From Rational Design of Drug Crystals to Understanding of Nucleic Acid Structures: Lamivudine Duplex

A DNA-like duplex of nucleosides is probable to exist even without the 5`-phosphate groups needed to assemble the chain backbone. However, double-stranded helical structures of nucleosides are unknown. Here, we report a duplex of nucleoside analogs that is spontaneously assembled due to stacking of the neutral and protonated molecules of lamivudine, a nucleoside reverse transcriptase inhibitor (NTRI) widely used in anti-HIV drug combinatory medication. The left-handed lamivudine duplex has features similar to those of i-motif DNA, as the face-to-face base stacking and the helix rise per base pair. Furthermore, the protonation pattern on alternate bases expected for it DNA-like duplex stabilized by pairing of neutral and protonated cytosine fragments was observed for the first time in the lamivudine double-stranded helix. This structure demonstrates that hydrogen bonds can substitute for covalent phosphodiester linkage in the stabilization of the duplex backbone. This interesting example of spontaneous molecular self-organization indicates that the 5`-phosphate group could not be a requirement for duplex assembly.

Potential sites of triple-helical nucleic acid formation in chromosomes of Rhynchosciara (Diptera: Sciaridae) and Drosophila melanogaster

Antibodies to specific nucleic acid conformations are amongst the methods that have allowed the study of non-canonical (Watson-Crick) DNA structures in higher organisms. In this work, the structural limitations for the immunological detection of DNA.RNA hybrid duplexes were examined using specific RNA homopolymers as probes for homopolymer polydeoxyadenylic acid (poly(dA)).polydeoxythymidylic acid (poly(dT))-rich regions of Rhynchosciara americana (Diptera: Sciaridae) chromosomes. Anti-DNA.RNA duplexes did not react with the complex formed between chromosomal poly(dA) and exogenous polyuridylic acid (poly(rU)). Additionally, poly(rU) prevented the detection of polyadenylic acid.poly(dT) hybrid duplexes preformed in situ. These results raised the possibility that three-stranded structures rather than duplexes were formed in chromosomal sites. To test this hypothesis, the specificity of antibodies to triple-helical nucleic acids was reassessed employing distinct nucleic acid configurations. These antibodies were raised to the poly(dA).poly(rU).poly(rU) complex and have been used here for the first time in immunocytochemistry. Anti-triplex antibodies recognised the complex poly(dA).poly(rU).poly(rU) assembled with poly(rU) in poly(dA).poly(dT)-rich homopolymer regions of R. americana chromosomes. The antibodies could not detect short triplex stretches, suggesting the existence of constraints for triple-helix detection, probably related to triplex tract length. In addition, anti-poly(dA).poly(rU).poly(rU) antibodies reacted with the pericentric heterochromatin of RNase-treated polytene chromosomes of R. americana and Drosophila melanogaster. In apparent agreement with data obtained in cell types from other organisms, the results of this work suggest that significant triple-helix DNA extensions can be formed in pericentric regions of these species.

Acid-base transport by the renal distal nephron

The functional versatility of the distal nephron is mainly due to the large cytological heterogeneity of the segment. Part of Na(+) uptake by distal tubules is dependent on Na(+)/H(+). exchanger 2 (NHE2), implicating a role of distal convoluted cells also in acid-base homeostasis. In addition, intercalated (IC) cells expressed in distal convoluted tubules, connecting tubules and collecting ducts are involved in the final regulation of acid-base excretion. IC cells regulate acid-base handling by 2 main transport proteins, a V-type H(+)-ATPase and a Cl/HCO(3)(-) exchanger, localized at different membrane domains. Type A IC cells are characterized by a luminal H(+)-ATPase in series with a basolateral Cl/HCO(3)(-) exchanger, the anion exchanger AE1. Type B IC cells mediate HCO(3)(-) secretion through the apical Cl(-)/HCO(3)(-) exchanger pendrin in series with a H(+)-ATPase at the basolateral membrane. Alternatively, H(+)/K(+)-ATPases have also been found in several distal tubule cells, particularly in type A and B IC cells. All of these mechanisms are finely regulated, and mutations of 1 or more proteins ultimately lead to expressive disorders of acid-base balance.

