Branchpoint sugar stereochemistry determines the hydrolytic susceptibility of branched RNA fragments by the yeast debranching enzyme (YDBR)

A series of branched RNAs (Y-shaped) related to yeast pre-mRNA splicing intermediates were synthesized incorporating both natural (i.e., ribose) and non-natural (i.e., arabinose, xylose and acyclic nucleoside) branchpoints in order to examine the effect of sugar conformation and phosphodiester configuration on yDBR hydrolytic efficiency. The results indicate that 2'-phosphodiester scission with yDBR occurs only with a cis-arrangement of phosphate groups at the branchpoint (i.e., ribose) thereby discriminating between all other configurations.     

Preference for Ribose Over Deoxyribose in Loop-Closing Base Pairs of Extra Stable Nucleic Acid Hairpins

We have investigated the effect of switching ribose to deoxyribose at the closing base-pair of an extra-stable RNA hairpin. Specifically, we studied the sequence 5′-GGAC(UUCG)GUCC, a dodecanucleotide that folds into a well-characterized, “extra stable” RNA hairpin structure. Recently, we showed that hairpins containing a 2′,5′-linked (UUCG) loop instead of the native 3′,5′-linked loop also exhibit extra-stability (Hannoush and Damha, J. Am. Chem. Soc., 2001, 123, 12368–12374). In this article, we show that the ribose units located at the loop-closing positions (i.e., rC ₄ and rG ₉ ) contribute significantly to the stabilization of RNA hairpins, particularly those containing the 3′,5′-UUCG loop. Interestingly, the requirement of rC4 and rG9 is more relaxed for DNA hairpins containing the 2′,5′-UUCG loop and, in fact, they may be replaced altogether (ribose → deoxyribose) without affecting stability. The results broaden our understanding of the behavior of highly stable (UUCG) hairpin loops and how they respond to structural perturbation of the loop-closing base pairs.     

Xanthine-7-Ribosides as Adenosine Receptor Antagonists: Further Evidence for Adenosine'S Anti Mode Of Binding

Abstract

With the aid of computer graphics methods, we recently developed a model for the antagonist binding site of the adenosine A₁ receptor (J. Med. Chem. 1990, 33, 1708-1713). According to this model, xanthines should bind to the receptor in a flipped orientation, i.e. the ring atoms N1, N3, N7 and N9 in adenosine coincide with C2, C6, N9 and N7 respectively in theophylline (FIG. la and 1 b). This implicates that the domain where the ribose moiety of adenosine binds must be adjacent to N7 in xanthines, and furthermore that xanthine-7-ribosides should have affinity for the receptor. To further explore the role of the orientation of the ribose moiety in binding to the receptor, we have synthesized and determined the A₁ affinity of the 7-ribosides of theophylline, 13-dipropylxanthine and 1,3-dibutylxanthine (FIG. 1c). The orientation of the ribose moiety was studied with H-NMR spectroscopy and theoretical chemical calculations.     

Determination of 2′-O-methyl groups in 32P-labeled RNAs

A two-dimensional method for the detection of ribose methyl groups in³²P-labeled RNAs is described which is suitable for both qualitative and quantitative purposes. The method involves fractionation of an alkaline hydrolysate of the RNA by two-dimensional electrophoresis of the digest on DEAE-cellulose paper; prior to the second electrophoresis the products are dephosphorylated on the paper by alkaline phosphatase. After visualization of the ribose-methylated (i.e., alkali-stable) oligonucleotides by radioautography, quantitation of the number of ribose methyl groups is possible since each ribose methyl group corresponds to one phosphate group. When applied to a bacterial 23S rRNA the method proved to be accurate enough for determination of the low level (0.1%) of ribose-methylated nucleosides in this RNA. It could also be demonstrated by this sensitive method that the RNA from the small ribosomal subunit of yeast mitochondria is devoid of ribose methyl groups.     

