How the Conformations of an Internal Junction Contribute to Fold an RNA Domain

Like proteins, some RNAs fold to compact structures. We can model functional RNAs as a series of short, rigid, base-paired elements, connected by non-base-paired nucleotides that serve as junctions. These connecting regions bend and twist, facilitating the formation of tertiary contacts that stabilize compact states. Here, we explore the roles of salt and junction sequence in determining the structures of a ubiquitous connector: an asymmetric internal loop. We focus on the J5/5a junction from the widely studied P4-P6 domain of the Tetrahymena ribozyme. Following the addition of magnesium ions to fold P4-P6, this junction bends dramatically, bringing the two halves of the RNA domain together for tertiary contact engagement. Using single-molecule fluorescence resonance energy transfer (smFRET), we examine the role of sequence and salt on model RNA constructs that contain these junction regions. We explore the wild-type J5/5a junction as well as two sequence variants. These junctions display distinct, salt-dependent conformations. Small-angle X-ray scattering (SAXS) measurements verify that these effects persist in the full-length P4-P6 domain. These measurements underscore the importance of junction sequence and interactions with ions in facilitating RNA folding.

Tuning RNA Flexibility with Helix Length and Junction Sequence

The increasing awareness of RNA's central role in biology calls for a new understanding of how RNAs, like proteins, recognize biological partners. Because RNA is inherently flexible, it assumes a variety of conformations. This conformational flexibility can be a critical aspect of how RNA attracts and binds molecular partners. Structurally, RNA consists of rigid basepaired duplexes, separated by flexible non-basepaired regions. Here, using an RNA system consisting of two short helices, connected by a single-stranded (non-basepaired) junction, we explore the role of helix length and junction sequence in determining the range of conformations available to a model RNA. Single-molecule Förster resonance energy transfer reports on the RNA conformation as a function of either mono- or divalent ion concentration. Electrostatic repulsion between helices dominates at low salt concentration, whereas junction sequence effects determine the conformations at high salt concentration. Near physiological salt concentrations, RNA conformation is sensitive to both helix length and junction sequence, suggesting a means for sensitively tuning RNA conformations.

Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with wormlike chain models, but nonbase-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and divalent salt. We report measurements of the form factor and interparticle interactions using SAXS, end-to-end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent molecular dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers.

Revealing transient structures of nucleosomes as DNA unwinds

The modulation of DNA accessibility by nucleosomes is a fundamental mechanism of gene regulation in eukaryotes. The nucleosome core particle (NCP) consists of 147 bp of DNA wrapped around a symmetric octamer of histone proteins. The dynamics of DNA packaging and unpackaging from the NCP affect all DNA-based chemistries, but depend on many factors, including DNA positioning sequence, histone variants and modifications. Although the structure of the intact NCP has been studied by crystallography at atomic resolution, little is known about the structures of the partially unwrapped, transient intermediates relevant to nucleosome dynamics in processes such as transcription, DNA replication and repair. We apply a new experimental approach combining contrast variation with time-resolved small angle X-ray scattering (TR-SAXS) to determine transient structures of protein and DNA constituents of NCPs during salt-induced disassembly. We measure the structures of unwrapping DNA and monitor protein dissociation from Xenopus laevis histones reconstituted with two model NCP positioning constructs: the Widom 601 sequence and the sea urchin 5S ribosomal gene. Both constructs reveal asymmetric release of DNA from disrupted histone cores, but display different patterns of protein dissociation. These kinetic intermediates may be biologically important substrates for gene regulation.

Role of ion valence in the submillisecond collapse and folding of a small RNA domain

Following the addition of ions to trigger folding, RNA molecules undergo a transition from rigid, extended states to a compact ensemble. Determining the time scale for this collapse provides important insights into electrostatic contributions to RNA folding; however, it can be challenging to isolate the effects of purely nonspecific collapse, e.g., relaxation due to backbone charge compensation, from the concurrent formation of some tertiary contacts. To solve this problem, we decoupled nonspecific collapse from tertiary folding using a single-point mutation to eliminate tertiary contacts in the small RNA subdomain known as tP5abc. Microfluidic mixing with microsecond time resolution and Förster resonance energy transfer detection provides insight into the ionic strength-dependent transition from extended to compact ensembles. Differences in reaction rates are detected when folding is initiated by monovalent or divalent ions, consistent with equilibrium measurements illustrating the enhanced screening of divalent ions relative to monovalent ions at the same ionic strength. Ion-driven collapse is fast, and a comparison of the collapse time of the wild-type and mutant tP5abc suggests that site binding of Mg(2+) occurs on submillisecond time scales.

The kainate receptor antagonist 2S,4R-4-methylglutamate attenuates mechanical allodynia and thermal hyperalgesia in a rat model of nerve injury

Opioids and receptor antagonists of excitatory amino acids attenuate mechanical allodynia and thermal hyperalgesia in animal models of neuropathic pain. Recently, a kainate receptor antagonist, 2S,4R-4-methylglutamate, has been developed but has not been tested for antinociceptive effects in animal models of neuropathic pain. We evaluated whether 2S,4R-4-methylglutamate attenuated responses to mechanical and thermal stimuli in uninjured (control) rats and increased responsiveness in rats with chronic constriction injury. Rats were tested for a number of withdrawal responses using a calibrated von Frey filament (mechanical stimulus) and withdrawal latencies from a radiant heat source (thermal stimulus). In control rats, 2S,4R-4-methylglutamate produced a small but significant decrease in responses from the mechanical stimulus (25 mg/kg) and significantly increased withdrawal latencies from the thermal stimulus at the highest dose administered (100 mg/kg). In addition, 2S,4R-4-methylglutamate greatly attenuated increased responsiveness in rats with chronic constriction injury. At four to eight days following chronic constriction injury, animals that displayed increased responsiveness to mechanical and thermal stimuli were injected intraperitoneally with either dizocilpine maleate (0.1 mg/kg), morphine (4 mg/kg), vehicle as controls, or 2S,4R-4-methylglutamate (25, 50, 75 or 100 mg/kg). 2S,4R-4-Methylglutamate (25, 50, 75 and 100 mg/kg) significantly attenuated the frequency of responses to mechanical stimuli (Wilcoxon, P < 0.05) and the latency of responses to thermal stimuli (analysis of variance and Duncan's, P < 0.05). Dizocilpine maleate and morphine, as expected, also reduced these responses. These results suggest that, in addition to opioid and N-methyl-D-aspartate receptors, kainate receptors may play a role in the maintenance of mechanical allodynia and thermal hyperalgesia associated with peripheral nerve injury.