Metabolic acidosis in patients with severe sepsis and septic shock: A longitudinal quantitative study

Objective: To describe the composition of metabolic acidosis in patients with severe sepsis and septic shock at intensive care unit admission and throughout the first 5 days of intensive care unit stay. Design: Prospective, observational study. Setting: Twelve-bed intensive care unit. Patients: Sixty patients with either severe sepsis or septic shock. Interventions: None. Measurements and Main Results: Data were collected until 5 days after intensive care unit admission. We studied the contribution of inorganic ion difference, lactate, albumin, phosphate, and strong ion gap to metabolic acidosis. At admission, standard base excess was -6.69 +/- 4.19 mEq/L in survivors vs. -11.63 +/- 4.87 mEq/L in nonsurvivors (p < .05); inorganic ion difference (mainly resulting from hyperchloremia) was responsible for a decrease in standard base excess by 5.64 +/- 4.96 mEq/L in survivors vs. 8.94 +/- 7.06 mEq/L in nonsurvivors (p < .05); strong ion gap was responsible for a decrease in standard base excess by 4.07 +/- 3.57 mEq/L in survivors vs. 4.92 +/- 5.55 mEq/L in nonsurvivors with a nonsignificant probability value; and lactate was responsible for a decrease in standard base excess to 1.34 +/- 2.07 mEq/L in survivors vs. 1.61 +/- 2.25 mEq/L in nonsurvivors with a nonsignificant probability value. Albumin had an important alkalinizing effect in both groups; phosphate had a minimal acid-base effect. Acidosis in survivors was corrected during the study period as a result of a decrease in lactate and strong ion gap levels, whereas nonsurvivors did not correct their metabolic acidosis. In addition to Acute Physiology and Chronic Health Evaluation 11 score and serum creatinine level, inorganic ion difference acidosis magnitude at intensive care unit admission was independently associated with a worse outcome. Conclusions: Patients with severe sepsis and septic shock exhibit a complex metabolic acidosis at intensive care unit admission, caused predominantly by hyperchloremic acidosis, which was more pronounced in nonsurvivors. Acidosis resolution in survivors was attributable to a decrease in strong ion gap and lactate levels. (Crit Care Med 2009; 37:2733-2739)

Effects of glutamine supplementation on kidney of diabetic rat

Glutamine is the most important donor of NH(3) in kidney playing an important role in acid-base buffering system. Besides this effect, glutamine presents many other relevant functions in the whole body, such as a precursor of arginine in adult and neonates. In addition to these effects, some studies have shown that glutamine can potentiate renal disease. In the present study, the effect of short-term treatment (15 days) with glutamine on control and diabetic rats was investigated. Using biochemical, histological and molecular biology analysis from control and diabetic rats we verified that glutamine supplementation increase in pro-inflammatory interleukins (IL)-1 beta and IL-6 content in renal cortex and induce alteration in glomerular characteristics. This study showed that short-term treatment with glutamine in association with increased glucose levels could cause important alterations in glomerular morphology that may result in fast progression of kidney failure.

CspC and CspD are essential for Caulobacter crescentus stationary phase survival

The cold shock response in bacteria involves the expression of low-molecular weight cold shock proteins (CSPs) containing a nucleic acid-binding cold shock domain (CSD), which are known to destabilize secondary structures on mRNAs, facilitating translation at low temperatures. Caulobacter crescentus cspA and cspB are induced upon cold shock, while cspC and cspD are induced during stationary phase. In this work, we determined a new coding sequence for the cspC gene, revealing that it encodes a protein containing two CSDs. The phenotypes of C. crescentus csp mutants were analyzed, and we found that cspC is important for cells to maintain viability during extended periods in stationary phase. Also, cspC and cspCD strains presented altered morphology, with frequent non-viable filamentous cells, and cspCD also showed a pronounced cell death at late stationary phase. In contrast, the cspAB mutant presented increased viability in this phase, which is accompanied by an altered expression of both cspC and cspD, but the triple cspABD mutant loses this characteristic. Taken together, our results suggest that there is a hierarchy of importance among the csp genes regarding stationary phase viability, which is probably achieved by a fine tune balance of the levels of these proteins.