Residue Specific Ribose and Nucleobase Dynamics of the cUUCGg RNA Tetraloop Motif by MNMR 13C Relaxation

The dynamics of the nucleobase and the ribose moieties in a 14-nt RNA cUUCGg hairpin-loop uniformly labeled with ¹³C and ¹⁵N were studied by ¹³C spin relaxation experiments. R₁, R_1ρ and the ¹³C-{¹H} steady-state NOE of C₆ and C_1′ in pyrimidine and C₈ and C_1′ in purine residues were obtained at 298 K. The relaxation data were analyzed by the model-free formalism to yield dynamic information on timescales of pico-, nano- and milli-seconds. An axially symmetric diffusion tensor with an overall rotational correlation time τ_c of 2.31±0.13 ns and an axial ratio of 1.35±0.02 were determined. Both findings are in agreement with hydrodynamic calculations. For the nucleobase carbons, the validity of different reported ¹³C chemical shift anisotropy values (Stueber, D. and Grant, D. M., 2002 J. Am. Chem. Soc. 124, 10539–10551; Fiala et al., 2000 J. Biomol. NMR 16, 291–302; Sitkoff, D. and Case, D. A., 1998 Prog. NMR Spectroscopy 32, 165–190) is discussed. The resulting dynamics are in agreement with the structural features of the cUUCGg motif in that all residues are mostly rigid (0.82 < S² < 0.96) in both the nucleobase and the ribose moiety except for the nucleobase of U7, which is protruding into solution (S² = 0.76). In general, ribose mobility follows nucleobase dynamics, but is less pronounced. Nucleobase dynamics resulting from the analysis of ¹³C relaxation rates were found to be in agreement with ¹⁵N relaxation data derived dynamic information (Akke et al., 1997 RNA 3, 702–709). Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Plausible prebiotic synthesis of aldopentoses from simple substrates, glycolaldehyde and formaldehyde

Possible ways of abiotic catalytic synthesis of biologically significant aldopentoses (ribose, xylose, arabinose, lyxose) from elementary substrates, i.e., formaldehyde (FA) and glycolaldehyde (GA) in aqueous solutions are discussed. Conditions in which the process of synthesis of pentoses yields up to 65% relative to the initial concentration of GA: homogeneous borate catalyst NaOH + H₃BO₃, pH 9, [GA]₀ 5 mM, [FA]₀ 50–100 mM have been found.     

Cooperative interactions in single-strand oligomers of adenylic acid

Optical rotatory dispersion measurements were made on the oligonucleotides (pA)₂, (pA)₄, and (pA)₆ at neutral pH over the temperature range 5–85°C., and compared to similar data for polyriboadenylic acid. The data were interpreted in terms of a temperature-dependent stacking of the bases in the single-strand oligomers, with very little dependence of the degree of stacking on the chain length. These results can be explained by a theory of cooperative stacking. The degrees of freedom available per residue are rotations about the five backbone covalent bonds and the bond connecting the base to the ribose ring. To nucleate a stacking interaction between neighboring bases the backbone sequence must be ordered as must be the two bases. For this stack to grow by one base a backbone sequence must again be ordered, but only one additional base must be ordered. Thus, the degree of freedom of the base with respect to the ribose ring determines the extent of the cooperative effect and hence the effect of chain length. A matrix formulation of the partition function is presented which incorporates this cooperative nature of the interaction and is shown to be in fair agreement with the data. The entropy of ordering a base with respect to the ribose ring is found to be 0.68 e.u., which suggests that the purine has a torsional oscillation when unstacked, but does not have several isoenergetic positions of internal rotation available. The enthalpy of stacking is found to be ?6.5 kcal./mole. A model involving neighbor and next-nearest neighbor interactions could also account for the data. For all practical purposes, the stacking interactions of successive residues can be treated as independent, i.e., the state of one residue is essentially independent of the state of stacking of its neighbors.     

Quantifying CaCO3 Microprecipitates Within Developing Surface Mats of Marine Stromatolites Using GIS and Digital Image Analysis

The unique geochemical coupling of organic molecules and mineral CaCO₃ provides a fluorescence signature detectable using conventional confocal scanning laser microscopy (CSLM). The surface microbial mats of open-water marine stromatolites (Bahamas) exist in a continuum of states ranging from a Type 1 (i.e., nonlithifying) to Type 2 (i.e., lithified micritic laminae present) to Type 3 (i.e., fused grain layer). An approach was developed here, that utilizes geographical information systems (GIS) and digital image analysis, coupled with CSLM to estimate concentrations of calcium carbonate precipitates in developing marine stromatolites. We propose that the area occupied by particles within each image can be used to estimate concentrations of precipitates. Fluorescent polymeric microbeads and bacteria were used to calibrate the approach. We used this approach to demonstrate that CaCO₃ precipitates in lithifying layers were quantifiable and significantly different (p < 0.0001) from those in nonlithifying layers. The approach provided a useful tool for the unambiguous assessment of relative changes in microbial precipitates occurring over small ( μ m to mm) spatial scales, and that characterize the formation of lithified layers (micritic laminae) in open-water marine stromatolites.     

