Dynamics of 8-Oxoguanine in DNA: Decisive Effects of Base Pairing and Nucleotide Context.

8-Oxo-7,8-dihydroguanine (oxoG), an abundant DNA lesion, can mispair with adenine and induce mutations. To prevent this, cells possess DNA repair glycosylases that excise either oxoG from oxoG:C pairs (bacterial Fpg, human OGG1) or A from oxoG:A mispairs (bacterial MutY, human MUTYH). Early lesion recognition steps remain murky and may include enforced base pair opening or capture of a spontaneously opened pair. We adapted the CLEANEX-PM NMR protocol to detect DNA imino proton exchange and analyzed the dynamics of oxoG:C, oxoG:A, and their undamaged counterparts in nucleotide contexts with different stacking energy. Even in a poorly stacking context, the oxoG:C pair did not open easier than G:C, arguing against extrahelical base capture by Fpg/OGG1. On the contrary, oxoG opposite A significantly populated the extrahelical state, which may assist recognition by MutY/MUTYH.

Cluster halogenation of adamantane and its derivatives with bromine and iodine monochloride.

Noncatalytic halogenation of adamantane (AdH) with bromine or iodine monochloride was found to proceed according to the cluster mechanism featuring high kinetic order with respect to the halogen and a sharp decrease in the calculated energy barrier when additional halogen molecules are involved in the quantum chemical system. In the reaction with Br2, 1-AdBr formed selectively. This reaction proved to be first order in terms of AdH and approximately seventh order in Br2, and its rate does not depend on the rising concentration of HBr. It was demonstrated that the reaction of AdH with ICl is sixth order in ICl, and at the first stage, 1-AdCl forms. According to kinetic data, this reaction requires 3 equivalents of ICl. The rate of 1-AdCl chlorination leading to the 1,3-di-Cl derivative turned out to be 105 times slower than that of AdH. The halogen exchange reaction of 1-AdBr with ICl yielded 1-AdCl, and this reaction is fast and is first order in ICl. Another halogen exchange reaction, AdCl + Br2 = AdBr + BrCl, proceeded much more slowly, and the equilibrium is strongly shifted to the left (equilibrium constant: 10-6). With an excess of either Br2 or ICl, adamantanol (1-AdOH) was found to enter into a slow (compared to AdH) exchange reaction producing 1-AdBr or 1-AdCl, respectively. In all the studied reactions, ICl is ∼106-fold more active than Br2. According to DFT data, the reactions of AdH with Br2 and ICl have similar rate-limiting stages, where the H atom from AdH and X atom from polarized halogen cluster X2n move toward each other forming an HX molecule and ion pair Ad+X2n-1-.

Noncatalytic Bromination of Icosahedral Dicarboranes: The Key Role of Anionic Bromine Clusters Facilitating Br Atom Insertion into the B-H σ-Bond.

The mechanism of the noncatalytic bromination of carboranes was studied experimentally and theoretically. We found that the reactions of o- and m-carboranes 1 and 2 with elemental bromine are first order in the substrate but unusually high (approximately fifth) order in bromine. The calculated energy barriers of these reactions decrease sharply as more bromine molecules are added to the quantum-chemical system. A considerable primary deuterium kinetic isotope effect for the bromination of 2 indicates that the rate-limiting stage is B-H bond breakage. According to quantum-chemical reaction path calculations, the bond breakage proceeds after the intrusion of a bromine atom into the B-H σ-bond. The 9-Br and 9-OH substituents in carborane 1 strongly retard the bromination of the corresponding derivatives. The bromination mechanism of 9-OH-1 is complex and includes neutral, deprotonated, and protonated forms of the carborane. The high experimental kinetic reaction order in bromine, together with quantum chemical modeling, points to a specific mechanism of bromination facilitated by anionic bromine clusters which significantly stabilize the transition state.

Structural and Aggregation Features of a Human κ-Casein Fragment with Antitumor and Cell-Penetrating Properties.