Inhibition of Trypanosoma brucei glucose-6-phosphate dehydrogenase by human steroids and their effects on the viability of cultured parasites

Dehydroepiandrosterone ( DHEA) is known as an intermediate in the synthesis of mammalian steroids and a potent uncompetitive inhibitor of mammalian glucose-6-phosphate dehydrogenase (G6PDH), but not the enzyme from plants and lower eukaryotes. G6PDH catalyzes the first step of the pentose-phosphate pathway supplying cells with ribose 5-phosphate, a precursor of nucleic acid synthesis, and NADPH for biosynthetic processes and protection against oxidative stress. In this paper we demonstrate that also G6PDH of the protozoan parasite Trypanosoma brucei is uncompetitively inhibited by DHEA and epiandrosterone (EA), with K(i) values in the lower micromolar range. A viability assay confirmed the toxic effect of both steroids on cultured T. brucei bloodstream form cells. Additionally, RNAi mediated reduction of the G6PDH level in T. brucei bloodstream forms validated this enzyme as a drug target against Human African Trypanosomiasis. Together these findings show that inhibition of G6PDH by DHEA derivatives may lead to the development of a new class of anti-trypanosomatid compounds. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.

Catalytic mechanism of inulinase from Arthrobacter sp S37

Detailed catalytic roles of the conserved Glu323, Asp460, and Glu519 of Arthrobacter sp. S37 inulinase (EnIA), a member of the glycoside hydrolase family 32, were investigated by site-directed mutagenesis and pH-dependence studies of the enzyme efficiency and homology modeling were carried out for EnIA and for D460E mutant. The enzyme efficiency (k(cat)/K-m) of the E323A and E519A mutants was significantly lower than that of the wild-type due to a substantial decrease in k(cat), but not due to variations in K-m, consistent with their putative roles as nucleophile and acid/base catalyst, respectively. The D460A mutant was totally inactive, whereas the D460E and D460N mutants were active to some extent, revealing Asp460 as a catalytic residue and demonstrating that the presence of a carboxylate group in this position is a prerequisite for catalysis. The pH-dependence studies indicated that the pK(a) of the acid/base catalyst decreased from 9.2 for the wild-type enzyme to 7.0 for the D460E mutant, implicating Asp460 as the residue that interacts with the acid/base catalyst Glu519 and elevates its pK(a). Homology modeling and molecular dynamics simulation of the wild-type enzyme and the D460E mutant shed light on the structural roles of Glu323, Asp460, and Glu519 in the catalytic activity of the enzyme. (C) 2008 Elsevier Inc. All rights reserved.

Comparative study of liponucleosides in Langmuir monolayers as cell membrane models

Liponucleosides may assist the anchoring of nucleic acid nitrogen bases into biological membranes for tailored nanobiotechnological applications. To this end precise knowledge about the biophysical and chemical details at the membrane surface is required. In this paper, we used Langmuir monolayers as simplified cell membrane models and studied the insertion of five lipidated nucleosides. These molecules varied in the type of the covalently attached lipid group, the nucleobase, and the number of hydrophobic moieties attached to the nucleoside. All five lipidated nucleosides were found to be surface-active and capable of forming stable monolayers. They could also be incorporated into dipalmitoylphosphatidylcholine (DPPC) monolayers, four of which induced expansion in the surface pressure isotherm and a decrease in the surface compression modulus of DPPC. In contrast, one nucleoside possessing three alkyl chain modifications formed very condensed monolayers and induced film condensation and an increase in the compression modulus for the DPPC monolayer, thus reflecting the importance of the ability of the nucleoside molecules to be arranged in a closely packed manner. The implications of these results lie on the possibility of tuning nucleic acid pairing by modifying structural characteristics of the liponucleosides. (C) 2010 Elsevier B.V. All rights reserved.