RIBOSE MODIFIED NUCLEOSIDES AND NUCLEOTIDES AS LIGANDS FOR PURINE RECEPTORS

Molecular modeling of receptors for adenosine and nucleotide (P2) receptors with docked ligand, based on mutagenesis, was carried out. Adenosine 3′,5′-bisphosphate derivatives act as selective P2Y₁ antagonists/partial agonists. The ribose moiety was replaced with carbocyclics, smaller and larger rings, conformationally constrained rings, and acyclics, producing compounds that retained receptor affinity. Conformational constraints were built into the ribose rings of nucleoside and nucleotide ligands using the methanocarba approach, i.e. fused cyclopropane and cyclopentane rings in place of ribose, suggesting a preference for the Northern (N) conformation among ligands for P2Y₁ and A₁ and A₃ARs.     

Structural and Chemical Characterization of a Natural Fracture Surface from 2.8 Kilometers Below Land Surface: Biofilms in the Deep Subsurface

A freshly intersected water-bearing fracture zone from the Mponeng Au mine located in the Witwatersrand Basin, Republic of South Africa was sampled, providing an opportunity to examine the natural, deep subsurface biosphere. The fracture, intersected by an advancing tunnel 2.8 kilometers below land surface, possessed a millimeter thick layer of chlorite group minerals, i.e., chamosite, at the water-mineral interface. Water flowing out from the fracture zone had a temperature of 52°C, pH of 9.16 and Eh of ?263 mV. Using scanning electron microscopy, the water-mineral interface was generally found to be clean, i.e., it did not possess any secondary mineral or dominant organic coatings. Irregular patches (10's of μm ² ) of organic material, however, resembling bacterial exopolysaccharides, occurred in the presence or absence of bacteria. The surface was colonized by highly dispersed individual bacteria or by microcolonies containing up to 5 cells, with an overall cell density of 5 × 10⁴ bacteria cm ^?2 . This biofilm population, although low, was 2 orders of magnitude greater than the bacteria present within the aqueous phase and provides the first direct observation of the sessile population from the terrestrial deep subsurface. Time of Flight-Secondary Ion Mass spectrometry revealed that the fracture surface was actually coated with a thin, i.e., molecular, organic conditioning film over much of its surface that was separate from the exopolysaccharide layers associated with the mineral water interface and with some of the attached cells.     

Treatment response to low-dose ketamine infusion for treatment-resistant depression: A gene-based genome-wide association study

BackgroundsEvidence suggested the crucial roles of brain-derived neurotrophic factor (BDNF) and glutamate system functioning in the antidepressant mechanisms of low-dose ketamine infusion in treatment-resistant depression (TRD).Methods65 patients with TRD were genotyped for 684,616 single nucleotide polymorphisms (SNPs). Twelve ketamine-related genes were selected for the gene-based genome-wide association study on the antidepressant effect of ketamine infusion and the resulting serum ketamine and norketamine levels.ResultsSpecific SNPs and whole genes involved in BDNF–TrkB signaling (i.e., rs2049048 in BDNF and rs10217777 in NTRK2) and the glutamatergic and GABAergic systems (i.e., rs16966731 in GRIN2A) were associated with the rapid (within 240 min) and persistent (up to 2 weeks) antidepressant effect of low-dose ketamine infusion and with serum ketamine and norketamine levels.DiscussionOur findings confirmed the predictive roles of BDNF–TrkB signaling and glutamatergic and GABAergic systems in the underlying mechanisms of low-dose ketamine infusion for TRD treatment.     

