Structures and dynamics of 8-oxo-7,8-dihydro-2'-deoxyguanosine in neutral and basic aqueous solutions by spectroscopy.

8-oxo-7,8-dihydro-2'-dexyoguanine (8-oxo-dG) can be tautomerized to a 6-enolate,8-keto tautomer through nearby-NH deprotonation at elevated pH. In this work, the N3-protonated 8-oxo-dG tautomers in deuterated pH-buffer solutions were studied using steady-state UV/Vis, FTIR, and ultrafast two-dimensional IR spectroscopies. The presence of 6,8-diketo and C6-anionic tautomers at neutral to basic conditions (pD = 7.4-12.0) was revealed by UV/Vis and FTIR results and was further confirmed by 2D IR signals in both diagonal and off-diagonal regions. However, the C6-enol tautomer, which may be an intermediate during the transition from 6,8-diketo to C6-enolate,C8-keto, was not observed appreciably due to its extreme low population. Furthermore, the neutral-to-anionic tautomeric transition of N3H-8-oxo-dG studied in this work occurs under more basic conditions than the N1H-8-oxo-dG reported previously, showing a higher pKa value for N3H than N1H. Finally, vibrational relaxation of the carbonyl stretching mode was found to be both molecular site dependent and pD dependent for 8oxo-dG. Taken together, this work shows that the ultrafast infrared spectroscopic method is effective for examining tautomers and their dynamics in nucleic acids.

Development of competitive and noncompetitive lateral flow immunoassays for pendimethalin using synthetic peptides.

Peptidomimetic and anti-immunocomplex peptides can be easily isolated from phage display libraries, and can be used as alternatives to chemical competing haptens to improve the sensitivity of small molecule immunoassay. In this work, 16 peptidomimetics and 7 anti-immunocomplex peptides of pendimethalin (PND) were obtained from cyclic 7-, 8-, 9-, and 10-residue peptide phage libraries. Peptidomimetic EJ-2 (CMFTGTDFPC) with the highest sensitivity in competitive phage enzyme-linked immunosorbent assay (ELISA) and immunocomplex peptide EF-30 (CNPGWPPIPC) with the highest sensitivity in noncompetitive phage ELISA were selected to prepare phage-free peptides with GGGSSK-biotin at the C-terminus. Competitive and noncompetitive lateral flow immunoassays (CLFIA and NLFIA) were developed by using the phage-free peptides. After optimization, the CLFIA and NLFIA showed visual limit of detections (vLODs) of 5 ng/mL and 2.5 ng/mL, respectively, which were improved two- and fourfold compared with a LFIA based on chemical hapten. The NLFIA showed better sensitivity than CLFIA in the detection of spiked samples, and can meet the detection requirements for agro-products regulated by EU and China. The detection results of CLFIA and NLFIA for blind samples were consistent with that of ultra performance liquid chromatography/tandem mass spectrometry.

Computational study on the prototropic tautomerism between simple oxo-, thio-, carbon-, aza-hydrazones, and their respective azines.

Most hydrazone compounds prefer the azine tautomeric states. However, oxygen-/sulfur-substituted compounds prefer hydrazone tautomers. In this study, density functional theory at M062X level with the basis set of 6-311 + + g(2d, 2p), with MP2/cc-pVTZ for reference, was used to investigate the different tautomeric mechanisms between hydrazone and azine forms with oxygen, sulfur, carbon, and nitrogen as negative centers. The energetic stabilities are in the order as oxygen- < sulfur- < imine- < amidino- < carbene-substituted hydrazones with respect to their azine tautomeric structures. Resonance of the molecular structures might be the geometrical basis for their energy stabilities and were estimated based on HOMED indices. Further, the increased proton affinities in the trend as hydroxyl < sulfhydryl < imine terminal groups account for their increasing azine preferences. Proton release was examined for the reversible equilibrium from azine to hydrazone by calculating the transition energy barrier of H transfer. It is favorable to form hydrazone tautomers for oxygen and sulfur containing groups, while it is less favorable for amino-substituted ones. Azine form is the most stable tautomer for methyl substituted.

Theoretical study of the oxidation reactions of methylacrylic acid and methyl methacrylate by triplet O2.

The oxidations of organic compounds and polymers by triplet O2 were called "dark oxidation" or "auto-oxidation", in contrast to their "photo-oxidation" by singlet O2. To study the relevant dark oxidation mechanism we take methylacrylic acid (MAA) and methyl methacrylate (MMA) as prototypes to study their reactions with triplet O2 by performing density functional theory calculations. Two reaction channels, the C-H bond oxidation and C=C bond oxidation, have been characterized in detail. The structures of the initial contact charge-transfer complexes, intermediates, transition states, and final oxides involved in the reactions have been localized at the UB3LYP/6-311+G(d,p) level. It is found that the C-H bond in the methyl group connected to the C=C bond presents relatively higher reactivity toward triplet O2 than the C=C bond itself. Thus, the reactions are expected to proceed via the C-H bond oxidation branch at room temperature and also via C=C bond oxidation at elevated temperature. In this sense, an effective method for preventing or retarding the dark oxidations of MAA and MMA in a natural environment is to chemically decorate or protect the C-H bond in the methyl connected to the C=C bond. The present results are expected to provide a general guide for understanding the dark oxidation mechanism of organic compounds and polymers.