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Depurination has attracted considerable attention since a long time for it is closely related to the damage and repair of nucleic acids. In the present study, depurination using a pool of 30-nt short DNA pieces with various sequences at diverse pH values was analyzed by High Performance Liquid Chromatography (HPLC). Kinetic analysis results showed that non-enzymatic depurination of oligodeoxynucleotides exhibited typical first-order kinetics, and its temperature dependence obeyed Arrhenius’ law very well. Our results also clearly showed that the linear relationship between the logarithms of rate constants and pH values had a salient point around pH 2.5. Interestingly and unexpectedly, depurination depended greatly on the DNA sequences. The depurination of poly (dA) was found to be extremely slow, and thymine rich sequences depurinated faster than other sequences. These results could be explained to some extent by the protonation of nucleotide bases. Moreover, two equations were obtained based on our data for predicting the rate of depurination under various conditions. These results provide basic data for gene mutagenesis and nucleic acids metabolism in acidic gastric juice and some acidic organelles, and may also help to rectify some misconceptions about depurination.

The ingestion of nucleic acids (NAs) as a nutritional supplement or in genetically modified food has attracted the attention of researchers in recent years. Discussions over the fate of NAs led us to study their digestion in the stomach. Interestingly, we found that NAs are digested efficiently by human gastric juice. By performing digests with commercial, recombinant and mutant pepsin, a protein-specific enzyme, we learned that the digestion of NAs could be attributed to pepsin rather than to the acidity of the stomach. Further study showed that pepsin cleaved NAs in a moderately site-specific manner to yield 3′-phosphorylated fragments and the active site to digest NAs is probably the same as that used to digest protein. Our results rectify the misunderstandings that the digestion of NAs in the gastric tract begins in the intestine and that pepsin can only digest protein, shedding new light on NA metabolism and pepsin enzymology.

In this study, genomic DNA was screened from Halobacillus andaensis NEAU-ST10-40T by selection in Escherichia coli KNabc lacking three major Na+/H+ antiporters. One gene designated upf0118 exhibiting Na+(Li+)/H+ antiport activity was finally cloned. Protein alignment showed that UPF0118 shares the highest identity of 81.5% with an unannotated gene encoding a protein with uncharacterized protein function belonging to UPF0118 family from H. kuroshimensis, but shares no identity with all known specific Na+(Li+)/H+ antiporter genes or genes with Na+(Li+)/H+ antiport activity. Growth test, western blot and Na+(Li+)/H+ antiport assay revealed that UPF0118 as a transmembrane protein exhibits pH-dependent Na+(Li+)/H+ antiport activity. Phylogenetic analysis indicated that UPF0118 clustered with all its homologs belonging to UPF0118 family at a wide range of 22–82% identities with the bootstrap value of 92%, which was significantly distant with all known specific single-gene Na+(Li+)/H+ antiporters and single-gene proteins with the Na+(Li+)/H+ antiport activity. Taken together, we propose that UPF0118 should represent a novel class of Na+(Li+)/H+ antiporter. To the best of our knowledge, this is the first report on the functional analysis of a protein with uncharacterized protein function as a representative of UPF0118 family containing the domain of unknown function, DUF20.

A controllable solid-state electrochemiluminescence (ECL) film based on efficient and stable quenching of ECL of ruthenium(II) tris-(bipyridine) (Ru(bpy)32+) by oxidizing ferrocene (Fc) at the electrode is developed. The ECL intensity is correlated to the distance which is controlled by the conformation of the ferrocene-labeled DNA molecular beacon (Fc-MB) between the Fc and Ru(bpy)32+ immobilized on the electrode. The conformation adjustment is conducted via complementary DNA hybridizing with the bases in the loop of the Fc-MB and changing the temperature of the Fc-MB and the resultant double-stranded DNA (dsDNA). Those events all result in change of the ECL intensity. With such characteristics, the solid-state Ru(bpy)32+-ECL film has the potential to be applied to reagentless DNA ECL biosensors and to calculate thermodynamic parameters of equilibrium constants of MB binding and the stem-loop formation.

Application of an X-ray fluorescence (XRF) microprobe for the analysis of single grains (80 to 1,000 m in diameter) of Clrich minerals for Br has been evaluated for fluorapatite, chlorapatite, scapolite-group minerals (marialite and meonite) and sodalite. A calibration curve based on the Br contents in four international reference materials has been confirmed by measurements on Brbearing standard solutions and by agreement with the results of Cl-rich minerals from instrumental neutron-activation analyses. Absolute errors associated with individual XRF microprobe analyses (i.e., counting statistics alone) are less than 5%, and the calculated limit of detection in the analysis of single mineral grains is ~1 ppm Br. Matrix and grain-size effects are shown to be negligible. Experiments at 1 atmosphere and 800 to 1000°C yield the following distribution coefficients for Br-Cl exchanges between marialite or sodalite and hydrous NaCl-NaBr melts: K D marialite-melt = 0.97 ± 0.08 and K D sodalite-melt = 0.9 ± 0.1. Therefore, the Cl/Br values in marialite and sodalite closely reflect the halogen proportions of their coexisting melts or fluids. The diffusivity of Br in sodalite follows an Arrhenius relation: D Br = 6.5 ϫ 10 -7 exp(-270 ± 10kJ/mol/RT) m 2 /s, over the temperature range from 800 to 1000°C. D Br in marialite is 1.7 ± 0.3 ϫ 10 -19 m 2 /s at 800°C. The Cl/Br weight ratios of marialite in the Tieshan Fe skarn deposit, China, cluster around 650 ± 40, supporting an origin involving hydrothermal brines from associated evaporites. Scapolitegroup minerals in the exoskarns of the Nickel Plate Au skarn deposit, British Columbia, have Cl/Br from 560 to 570, higher than those (130 to 180) of their counterparts in the endoskarns and vuggy cavities. This variation is attributable to an increased involvement of magmatic water from distal to proximal zones. Similarly, scapolite-group minerals in the Grenville U-Th-Mo-REE pegmatite-skarn-vein deposits vary widely in Cl/Br, from 80 to 380, indicative of mixed sources of hydrothermal fluids. This study shows the potential of Br analysis of Cl-rich silicate minerals for constraining the sources and evolution of hydrothermal fluids.Keywords: XRF microprobe, Br, scapolite-group minerals, sodalite, exchange experiments, distribution coefficient, diffusion coefficient, skarn deposits. SOMMAIRENous évaluons l'application d'une microsonde à fluorescence X pour l'analyse de grains isolés (de 80 à 1,000 m de diamètre) pour le Br dans les minéraux porteurs de Cl comme la fluorapatite, la chlorapatite, les minéraux du groupe de la scapolite tels marialite et méionite, et sodalite. Le calibrage a été fait au moyen des teneurs en brome de quatre étalons internationaux, et a été confirmé avec des résultats obtenus pour des solutions standards contenant du Br et des minéraux riches en Cl analysés par activation neutronique instrumentale. Les erreurs absolues associées à une seule analyse par microsonde à fluorescence X, dues aux seules erreurs de comptage, sont inférieures à 5%, et le ...

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