Inhibitors and Dipeptide Substrates for a Microsomal Tyrosylsulfotransferase from rat Brain

Abstract

The sulfotransferase associated with a microsomal fraction from rat brain was previously shown to transfer sulfate groups from 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to peptides derived from the chole cystokinin (CCK) molecule. Three tyrosine-containing dipeptide derivatives, i.e., Cbz-Glu-Tyr, Cbz-Gly-Tyr and Ac-Phe-Tyr are shown here to accept the [³⁵S] sulfate group from [³⁵S] PAPS under the action of this sulfotransferase. The sulfotransferase activity evaluated with either any of these dipeptide derivatives or CCK-8 as acceptors is similarly inhibited by a series of compounds, i.e., lipophilic polycyclic compounds like fluphenazine, tyrosine derivatives like Boc-O-benzyl-tyrosine and phenolsulfotransferase inhibitors like 4,4-di-isothiocyano 2′,2′-disulfonic acid stilbene.     

John Montgomery's Legacy: Carbocyclic Adenosine Analogues as Sah Hydrolase Inhibitors with Broad-Spectrum Antiviral Activity

Ever since the S-adenosylhomocysteine (AdoHcy, SAH) hydrolase was recognized as a pharmacological target for antiviral agents (J. A. Montgomery et al., J. Med. Chem. 25:626–629, 1982), an increasing number of adenosine, acyclic adenosine, and carbocyclic adenosine analogues have been described as potent SAH hydrolase inhibitors endowed with broad-spectrum antiviral activity. The antiviral activity spectrum of the SAH hydrolase inhibitors include pox-, rhabdo-, filo-, arena-, paramyxo-, reo-, and retroviruses. Among the most potent SAH hydrolase inhibitors and antiviral agents rank carbocyclic 3-deazaadenosine (C-c³Ado), neplanocin A, 3-deazaneplanocin A, the 5′-nor derivatives of carbocyclic adenosine (C-Ado, aristeromycin), and the 2-halo (i.e., 2-fluoro) and 6′-R-alkyl (i.e., 6′-R-methyl) derivatives of neplanocin A. These compounds are particularly active against poxviruses (i.e., vaccinia virus), and rhabdoviruses (i.e., vesicular stomatitis virus). The in vivo efficacy of C-c³Ado and 3-deazaneplanocin A has been established in mouse models for vaccinia virus, vesicular stomatitis virus, and Ebola virus. SAH hydrolase inhibitors such as C-c³Ado and 3-deazaneplanocin A should in the first place be considered for therapeutic (or prophylactic) use against poxvirus infections, including smallpox, and hemorrhagic fever virus infections such as Ebola.     

Uterine Volume and Endometrial Thickness in the Early Follicular Phase in Patients with Polycystic Ovary Syndrome

ObjectiveWe aimed to evaluate uterine volume and endometrial thickness during the early follicular phase in patients with polycystic ovary syndrome (PCOS) and healthy controls.MethodsWe studied 1,016 PCOS patients and 182 healthy controls. The anthropometric, endocrine, and metabolic characteristics of PCOS were determined. Uterine volume and endometrial thickness were also recorded.ResultsUterine volume progressively increased with age both in PCOS patients and controls. Patients with PCOS and body mass index (BMI) ≥ 25 kg/m² had greater uterine volumes than PCOS patients with BMI < 25 kg/ m² (P < .001). Patients with the classic PCOS phenotypes (i.e., with oligo-ovulation and/or anovulation [ANOV] and hyperandrogenemia [HA] with or without polycystic ovaries [PCO]) had smaller uterine volume than PCOS patients with the additional phenotypes introduced by the Rotterdam criteria (i.e., with PCO and either ANOV or HA; P = .033) and controls (P = .045).ConclusionUterine volume increases progressively with age and obesity in PCOS patients. The smaller uterine volumes and endometrial thicknesses in the classic PCOS phenotypes might be attributed to the more severe HA of these patients. (Endocr Pract. 2014;20:540-547)     

Sequential correlation of anomeric ribose protons and intervening phosphorus in RNA oligonucleotides by a 1H,13C,31P triple resonance experiment: HCP-CCH-TOCSY