Intrinsically disordered proteins play a central role in dynamic regulatory and assembly processes in the cell. Recently, a human κ-casein proteolytic fragment called lactaptin (8.6 kDa) was found to induce apoptosis of human breast adenocarcinoma MCF-7 and MDA-MB-231 cells with no cytotoxic activity toward normal cells. Earlier, we had designed some recombinant analogs of lactaptin and compared their biological activity. Among these analogs, RL2 has the highest antitumor activity, but the amino acid residues and secondary structures that are responsible for RL2's activity remain unclear. To elucidate the structure-activity relations of RL2, we studied the structural and aggregation features of this fairly large intrinsically disordered fragment of human milk κ-casein by a combination of physicochemical methods: NMR, paramagnetic relaxation enhancement (PRE), Electron Paramagnetic Resonance (EPR), circular dichroism, dynamic light scattering, atomic force microscopy, and a cytotoxic activity assay. It was found that in solution, RL2 exists as stand-alone monomeric particles and large aggregates. Whereas the disulfide-bonded homodimer turned out to be more prone to assembly into large aggregates, the monomer predominantly forms single particles. NMR relaxation analysis of spin-labeled RL2 showed that the RL2 N-terminal region, which is essential not only for multimerization of the peptide but also for its proapoptotic action on cancer cells, is more ordered than its C-terminal counterpart and contains a site with a propensity for α-helical secondary structure.

Data for isolation and properties analysis of diastereomers of a mono-substituted phosphoryl guanidine trideoxyribonucleotide.

This article presents new data on the properties of the diastereomers of a mono-substituted phosphoryl guanidine trideoxyribonucleotides d(TpCp*A) [1,2]. The data include information on isolation, identification, treatment with snake venom phosphodiesterase and structural analysis by 1D and 2D NMR spectroscopy and restrained molecular dynamics analysis. The data can be used for preparation, analysis, application of phosphoryl guanidine oligonucleotide and for development of new nucleic acids derivatives. This data article is associated with the manuscript titled "Diastereomers of a mono-substituted phosphoryl guanidine trideoxyribonucleotide: isolation and properties" [1].

Acid-Catalyzed Versus Thermally Induced C1-C1' Bond Cleavage in 1,1'-Bi-2-naphthol: An Experimental and Theoretical Study.

Experiments show that 1,1'-bi-2-naphthol (BINOL) undergoes facile C1-C1' bond cleavage under action of triflic acid at temperatures above 0 °C to give mainly 2-naphthol along with oligomeric material. CASSCF and MRMP//CASSCF computations have demonstrated unambiguously that this unusual mode of scission of the biaryl bond can occur in the C1,C1'-diprotonated form of BINOL via a mechanism involving homolytic cleavage prompted by the intramolecular electrostatic repulsion. These findings also provide insights into the mechanism of a comparatively easy thermal cleavage of BINOL, implying the intermediacy of its neutral diketo form.

Diastereomers of a mono-substituted phosphoryl guanidine trideoxyribonucleotide: Isolation and properties.

Recently, a new type of nucleic acid analogues with modified phosphate group, namely, phosphoryl guanidine oligonucleotides, has been described. In the present work, we assess the difference between diastereomers of a mono-substituted phosphoryl guanidine oligonucleotide and analyze their resistance to nuclease digestion. Individual diastereomers ('fast' and 'slow') of a trideoxynucleotide d (TpCp*A) were isolated by reverse-phase HPLC. Snake venom phosphodiesterase digestion showed that the native trideoxynucleotide was fully degraded after 30 min, whereas both 'fast' and 'slow' diastereomers of d (TpCp*A) were not completely digested even after 7 days. UV and CD spectra revealed similarities in the structure of the diastereomers. Structural analysis by 1D and 2D NMR spectroscopy also uncovered significant similarity in the properties of Rp and Sp diastereomers. Structural analysis of nuclear Overhauser effect spectroscopy (NOESY) data and restrained molecular dynamics methods showed very flexible single-stranded oligonucleotide structures. Detailed computational analysis of restraint penalty energies via restrained molecular dynamics simulations with the 2D NMR interproton distance data allowed us to conclude that most likely, the 'fast' isomer is the Sp diastereomer, and the 'slow' isomer is the Rp diastereomer.

Elevated reaction order of 1,3,5-tri-tert-butylbenzene bromination as evidence of a clustered polybromide transition state: a combined kinetic and computational study.

