Human apurinic/apyrimidinic (AP) endonuclease APE1 catalyses the hydrolysis of phosphodiester bonds on the 5′ side of an AP-site (in the base excision repair pathway) and of some damaged nucleotides (in the nucleotide incision repair pathway). The range of substrate specificity includes structurally unrelated damaged nucleotides. Here, to examine the mechanism of broad substrate specificity of APE1, we performed pulsed electron–electron double resonance (PELDOR) spectroscopy and pre-steady-state kinetic analysis with Förster resonance energy transfer (FRET) detection of DNA conformational changes during DNA binding and lesion recognition. Equilibrium PELDOR and kinetic FRET data revealed that DNA binding by APE1 leads to noticeable damage-dependent bending of a DNA duplex. Molecular dynamics simulations showed that the damaged nucleotide is everted from the DNA helix and placed into the enzyme’s binding pocket, which is formed by Asn-174, Asn-212, Asn-229, Ala-230, Phe-266 and Trp-280. Nevertheless, no damage-specific contacts were detected between these amino acid residues in the active site of the enzyme and model damaged substrates containing 1,N6-ethenoadenosine, α-adenosine, 5,6-dihydrouridine or F-site. These data suggest that the substrate specificity of APE1 is controlled by the ability of a damaged nucleotide to flip out from the DNA duplex in response to an enzyme-induced DNA distortion.

Pulsed double electron–electron resonance technique (PELDOR or DEER) is often applied to study conformations and aggregation of spin-labelled macromolecules. Because of the ill-posed nature of the integral equation determining the distance distribution function, a regularization procedure is required to restrict the smoothness of the solution. In this work, we performed PELDOR measurements for new flexible nitroxide biradicals based on trolox, which is the synthetic analogue of

The dissociation constants of (4-amino-1-hydroxybutylidene)bisphosphonic (alendronic) acid, (3-(dimethylamino)-1-hydroxypropylidene)bisphosphonic (olpadronic) acid and (3-amino-1-hydroxypropylidene)bisphosphonic (pamidronic) acid were obtained in aqueous solutions (0.10 M KCl) and micellar solutions of cetylpyridinium chloride (0.10 M CPC) at 25.0°C. With the exception of the third dissociation constant of alendronic acid, the dissociation constants of alendronic, olpadronic and pamidronic acids in aqueous solutions matched literature data. The possibility of sodium alendronate determination by acid-base titration by NaOH solution was theoretically grounded on the basis of re-evaluated data of alendronic acid dissociation constants.

We describe a new model-free approach to solve the inverse problem in pulsed double electron-electron resonance (PELDOR, also known as DEER) spectroscopy and obtain the distance distribution function between two radicals from time-domain PELDOR data. The approach is based on analytical solutions of the Fredholm integral equations of the first kind using integral Mellin transforms to provide the distance distribution function directly. The approach appears to confine the noise in the computed distance distribution to short distances and does not introduce systematic distortions. Thus, the proposed analysis method can be a useful supplement to current methods to determine complicated distance distributions.

Non-uniform schemes for collection of pulse dipole spectroscopy data can decrease and redistribute noise in the distance spectrum for increased sensitivity and throughput.

Mechanisms of carbazole photoluminescence quenching by the free and chemically bound nitroxyl radicals in the model bound system "carbazole (CBZ)-imidazolidine nitroxyl radical R • " were investigated and the photophysical properties of the system were studied and com pared with those of free CBZ and R • in solution. The quantum yield and lifetime of fluores cence from the local singlet excited state of the carbazole moiety in the bound CBZ-R • system is three orders of magnitude lower than in free CBZ. The lifetime of the local triplet excited state of the carbazole moiety in the bound system is shorter than 50 ns. The rate constants for intermolecular quenching of the singlet and triplet excited states of free CBZ by R • in acetoni trile were found to be (1.4±0.1)•10 10 and (1.5±0.2)•10 9 L mol -1 s -1 , respectively. The most plausible mechanisms of both free and covalently bound carbazole luminescence quenching by nitroxyl radicals are exchange energy transfer and acceleration of internal conversion due to electron exchange.Keywords: spin labeled luminophores, laser flash photolysis, fluorescence quenching.Spin catalysis of chemical reactions by paramagnetic species occurs in triads of paramagnetic species where spin conversion in a pair of species is initiated by the third electron spin. 1,2 This phenomenon was experimentally confirmed for a number of photochemical, biochemical, and radiation chemical systems. 3-5 The third spin plays the role of the source of external magnetic field in which a spin correlated radical pair created in some (e.g., radia tion chemical) way is placed. Systematic research on spin catalysis requires some model compounds comprising a paramagnetic fragment bound to a partner from the rad ical pair.In this connection, spin labeled luminophores are of particular interest. Theoretical calculations predict a num ber of interesting effects in radiation processes involving them. 6 However, in most cases the paramagnetic center acts as an efficient quencher of the luminescence of such compounds. 4,7-9 It should be noted that it was proposed to use the reverse effect, viz., the rise of the luminescence of fluorophore-nitroxide radical dyads due to reduction of the nitroxide group, for the design of sensors for the superoxide radical, antioxidants, hydrogen peroxide in bi ological systems, 10 and for alkyl radicals in polymers. 11The accelerated internal conversion proceeding by the electron exchange mechanism is the main quenching mechanism of the fluorescence of chemically bound sys tems "luminophore-nitroxide radical". 7,8 However, some other mechanisms of quenching in these systems were pro posed, e.g., acceleration of intersystem crossing (ISC) from the excited singlet to triplet state. 7 These assumptions are based on the fact that quenching of singlet states of lumi nophores by free (chemically unbound) nitroxide radicals (this process has been studied in more details) can follow all known channels including energy transfer, 12,13 elec tron transfer, 14 ISC, 15,16 and internal convers...

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