring.

The role of quantum coherence in photochemical functions of molecular systems such as photosynthetic complexes is a broadly debated topic. Coexistence and intermixing of electronic and vibrational coherences has been proposed to be responsible for the observed long-lived coherences and high energy transfer efficiency. However, clear experimental evidence of coherences with different origins operating at the same time has been elusive.

Disorder-Induced Quantum Beats in Two-Dimensional Spectra of Excitonically Coupled Molecules.

Quantum superposition of molecular electronic states is very fragile because of thermal energy fluctuations and the static conformational disorder induced by the intimate surrounding of constituent molecules of the system. However, the nature of the long-lived quantum beats, observed in time-resolved spectra of molecular aggregates at physiological conditions, is still being debated. We present our study of the conditions when long-lived electronic quantum coherences originating from recently proposed inhomogeneous broadening mechanism are enhanced and reflected in the two-dimensional electronic spectra of the excitonically coupled molecular dimer.

Coherence and population dynamics of chlorophyll excitations in FCP complex: Two-dimensional spectroscopy study.

Energy transfer processes and coherent phenomena in the fucoxanthin-chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Qy transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds.

Vibronic phenomena and exciton-vibrational interference in two-dimensional spectra of molecular aggregates.

A general theory of electronic excitations in aggregates of molecules coupled to intramolecular vibrations and the harmonic environment is developed for simulation of the third-order nonlinear spectroscopy signals. It is applied in studies of the time-resolved two-dimensional coherent spectra of four characteristic model systems: weakly/strongly vibronically coupled molecular dimers interacting with high/low frequency intramolecular vibrations. The results allow us to (i) classify and define the typical spectroscopic features of vibronically coupled molecules, (ii) separate the cases, when the long-lived quantum coherences due to vibrational lifetime borrowing should be expected, (iii) define when the complete exciton-vibrational mixing occurs, and (iv) when separation of excitonic and vibrational coherences is possible.

Mapping energy transfer channels in fucoxanthin-chlorophyll protein complex.

Fucoxanthin-chlorophyll protein (FCP) is the key molecular complex performing the light-harvesting function in diatoms, which, being a major group of algae, are responsible for up to one quarter of the total primary production on Earth. These photosynthetic organisms contain an unusually large amount of the carotenoid fucoxanthin, which absorbs the light in the blue-green spectral region and transfers the captured excitation energy to the FCP-bound chlorophylls. Due to the large number of fucoxanthins, the excitation energy transfer cascades in these complexes are particularly tangled.

Vibronic coherence in oxygenic photosynthesis.

Photosynthesis powers life on our planet. The basic photosynthetic architecture consists of antenna complexes that harvest solar energy and reaction centres that convert the energy into stable separated charge. In oxygenic photosynthesis, the initial charge separation occurs in the photosystem II reaction centre, the only known natural enzyme that uses solar energy to split water.

Vibronic models for nonlinear spectroscopy simulations.

It is already well established that the high-frequency intramolecular vibrations are responsible for many observed dynamic phenomena in linear and nonlinear electronic spectroscopy such as the spectral lineshape formation, the transition dipole moment, the lifetime borrowing, and vibrational and mixed coherence beats. All these implications together with the vibronic enhancement of the energy and charge transfer can be explained by the vibronic molecular exciton theory and are highly relevant for the description of the spectral dynamics in photosynthetic pigment-protein complexes. In this paper, a few critical points of the vibronic theory application to linear and nonlinear signals are discussed.

Molecular vibrations-induced quantum beats in two-dimensional electronic spectroscopy.

Quantum beats in nonlinear spectroscopy of molecular aggregates are often attributed to electronic phenomena of excitonic systems, while nuclear degrees of freedom are commonly included into models as overdamped oscillations of bath constituents responsible for dephasing. However, molecular systems are coupled to various high-frequency molecular vibrations, which can cause the spectral beats hardly distinguishable from those created by purely electronic coherences. Models containing damped, undamped, and overdamped vibrational modes coupled to an electronic molecular transition are discussed in this paper in context of linear absorption and two-dimensional electronic spectroscopy.

Quantum coherence and disorder-specific effects in simulations of 2D optical spectra of one-dimensional J-aggregates.

Time-resolved two-dimensional photon-echo (2D PE) spectra of linear J-aggregates containing four molecules per unit cell--a model system for a concentrated water solution of the pseudo-isocyanine dye--is theoretically considered. Analysis of a single unit cell and the full-sized aggregate is consistently carried out. Spectral features of a single unit cell are sorted out by assigning them to specific double-sided Feynman diagrams.

Sequence similarity among type-II restriction endonucleases, related by their recognized 6-bp target and tetranucleotide-overhang cleavage.