The kinetics and mechanism of concurrent bromo-de-protonation and bromo-de-tert-butylation of 1,3,5-tri-tert-butylbenzene at different bromine concentrations were studied experimentally and theoretically. Both reactions have high order in bromine (experimental kinetic orders ∼5 and ∼7, respectively). According to quantum chemical DFT calculations, such high reaction orders are caused by participation of clustered polybromide anions Br2n-1- in transition states. Bromo-de-tert-butylation has a higher order due to its bigger reaction center demanding clusters of extended size. A significant primary deuterium kinetic isotope effect (KIE) for bromo-de-protonation is measured indicating proton removal is rate limiting, as confirmed by computed DFT models. The latter predict a larger value for the KIE than measured and possible explanations for this are discussed.

Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.

DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI→BII transition in the backbone 3' to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.

Protonation Behavior of 1,1'-Bi-2-naphthol and Insights into Its Acid-Catalyzed Atropisomerization.

The behavior of 1,1'-bi-2-naphthol (BINOL) in variety of (super)acid media has been studied by NMR. The results are combined with the theoretical (DFT) study of the role of mono- and diprotonated forms of BINOL in the acid-catalyzed atropisomerization of this compound. It is demonstrated that the process of enantiomeric configuration exchange proceeds mainly via internal rotation around the C1(sp3)-C1'(sp3) bond in intermediates such as C1-monoprotonated keto or C1,C1'-diprotonated forms of BINOL, depending on the acidity level.

Noncatalytic bromination of benzene: A combined computational and experimental study.

The noncatalytic bromination of benzene is shown experimentally to require high 5-14 M concentrations of bromine to proceed at ambient temperatures to form predominantly bromobenzene, along with detectable (<2%) amounts of addition products such as tetra and hexabromocyclohexanes. The kinetic order in bromine at these high concentrations is 4.8 ± 0.06 at 298 K and 5.6 ± 0.11 at 273 K with a small measured inverse deuterium isotope effect using D6 -benzene of 0.97 ± 0.03 at 298 K. These results are rationalized using computed transition states models at the B3LYP+D3/6-311++G(2d,2p) level with an essential continuum solvent field for benzene applied. The model with the lowest predicted activation free energies agrees with the high experimental kinetic order in bromine and involves formation of an ionic, concerted, and asynchronous transition state with a Br8 cluster resembling the structure of the known Br9 (-). This cluster plays three roles; as a Br(+) donor, as a proton base, and as a stabilizing arm forming weak interactions with two adjacent benzene CH hydrogens, these aspects together combining to overcome the lack of reactivity of benzene induced by its aromaticity. The computed inverse kinetic isotope effect of 0.95 agrees with experiment, and arises because C-Br bond formation is essentially complete, whereas C-H cleavage has not yet commenced. The computed free energy barriers for the reaction with 4Br2 and 5Br2 for a standard state of 14.3 M in bromine are reasonable for an ambient temperature reaction, unlike previously reported theoretical models involving only one or two bromines.

Discovery of a new class of antiviral compounds: camphor imine derivatives.

A new class of compounds featuring a camphor moiety has been discovered that exhibits potent inhibitory activity against influenza A(H1N1)pdm09 and A(H5N1) viruses. The synthesized compounds were characterized by spectroscopic analysis; in addition the structures of compound 2 and 14 were elucidated by the X-ray diffraction technique. Structure-activity relationship studies have been conducted to identify the 1,7,7-trimethylbicyclo[2.2.1]heptanes2-ylidene group as the key functional group responsible for the observed antiviral activity. The most potent antiviral compound is imine 2 with therapeutic index more than 500.

Synthesis and biological activity of novel deoxycholic acid derivatives.

We report the synthesis and biological activity of new semi-synthetic derivatives of naturally occurring deoxycholic acid (DCA) bearing 2-cyano-3-oxo-1-ene, 3-oxo-1(2)-ene or 3-oxo-4(5)-ene moieties in ring A and 12-oxo or 12-oxo-9(11)-ene moieties in ring C. Bioassays using murine macrophage-like cells and tumour cells show that the presence of the 9(11)-double bond associated with the increased polarity of ring A or with isoxazole ring joined to ring A, improves the ability of the compounds to inhibit cancer cell growth.