Summary A three-dimensional ¹H,¹³C,³¹P triple resonance experiment, HCP-CCH-TOCSY, is presented which provides unambiguous through-bond correlation of all ¹H ribose protons on the 5′ and 3′ sides of the intervening phosphorus along the backbone bonding network in ¹³C-labeled RNA oligonucleotides. The correlation of the complete ribose spin system to the intervening phosphorus is obtained by adding a C,C-TOCSY coherence transfer step to the triple resonance HCP experiment. The C,C-TOCSY transfer step, which utilizes the large and relatively uniform ¹J(C,C) coupling constant (∼40 Hz for ribose carbons), efficiently correlates the phosphorus-coupled carbons observed in the HCP correlation experiment (i.e., C4′ and C5′ in the 5′ direction and C4′ and C3′ in the 3′ direction) to all other carbons in the ribose spin system. Of the additional correlations observed in the HCP-CCH-TOCSY, that to the relatively well-resolved anomeric H1′, C1′ resonance pairs provides the greatest gain in terms of facilitating assignment. The gain in spectral resolution afforded by chemical shift labeling with the anomeric resonances should provide a more robust pathway for sequential assignment over the intervening phosphorus in larger RNA oligonucleotides. The HCP-CCH-TOCSY experiment is demonstrated on a uniformly ¹³C,¹⁵N-labeled 19-nucleotide RNA stem-loop, derived from the antisense RNA I molecule found in the ColE1 plasmid replication control system.     

Regulation of and intervention into the oxidative pentose phosphate pathway and adenine nucleotide metabolism in the heart

The capacity of the oxidative pentose phosphate pathway (PPP) in the heart is limited, since the activity of glucose-6-phosphate dehydrogenase (G-6-PD), the first and regulating enzyme of this pathway, is very low. Two mechanisms are involved in the regulation of this pathway. Under normal conditions, G-6-PD is inhibited by NADPH. This can be overcome in the isolated perfused rat heart by increasing the oxidized glutathione and by elevating the NADP⁺/NADPH ratio. Besides this rapid control mechanism, there is a long-term regulation which involves the synthesis of G-6-PD. The activity of G-6-PD was elevated in the rat heart during the development of cardiac hypertrophy due to constriction of the abdominal aorta and in the non-ischemic part of the rat heart subsequent to myocardial infarction. The catecholamines isoproterenol and norepinephrine stimulated the activity of myocardial G-6-PD in a time- and dose-dependent manner. The isoproterenol-induced stimulation was cAMP-dependent and due to increased new synthesis of enzyme protein. The G-6-PD mRNA was elevated by norepinephrine. As a consequence of the stimulation of the oxidative PPP, the available pool of 5-phosphoribosyl-l-pyrophosphate (PRPP) was expanded. PRPP is an important precursor substrate for purine and pyrimidine nucleotide synthesis. The limiting step in the oxidative PPP, the G-6-PD reaction, can be bypassed with ribose. This leads to an elevation of the cardiac PRPP pool. The decline in ATP that is induced in many pathophysiological conditions was attenuated or even entirely prevented by i.v. infusion of ribose. In two in vivo rat models, the overloaded and catecholamine-stimulated heart and the infarcted heart, the normalization of the cardiac adenine nucleotide pool by ribose was accompanied by an improvement of global heart function. Combination of ribose with adenine or inosine in isoproterenol-treated rats was more effective to restore completely the cardiac ATP level within a short period of time than either intervention alone. (Mol Cell Biochem 160/161: 101–109, 1996)     

The Conserved Motif in Hydrophilic Loop 2/3 and Loop 8/9 of the Lactose Permease of Escherichia coli. Analysis of Suppressor Mutations