The type-II restriction endonucleases (ENases) EcoRI (recognition sequence G decreases AATTC), RsrI (G decreases AATTC), XcyI (C decreases CCGGG), Cfr9I (C decreases CCGGG) and MunI (C decreases AATTG), all cleave hexanucleotide palindromic sequences, leaving tetranucleotide 5'-overhangs. Two regions of similarity that appear in the same order and relative position were identified among the amino-acid sequences of ENases. These regions map to the structural elements of EcoRI involved in the building of the catalytic site and in interactions with the central nucleotides of the recognized sequence.

Sequence motifs characteristic for DNA [cytosine-N4] and DNA [adenine-N6] methyltransferases. Classification of all DNA methyltransferases.

Two additional conserved motifs (CM), CM Is and CM III, have been found in addition to well-known CM I and CM II within the primary amino acid sequences of almost all m6A- and m4C-methyltransferases (MTases). The boundaries of all four CM were defined and their consensus sequences characteristic both for different classes, as well as for all N-MTases, were derived. Some regular deviations at fixed positions of the consensus sequences CM Is, CM I and CM II, typical for separate classes of N-MTases, were presumed to correlate.

CAATTG-specific restriction-modification munI genes from Mycoplasma: sequence similarities between R.MunI and R.EcoRI.

The genes coding for the MunI restriction-modification (R-M) system, which recognize the sequence 5'-CAATTG, have been cloned and expressed in Escherichia coli, and their nucleotide sequences have been determined. The restriction endonuclease (ENase; R.MunI) is encoded by an open reading frame (ORF) of 606 bp, and a 699-bp ORF codes for the methyltransferase (MTase).

Cloning and analysis of translational control for genes encoding the Cfr9I restriction-modification system.

The complete type-II Cfr9I restriction-modification (R-M) system of Citrobacter freundii strain RFL9, recognizing the DNA sequence CCCGGG, has been cloned and expressed, and functionally active enzymes have been produced in Escherichia coli. Both the methyltransferase (MTase; M.Cfr9I) and restriction endonuclease (ENase; R.

Cloning and sequence analysis of the genes coding for Eco57I type IV restriction-modification enzymes.

A 6.3 kb fragment of E.coli RFL57 DNA coding for the type IV restriction-modification system Eco57I was cloned and expressed in E.

Purification and properties of the Eco57I restriction endonuclease and methylase--prototypes of a new class (type IV).

The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa.

Alw26I, Eco31I and Esp3I--type IIs methyltransferases modifying cytosine and adenine in complementary strands of the target DNA.

The specificity of three DNA methyltransferases M.Alw26I, M.Eco31I and M.

[Mycoplasma restriction-modification system MunI and its possible role in pathogenesis processes].

The restriction-modification system, named RMMunI, has been purified and characterised from Friend murine erythroleukemia cells. The site-specific endonuclease recognizes and cleaves the 5'C1AATTG nucleotide sequence. RMunI is an isoschizomer of RMfeI from Mycoplasma fermentans.

M.Smal is an N4-methylcytosine specific DNA-methylase.

An enzymatic activity rendering DNA immune to the action of the Smal restriction endonuclease in the presence of S-adenosyl-L-methionine has been detected in Serratia marcescens Sb. This methylase, M.Smal, modifies the second cytosine residue of the substrate sequence CCCGGG yielding N4-methylcytosine.

An improved method for the detection of Dcm methylation in DNA molecules.

The intrinsic insensitivity of EcoRII recognition sites in RF DNAs of phage M13 and vector M13mp18 towards this restriction endonuclease can be overcome by adding site-specific oligodeoxyribonucleotide duplexes to the restriction sample. Since Dcm- DNA but not Dcm(+)-methylated DNA becomes susceptible under these conditions, this procedure constitutes an improvement of the Dcm methylation assay.

[Site-specific endonucleases LplI and AagI].

New site-specific endonucleases LplI and AagI have been isolated from the Lactobacillus plantarum and Achromobacter agile cells, respectively. The enzymes' purification stages included treatment of cell-free extracts with polyethylenimine, fractionation in two-phase system by Albertsson's method, chromatography on blue Sepharose and DEAE-cellulose. The results of cleavage of a 5'-32P-labelled oligodeoxynucleotide duplex by restriction endonucleases LplI and AagI indicate that these enzymes recognize and cut the sequence AT decreases CGAT, being therefore true isoschizomers of the ClaI restriction endonuclease from Caryophanon latum.

[Isolation and characteristics of new restriction endonucleases from Haemophilus influenzae].

Various strains of Haemophilus influenzae have been examined for the presence of site-specific endonuclease activities, and eleven restriction endonucleases have been isolated from seven strains. For all the endonucleases recognition sequences were determined, for three of them cleavage sites being identified. The enzymes proved to be isoschizomers of known endonucleases, viz.

Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases.

The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been determined. The predicted methylases are proteins of 454 and 300 amino acids, respectively. Primary structure comparison of M.