Role of the triad N46, S106 and T107 and the surface charges in the determination of the acidic pH optimum of digestive lysozymes from Musca domestica

Structures of digestive lysozymes 1 and 2 from housefly (MdL1 and MdL2) show that S106-T107 delimit a polar pocket around E32 (catalytic acid/base) and N46 contributes to the positioning of 050 (catalytic nucleophile), whereas those residues are replaced by V109-A110 and D48 in the non-digestive lysozyme from hen egg-white (HEWL). Further analyses revealed that MdL1 and MdL2 surfaces are less positively charged than HEWL surface. To verify the relevance of these differences to the acidic pH optimum of digestive lysozymes it was determined that pKas of the catalytic residues of the triple mutant MdL2 (N46D-S106V-T107A) are similar to HEWL pKas and higher than those for MdL2. In agreement, triple mutant MdL2 and HEWL exhibits the same pH optimum upon methylumbelliferylchitotrioside. In addition to that, the introduction of six basic residues on MdL1 surface increased by 1 unit the pH optimum for the activity upon bacterial walls. Thus, the acidic pH optimum for MdL2 and MdL1 activities upon methylumbelliferylchitotrioside is determined by the presence of N46, S106 and T107 in the environment of their catalytic residues, which favors pKas reduction. Conversely, acidic pH optimum upon bacterial walls is determined by a low concentration of positive charges on the MdL2 and MdL1 surfaces. (C) 2010 Elsevier Inc. All rights reserved.

Picosecond Dynamics of the Prototropic Reactions of 7-Hydroxyflavylium Photoacids Anchored at an Anionic Micellar Surface

Three water-insoluble, micelle-anchored flavylium salts, 7-hydroxy-3-octyl-flavylium chloride, 4`-hexyl-7-hydroxyflavylium chloride, and 6-hexyl-7-hydroxy-4-methyl-flavylium chloride, have been employed to probe excited-state prototropic reactions in micellar sodium dodecyl sulfate (SDS). In SDS micelles, the fluorescence decays of these three flavylium salts are tetraexponential functions in the pH range from 1.0 to 4.6 at temperatures from 293 to 318 K. The four components of the decays are assigned to Four kinetically coupled excited species in the micelle: specifically, promptly deprotonable (AH(+)*) and nonpromptly deprotonable (AH(h)(+)*) orientations of the acid in the micelle. the base-proton geminate pair (A*center dot center dot center dot H(+)), and the free conjugate base (A*). The initial prompt deprotonation to form the germinate pair occurs at essentially the same rate (k(d) similar to 6-7 x 10(10) s(-1)) for all three photoacids. Recombination of the germinate pair is similar to 3-fold faster than the rate of proton escape from the pair (k(rec) similar to 3 x 10(10) s(-1) and k(diss) similar to 1 x 10(10) s(-1)), corresponding to an intrinsic recombination efficiency of the pair of similar to 75%. Finally, the reprotonation of the short-lived free A* (200-350 ps, depending oil the photoacid) has two components, only one of which depends oil the proton concentration in the intermicellar aqueous phase. Ultrafast transfer of the proton to water and substantial compartmentalization of the photogenerated proton at the micelle surface Oil the picosecond time scale strongly suggest preferential transfer of the proton to preformed hydrogen-bonded water bridges between the photoacid and the anionic headgroups. This localizes the proton in the vicinity of the excited base much more efficiently than ill bulk water, resulting ill the predominance of geminate re reprotonation at the micelle surface.

Electrostatic and Hydrophobic Interactions Involved in CNT Biofunctionalization with Short ss-DNA

This work is aimed at studying the adsorption mechanism of short chain 20-mer pyrimidinic homoss-DNA (oligodeoxyribonucleotide, ODN: polyC(20) and polyT(20)) onto CNT by reflectometry. To analyze the experimental data, the effective-medium theory using the Bruggemann approximation represents a Suitable optical model to account for the surface properties (roughness, thickness, and optical constants) and the size of the adsorbate. Systematic information about the involved interactions is obtained by changing the physicochemical properties of the system. Hydrophobic and electrostatic interactions are evaluated by comparing the adsorption oil hydrophobic CNT and oil hydrophilic silica and by Modulating the ionic Strength With and without Mg(2+). The ODN adsorption process oil CNT is driven by hydrophobic interactions only when the electrostatic repulsion is Suppressed. The adsorption mode results in ODN molecules in a side-on orientation with the bases (nonpolar region) toward the surface. This unfavorable orientation is partially reverse by adding Mg(2+). On the other hand, the adsorption oil silica is dominated by the strong repulsive electrostatic interaction that is screened at high ionic strength or mediated by Mg(2+). The cation-mediated process induces the interaction of the phosphate backbone (polar region) with the surface, leaving the bases free for hybridization. Although the general adsorption behavior of the pyrimidine bases is the same, polyC(20) presents higher affinity for the CNT Surface due to its acid-base properties.

