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Characterization of Mg2+ Distributions around RNA in Solution.

ABSTRACT: Binding of metal ions is an important factor governing the folding and dynamics of RNA. Shielding of charges in the polyanionic backbone allows RNA to adopt a diverse range of folded structures that give rise to their many functions within the cell. Some RNA sequences fold only in the presence of Mg2+, which may be bound via direct interactions or occupy the more diffuse "ion atmosphere" around the RNA. To understand the driving forces for RNA folding, it is important to be able to fully characterize the distribution of metal ions around the RNA. In this work, a combined Grand Canonical Monte Carlo-Molecular Dynamics (GCMC-MD) method is applied to characterize Mg2+ distributions around folded RNA structures. The GCMC-MD approach identifies known inner- and outer-shell Mg2+ coordination, while also predicting new regions occupied by Mg2+ that are not observed in crystal structures but that may be relevant in solution, including the case of the Mg2+ riboswitch, for which alternate Mg2+ binding sites may have implications for its function. This work represents a significant step forward in establishing a structural and thermodynamic description of RNA-Mg2+ interactions and their role in RNA structure and function.

SUBMITTER: Lemkul JA

PROVIDER: S-EPMC5088455 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Characterization of Mg<sup>2+</sup> Distributions around RNA in Solution.

Lemkul Justin A JA Lakkaraju Sirish Kaushik SK MacKerell Alexander D AD

ACS omega 20161026 4

Binding of metal ions is an important factor governing the folding and dynamics of RNA. Shielding of charges in the polyanionic backbone allows RNA to adopt a diverse range of folded structures that give rise to their many functions within the cell. Some RNA sequences fold only in the presence of Mg<sup>2+</sup>, which may be bound via direct interactions or occupy the more diffuse "ion atmosphere" around the RNA. To understand the driving forces for RNA folding, it is important to be able to fu ...[more]

PMID: 27819065

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Project description:BackgroundThe feline lungworm Aelurostrongylus abstrusus affects the lower respiratory tract in cats worldwide. As infections may lead to chronic respiratory changes or even death, preventive treatment in cats with outdoor access is warranted.MethodsThe preventive efficacy of a spot-on solution (Bravecto® Plus spot-on solution for cats, MSD) against cat aelurostrongylosis was evaluated using three different preventive treatment regimes in a negative controlled, randomized and partially blinded laboratory efficacy study with 31 purposed-bred cats. The minimum recommended dose of 2.0 mg moxidectin + 40 mg fluralaner/kg bodyweight was applied once 12 (Group [G]1), 8 (G2) or 4 (G3) weeks before experimental infection with 300 third-stage larvae (L3) of A. abstrusus. Another group served as untreated control (G4). Individual faecal samples were analysed as of day 30 post infection (pi) to monitor larvae excretion. Necropsy was performed at days 47-50 pi. The lungs were examined macroscopically for pathological findings and (pre-)adult worms were counted to assess preventive efficacy.ResultsBeginning at day 32-40 pi, all cats of the control group were constantly shedding larvae of A. abstrusus, whereas only one animal of G1 excreted larvae at several consecutive days. In addition, two cats of G1 and G3 and three of G2 were positive on a single occasion. The geometric mean (GM) of the maximum number of excreted larvae was 7574.29 in the control group compared to 1.10 (G1), 1.19 (G2) and 0.53 (G3), resulting in a GM reduction of > 99.9% in all treatment groups. All lungs of the control animals showed severe or very severe alterations at necropsy, while in 94.44% of the treated cats lung pathology was rated as absent or mild. The GM number of (pre-)adult A. abstrusus retrieved from the lungs was 26.57 in the control group, 0.09 in G1 and 0.00 in G2 and G3. Thus, GM worm count reduction was 99.66% in G1 and 100% in G2 and G3.ConclusionsA single application of Bravecto® Plus spot-on solution at a dose of 2.0 mg moxidectin + 40 mg fluralaner/kg bodyweight reliably prevents cat aelurostrongylosis for at least 12 weeks.

Dataset Information

Characterization of Mg2+ Distributions around RNA in Solution.

Publications

Characterization of Mg<sup>2+</sup> Distributions around RNA in Solution.

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