Geotrichum candidum produces several lipases with markedly different substrate specificities

We have purified and examined the substrate specificity of four lipases from two strains of the mould Geotrichum candidum, ATCC 34614 and CMICC 335426. We have designated the lipases I and II (ATCC 34614), and A and B (CMICC 335426). The enzymes are monomeric and have similar molecular masses and pI. Thus, lipases I and II have native molecular masses of 50.1 kDa and 55.5 kDa, and pI of 4.61 and 4.47, respectively. Lipases A and B are very similar to lipases I and II with native molecular masses of 53.7 kDa and 48.9 kDa, and pI of 4.71 and 4.50, respectively. Treatment with endo-beta-N-acetylglucosaminidase caused a reduction in molecular mass of approximately 4.5 kDa for all four lipases, indicating that these enzymes are glycosylated. Western blotting shows that the lipases are related. However, lipase B from CMICC 335426 shows a remarkable specificity for unsaturated substrates with a double bond at position 9 (cis configuration), and this specificity is not exhibited by the other three lipases. No lipase of this unique specificity has previously been purified to homogeneity. Structural studies using these four lipases should allow insight into the molecular basis of this remarkable specificity.

Effect of large doses of ascorbic acid in man on some nitrogenous components of urine

Base-line values for the excretion of urea N, amine N, creatinine, uric acid and cysteine were measured in three consecutive 24-h urine collections from 16 healthy volunteers. The subjects then took 1 g ascorbic acid three times a day after meals for 7 days. Twenty-four hour urine samples were collected on the 1st, 3rd, 5th and 7th days of the study. Where possible, a further 24-h sample was collected a minimum of 10 d after the end of the study. Administration of 3 g/d of ascorbic acid had no effect on urine volume, pH or the excretion of urea, amino N or creatinine. It caused a transient increase in uric acid excretion but an immediate and sustained increase in the excretion of cysteine. This study provides no evidence for an effect of high doses of ascorbic acid on urinary stone formation but does suggest competition for important co-factors in the metabolism of drugs.

Effect of pharmacological doses of ascorbic acid on the hepatic microsomal haemoproteins in the guinea-pig

1. Ascorbic acid deficiency results in a reduction in the activity of the hepatic mixed function oxidase systems in the guinea-pig. In this study, male Dunkin-Hartley guinea-pigs were given 0, 50, 100, 200 or 300 mg ascorbic acid/d in two equal doses in buffered sucrose solution (200 g/l) for 4 d. Controls received an equal volume of sucrose solution. 2. A dose of 50 mg ascorbic acid/d resulted in a significant rise in the specific activities of both cytochromes P-450 and b5. At doses of 200 and 300 mg ascorbic acid/d the concentration of both haemoproteins was significantly lower than the control values. These effects were mirrored by total microsomal haem concentration. 3. These results suggest that when given in large doses, ascorbic acid ceases to act simply as a vitamin and should be considered a drug competing for substrates and cofactors with co-administered drugs and endogenous substrates such as cholesterol.

Effect of large doses of ascorbic acid on the mixed function oxidase system in guinea pig liver

Reports of the beneficial effects of large doses of ascorbic acid have stressed its water solubility and non-toxic properties. In this study male guinea pigs, dosed with 150 mg twice daily, ascorbic acid, demonstrated no differences in effect on liver weight, body weight or hepatic total protein when compared with controls. The activities of NADPH-dependent cytochrome c reductase, N-demethylase (Type I) and O-de-ethylase enzymes (Type II) remained unaffected, but the activity of the Type I hydroxylating enzyme, biphenyl-4-hydroxylase, and the amounts of cytochromes P-450 and b5 were significantly reduced. Total microsomal haem proteins were reduced and mirrored the effects in cytochromes P-450 and b5. The rate-limiting enzyme in haem synthesis, delta-amino-laevulinic acid synthetase, rose in the ascorbic acid group and this was associated with a fall in activity of the haem degrading enzyme, microsomal haem oxygenase. Thus, large amounts of ascorbic acid have similar effects to those found in scorbutic animals and appear to interfere with the construction of the cytochrome P-450 molecule.

Hymenoptera venom allergy: a geographic study

RAST results for the five common venoms from 1,024 positive sera obtained from patients who experienced recent severe allergic reactions to insect stings were analyzed for nine different geographic areas of the United States. Substantial differences were found as a function of geography and insect distribution. The results suggest that multiple reactivity is most common in areas with the most variety of insects, that cross reactivity is not the only important cause of multiple reactivity and that sensitization by multiple stings is more common than suggested by patient histories.

Metabolism of nicotinic acid in children with burns and scalds

The excretions of two metabolites of nicotinic acid, N1-methylnicotinamide and N1-methyl-2-pyridone-5-carboxamide have been measured at varying times after injury in a group of 27 burned or scalded children. Compared with control patients the excretions of both of these metabolites were significantly raised after injury, which suggests that the utilisation of nicotinic acid is increased.