Jürgen Sühnel

DiProDB: a database for dinucleotide properties

DiProDB (http://diprodb.fli-leibniz.de) is a database of conformational and thermodynamic dinucleotide properties. It includes datasets both for DNA and RNA, as well as for single and double strands. The data have been shown to be important for understanding different aspects of nucleic acid structure and function, and they can also be used for encoding nucleic acid sequences. The database is intended to facilitate further applications of dinucleotide properties. A number of property datasets is highly correlated. Therefore, the database comes with a correlation analysis facility. Authors having determined new sets of dinucleotide property values are invited to submit these data to DiProDB.

Cross-link formation of phage lambda DNA in situ photochemically induced by the furocoumarin derivative angelicin.

The combined action of 365 nm ultraviolet light and xanthotoxin or angelicin inhibits the injection of phage lambda into the host. For both furocoumarin derivatives the inhibition of injection is discussed in terms of photochemically induced cross-linking of the DNA inside the phage heads; Cross-linking of DNA has previously been described for xanthotoxin (Musajo, L. and Rodighiero, G. (1972) in Photophysiology (Giese, A.C., ed.), Vol. VII, pp. 115-147, Academic Press, New York and Scott, B.R., Pathak, M.A. and Mohn, G.R. (1976) Mutation Res. 39, 30-74) but not for angelicin. The electronic structures in the first excited states calculated by means of quantum chemistry according to the Pariser-Parr-Pople method are very similar for xanthotoxin, psoralen and angelicin. Hence angelicin should be capable of acting bifunctionally like xanthotoxin, but for sterical reasons such reaction should be possible only for the folded DNA, as in phage heads, but not for diluted aqueous solution of DNA.

Molecular geometry and excited electronic states. Theoretic study on the molecular geometry and the fluorescence lifetime difference of isometric phenylnapkthalenes

Abstract The equilibrium molecular geometries of 1-phenyl- and 2-phenyl-naphthalenes in the electronic So and S1 states have been calculated by minimization of the total energy with respect to all molecular coordinates. The singlet term systems of both isomers have been determined using these results. Although the fluorescence transition energy is nearly the same in both cases it was found that the corresponding electronic transitions were allowed in 1-phenylnaphthalene but were forbidden in 2-phenylnaphthalene. The result explains the different fluorescence lifetimes observed.

Theoretical study of the kinetic isotope effect in proton-transfer reactions. Influence of the interaction potential of reactants on the kinetic isotope effect

Abstract The dependence of the kinetic isotope effect of proton-transfer reactions on the shape of the interaction potential of reactants is investigated within the framework of the quantum-statistical mechanical theory of rate processes for polar media. It is shown that the assumption of equal transfer distances for H + and D + is not justified for realistic interaction potentials. The difference of the transfer distances exhibits a maximum in passing from flat to steep potentials. The results obtained are discussed with regard to the influence on steric hindrance and hydrogen bonding. The influence of the interaction potential between the reactants on the kinetic isotope effect was investigated utilizing the quantum-statistical mechanical theory of rate processes in polar media for reactions with Δ E = 0 and T = 300 K. It was found that the difference of the effective transfer distances r 00 H − r 00 D exhibits a maximum in passing from very flat to steep potentials. The assumption r 00 H = r 00 D is not justified for realistic interaction potentials. The kinetic isotope effect is very sensitive to variations in the intermolecular potential. The isotope effect should be increased by steric hindrance and decreased by hydrogen bonding of the reactants. The first result is supported by experimental facts the second one requires further experimental efforts. After submission of the present work calculations on the KIE using a Morse intermolecular potential were published [37]. It has also been found that the assumption r 00 H = r 00 D is not justified for realistic interaction potentials. The calculations in ref. [37] are restricted to several sets of potential parameters all reproducing the same value of a KIE observed experimentally. The effect of a systematic variation of the potential shape was not investigated.