Development of a heavy metal sorption system through the P=S functionalization of coconut (Cocos nucifera) fibers

Lignocellulosic residues are interesting materials for the production of heavy metal adsorbents for aquatic systems. Whole fibers taken from coconut (Cocos nucifera) husks were functionalized with the thiophosphoryl (P=S) group by means of the direct reaction with CI(3)P=S, (CH(3)O)(2)CIP=S or (CH(3)CH(2)O)(2)CIP=S in order to obtain an adsorptive system for `soft` metal ions, particularly Cd(2+). These functionalized fibers (FFs) were characterized by means of elemental analysis, infrared spectroscopy, thermal analysis and acid-base titration. Adsorption isotherms for Cd(2+) fitted the Langmuir model, with binding capacities of 0.2-5 mmol g(-1) of FF at 25 degrees C. (C) 2009 Elsevier Ltd. All rights reserved.

Flow injection analysis using carbon film resistor electrodes for amperometric determination of ambroxol

Flow injection analysis (FIA) using a carbon film sensor for amperometric detection was explored for ambroxol analysis in pharmaceutical formulations. The specially designed flow cell designed in the lab generated sharp and reproducible current peaks, with a wide linear dynamic range from 5 x 10(-7) to 3.5 x 10(-4) mol L-1, in 0.1 mol L-1 sulfuric acid electrolyte, as well as high sensitivity, 0.110 A mol(-1) L cm(-2) at the optimized flow rate. A detection limit of 7.6 x 10(-8) mol L-1 and a sampling frequency of 50 determinations per hour were achieved, employing injected volumes of 100 mu L and a flow rate of 2.0 mL min(-1). The repeatability, expressed as R.S.D. for successive and alternated injections of 6.0 x 10(-6) and 6.0 x 10(-5) mol L-1 ambroxol solutions, was 3.0 and 1.5%, respectively, without any noticeable memory effect between injections. The proposed method was applied to the analysis of ambroxol in pharmaceutical samples and the results obtained were compared with UV spectrophotometric and acid-base titrimetric methods. Good agreement between the results utilizing the three methods and the labeled values was achieved, corroborating the good performance of the proposed electrochemical methodology for ambroxol analysis. (C) 2008 Elsevier B.V. All rights reserved.

On the Relaxation Mechanisms of 6-Azauracil

The nonadiabatic photochemistry of 6-azauracil has been studied by means of the CASPT2//CASSCF protocol and double-zeta plus polarization ANO basis sets. Minimum energy states, transition states, minimum energy paths, and surface intersections have been computed in order to obtain an accurate description of several potential energy hypersurfaces. It is concluded that, after absorption of ultraviolet radiation (248 nm), two main relaxation mechanisms may occur, via which the lowest (3)(pi pi*) state can be populated. The first one takes place via a conical intersection involving the bright (1)(pi pi*) and the lowest (1)(n pi*) states, ((1)pi pi*/(1)n pi*)(CI), from which a low energy singlet-triplet crossing, ((1)n pi*/(3)pi pi*)(STC), connecting the (1)(n pi*) state to the lowest (3)(pi pi*) triplet state is accessible. The second mechanism arises via a singlet-triplet crossing, ((1)pi pi*/(3)n pi*)(STC), leading to a conical intersection in the triplet manifold, ((3)n pi*/(3)pi pi*)(CI), evolving to the lowest (3)(pi pi*) state. Further radiationless decay to the ground state is possible through a (gs/(3)pi pi*)(STC).