Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target.

A fragment of 23S ribosomal RNA (nucleotides 1906-1924 in E. coli), termed Helix 69, forms a hairpin that is essential for ribosome function. Helix 69 forms a conformationally flexible inter-subunit connection with helix 44 of 16S ribosomal RNA, and the nucleotide A1913 of Helix 69 influences decoding accuracy. Nucleotides U1911 and U1917 are post-transcriptionally modified with pseudouridines (Ψ) and U1915 with 3-methyl-Ψ. We investigated Helix 69 as a target for a complementary synthetic oligonucleotide - peptide nucleic acid (PNA). We determined thermodynamic properties of Helix 69 and its complexes with PNA and tested the performance of PNA targeted at Helix 69 in inhibiting translation in cell-free extracts and growth of E. coli cells. First, we examined the interactions of a PNA oligomer complementary to the G1907-A1919 fragment of Helix 69 with the sequences corresponding to human and bacterial species (with or without pseudouridine modifications). PNA invades the Helix 69 hairpin creating stable complexes and PNA binding to the pseudouridylated bacterial sequence is stronger than to Helix 69 without any modifications. Second, we confirmed the binding of PNA to 23S rRNA and 70S ribosomes. Third, we verified the efficiency of translation inhibition of these PNA oligomers in the cell-free translation/transcription E. coli system, which were in a similar range as tetracycline. Next, we confirmed that PNA conjugated to the (KFF)3K transporter peptide inhibited E. coli growth in micromolar concentrations. Overall, targeting Helix 69 with PNA or other sequence-specific oligomers could be a promising way to inhibit bacterial translation.

Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies.

Amikacin is a 2-deoxystreptamine aminoglycoside antibiotic possessing a unique l-HABA (l-(-)-γ-amino-α-hydroxybutyric acid) group and applied in the treatment of hospital-acquired infections. Amikacin influences bacterial translation by binding to the decoding region of the small ribosomal subunit that overlaps with the binding site of aminoacylated-tRNA (A-site). Here, we have characterized thermodynamics of interactions of amikacin with a 27-mer RNA oligonucleotide mimicking the aminoglycoside binding site in the bacterial ribosome. We applied isothermal titration and differential scanning calorimetries, circular dichroism and thermal denaturation experiments, as well as computer simulations. Thermal denaturation studies have shown that amikacin affects only slightly the melting temperatures of the A-site mimicking RNA model suggesting a moderate stabilization of RNA by amikacin. Isothermal titration calorimetry gives the equilibrium dissociation constants for the binding reaction between amikacin and the A-site oligonucleotide in the micromolar range with a favorable enthalpic contribution. However, for amikacin we observe a positive entropic contribution to binding, contrary to other aminoglycosides, paromomycin and ribostamycin. Circular dichroism spectra suggest that the observed increase in entropy is not caused by structural changes of RNA because amikacin binding does not destabilize the helicity of the RNA model. To investigate the origins of this positive entropy change we performed all-atom molecular dynamics simulations in explicit solvent for the 27-mer RNA oligonucleotide mimicking one A-site and the crystal structure of an RNA duplex containing two A-sites. We observed that the diversity of the conformational states of the l-HABA group sampled in the simulations of the complex was larger than for the free amikacin in explicit water. Therefore, the larger flexibility of the l-HABA group in the bound form may contribute to an increase of entropy upon binding.

Use of different types of mesoporous materials as tools for organic synthesis.

Mesoporous materials have been investigated as auxiliary agents for organic synthesis comprising reactants with widely different solubility characteristics. The finely divided oxide material was immersed in an aqueous solution of a water-soluble reactant, potassium iodide, and the loaded particles were kept under stirring in the hydrophobic reactant, 4-tert-butylbenzyl bromide, or in a hydrocarbon solution of this reactant. The reaction proceeded well in alumina and silica of either bicontinuous cubic or hexagonal geometry. It was shown for silica that the particle size was an important parameter; the smaller the size the faster the reaction. Titania gave a much lower reaction rate than alumina and silica. It was found that the hexagonal mesoporous alumina could be reused either as a slurry or in a column procedure. Attempts were also made to use hydrophobic mesoporous materials, either mesoporous graphite or mesoporous oxide treated with chlorotrimethylsilane, in the reversed mode. The hydrophobic solid was then immersed in a solution of the hydrophobic reactant and subsequently dispersed in an aqueous solution of the water-soluble reactant. Two nucleophilic substitution reactions and one oxidation reaction were investigated but the yields were low in all cases.

Use of a mesoporous material for organic synthesis.

A common problem in synthetic organic chemistry is attaining proper contact between lipophilic organic compounds and inorganic salts. Various strategies, for example, phase transfer catalysis (Starks, C. M.; Liotta, C. L.; Halpern, M. Phase Transfer Catalysis: Fundamentals, Applications and Industrial Perspectives; Chapman & Hall: New York, 1994) or use of a microheterogeneous medium such as a microemulsion (Hager, M.; Currie, F.; Holmberg, K. Organic Reactions in Microemulsions. In Colloid Chemistry II; Antonietti, M., Ed.; Topics in Current Chemistry 227; Springer-Verlag: Heidelberg, 2003; p 53) have been worked out to tackle the issue. Here, we report that mesoporous solid materials made from surfactant self-assembly can be used as medium for such reactions. The material is made from silica, and the pore size is large, relatively uniform, and can be controlled with a high degree of precision by the choice of surfactant that is being used as template (Palmqvist, A. E. C. Curr. Opin. Colloid Interface Sci. 2003, 8, 145). The pores are hydrophilic and are filled with an aqueous solution containing the inorganic salt. The porous material is dispersed in the lipophilic organic substrate, that is, 4-tert-butylbenzyl bromide, or in a hydrocarbon solution of this substrate. The reaction occurs at the hydrophilic/lipophilic interface, and, because the interface is large, the reaction is fast. A considerable advantage with this new reaction medium is that the workup procedure is extremely facile. After the reaction is completed, the solid is simply removed by filtering or centrifugation.