The major facilitator superfamily (MFS) of transport proteins, which includes the lactose permease of Escherichia coli, contains a conserved motif G-X-X-X-D/E-R/K-X-G-R/K-R/K in the loops that connect transmembrane segments 2 and 3, and transmembrane segments 8 and 9. In three previous studies (Jessen-Marshall, A.E., & Brooker, R.J. 1996. J. Biol. Chem. 271:1400–1404; Jessen-Marshall, A.E., Parker, N., & Brooker, R.J. 1997. J. Bacteriol. 179:2616–2622; and Pazdernik, N., Cain, S.M., & Brooker, R.J. 1997. J. Biol. Chem. 272:26110–26116), suppressor mutations at twenty different sites were identified which restore function to mutant permeases that have deleterious mutations in the conserved loop 2/3 or loop 8/9 motif. In the current study, several of these second-site suppressor mutations have been separated from the original mutation in the conserved motif. The loop 2/3 suppressors were then coupled to a loop 8/9 mutation (P280L) and the loop 8/9 suppressors were coupled to a loop 2/3 mutation (i.e., G64S) to determine if the suppressors could restore function only to a loop 2/3 mutation, a loop 8/9 mutation, or both. The single parent mutations changing the first position in loop 2/3 (i.e., G64S) and loop 8/9 (i.e., P280L) had less than 4% lactose transport activity. Interestingly, most of the suppressors were very inhibitory when separated from the parent mutation. Two suppressors, A50T and G370V, restored substantial transport activity when individually coupled to the mutation in loop 2/3 and also when coupled to the corresponding mutation in loop 8/9. In other words, these suppressors could alleviate a defect imposed by mutations in either half of the permease. From a kinetic analysis, these suppressors were shown to exert their effects by increasing the V _max values for lactose transport compared with the single G64S and P280L strains. These results are discussed within the context of our model in which the two halves of the lactose permease interact at a rotationally symmetrical interface, and that lactose transport is mediated by conformational changes at the interface. Received: 18 November 1999/Revised: 11 April 2000     

Size‐dependent and environment‐mediated shifts in leaf traits of a deciduous tree species in a subtropical forest

AimsUnderstanding the joint effects of plant development and environment on shifts of intraspecific leaf traits will advance the understandings of the causes of intraspecific trait variation. We address this question by focusing on a widespread species Clausena dunniana in a subtropical broad‐leaved forest.MethodsWe sampled 262 individuals of C. dunniana at two major topographic habitat types, the slope and hilltop, within the karst forests in Maolan Nature Reserve in southwestern China. We measured individual plant level leaf traits (i.e., specific leaf area (SLA), leaf area, leaf dry‐matter content (LDMC), and leaf thickness) that are associated with plant resource‐use strategies. We adopted a linear mixed‐effects model in which the plant size (i.e., the first principal component of plant basal diameter and plant height) and environmental factors (i.e., topographic habitat, canopy height, and rock‐bareness) were used as independent variables, to estimate their influences on the shifts of leaf traits.Key ResultsWe found that (1) plant size and the environmental factors independently drove the intraspecific leaf trait shifts of C. dunniana, of which plant size explained less variances than environmental factors. (2) With increasing plant size, C. dunniana individuals had increasingly smaller SLA but larger sized leaves. (3) The most influential environmental factor was topographic habitat; it drove the shifts of all the four traits examined. Clausena dunniana individuals on hilltops had leaf traits representing more conservative resource‐use strategies (e.g., smaller SLA, higher LDMC) than individuals on slopes. On top of that, local‐scale environmental factors further modified leaf trait shifts.ConclusionsPlant size and environment independently shaped the variations in intraspecific leaf traits of C. dunniana in the subtropical karst forest of Maolan. Compared with plant size, the environment played a more critical role in shaping intraspecific leaf trait variations, and potentially also the underlying individual‐level plant resource‐use strategies.     

A Simple Method for Synthesis of Spongosine,Azaspongosine, and Their Antiplatelet Effects

Abstract

Reaction of 2-ethylthioadenine (1) with protected ribose (2) in the presence of stannic chloride gave 2-ethylthioadenosine (4). Oxidation of 5 with potassium permanganate yielded the corresponding sulfone (6) which furnished spongosine (7) after treatment with sodium methoxide. Similarly, reactions of 7-amino-5-ethylthio-1,2,3-triazolo[4,5-d]pyrimidine (8) with the ribose (2) gave 8-azaspongosine (13). The compounds (4) and 7 demonstrated potent antiaggregatory effects both in human platelet-rich plasma and whole blood, whereas, the aza analog (13) showed no inhibitory activity on platelet aggregation. Both (4) and (7) inhibit platelet aggregation in the presence of adenosine deaminase, whereas, adenosine is non-inhibitory, suggesting that analogs (4) and (7) are poor substrates for adenosine deaminase.