Interpretation of the vibrational spectra and calculation of the geometries of cycloheptatriene, 7-d-cycloheptatriene and phenyl substituted cycloheptatrienes

Abstract Equilibrium geometries, vibrational frequencies and normal coordinates have been calculated quantum chemically for the strained ring compound cycl oheptatriene and its phenyl substituted derivatives. The calculated geometry of cycloheptatriene agrees with the experimental one. The 1-, 2- and 3-phenyl substituted derivatives have a more nearly planar shape for the seven membered ring than cycloheptatriene itself. Comparison with the experimental vibrational frequencies of cycloheptatriene and 7-d-cycloheptatriene results in a satisfactory interpretation of the vibrational spectra. The three carbon—carbon stretching frequencies of the cycloheptatriene π-system show only minor effects caused by phenyl substitution.

Theory of proton-transfer reactions. The influence of adiabaticity on free energy relations

Abstract The influence of adiabaticity on free energy relations of proton-transfer reactions is investigated within the framework of the quantum-statistical mechanical rate theory. It is found that there may be both for the Bronsted plot and for the free energy dependence of the kinetic isotope effect qualitative differences between the non-adiabatic and the adiabatic case in the exergonic region.

Theory of proton-transfer reactions. On the solvent dependence of the kinetic isotope effect

Abstract For the proton-transfer reactions of trinitrotoluene and 1-(4-nitrophenyl)-1-nitroethane with 1,8-diazabicyclo[5.4.0]undec-7-ene a new interpretation of the marked solvent dependence of the kinetic isotope effect is presented utilizing the quantum-statistical mechanical rate theory. The solvent effect is mainly caused by the different intermolecular interaction potentials in the initial and final states of the reaction and their different solvent dependence originating from the fact that proton-transfer transforms in the cases under study two neutral molecules into an ion-pair. Moreover varying steric hindrance is invoked to explain the different values of the kinetic isotope effect in the same solvent or solvents of comparable polarity.

Computer analysis of phytochrome sequences and reevaluation of the phytochrome secondary structure by Fourier transform infrared spectroscopy.

A repertoire of various methods of computer sequence analysis was applied to phytochromes in order to gain new insights into their structure and function. A statistical analysis of 23 complete phytochrome sequences revealed regions of non-random amino acid composition, which are supposed to be of particular structural or functional importance. All phytochromes other than phyD and phyE from Arabidopsis have at least one such region at the N-terminus between residues 2 and 35. A sequence similarity search of current databases indicated striking homologies between all phytochromes and a hypothetical 84.2-kDa protein from the cyanobacterium Synechocystis. Furthermore, scanning the phytochrome sequences for the occurrence of patterns defined in the PROSITE database detected the signature of the WD repeats of the beta-transducin family within the functionally important 623-779 region (sequence numbering of phyA from Avena) in a number of phytochromes. A multiple sequence alignment performed with 23 complete phytochrome sequences is made available via the IMB Jena World-Wide Web server (http://www.imb-jena.de/PHYTO.html). It can be used as a working tool for future theoretical and experimental studies. Based on the multiple alignment striking sequence differences between phytochromes A and B were detected directly at the N-terminal end, where all phytochromes B have an additional stretch of 15-42 amino acids. There is also a variety of positions with totally conserved but different amino acids in phytochromes A and B. Most of these changes are found in the sequence segment 150-200. It is, therefore, suggested that this region might be of importance in determining the photosensory specificity of the two phytochromes. The secondary structure prediction based on the multiple alignment resulted in a small but significant beta-sheet content. This finding is confirmed by a reevaluation of the secondary structure using FTIR spectroscopy.

Molecular geometry and excited electronic states: Part IV. Theoretical study on molecular geometries and spectral properties of bipyrimidine compounds☆

Abstract The equilibrium geometry of two bipyrimidine photoproducts of nucleic acids in the electronic ground and first excited singlet states has been calculated by minimization of the total energy with respect to all molecular coordinates. Using these results and the method of configuration analysis, this paper discusses whether or not the model of individual chromophores can be invoked to rationalize the spectral properties.

Molecular geometry and excited electronic states

Abstract Equilibrium molecular geometries of styrene in the electronic S 0 , S 1 , and S 2 , states have been calculated within the scope of the adiabatic approximation by minimization of the total energy with respect to all molecular coordinates. Besides the most stable planar structures, some further conformers twisted about the single and/or double bonds have been found. An interpretation of the styrene dual fluorescence is given using these results.