Templates direct the sequence-specific anchoring of the C-terminus of peptido RNAs

When amino acids and ribonucleotides react in aqueous condensation buffer, they form peptido RNA with a phosphoramidate bond between the N-terminus of the peptide and the 5′-terminal phosphate of a ribonucleotide. If peptido RNA was the product of spontaneous reactions of amino acids and nucleotides, there must have been a transition to peptidyl tRNAs, where the C-terminus of the peptide is ester-linked to the 2′,3′-terminus of an oligonucleotide. Here we report how short peptido RNAs react with the 3′-terminus of oligodeoxynucleotides, templated by RNA strands. In our model system, the rate and yield of the anchoring of the C-terminus of the dipeptido dinucleotides to an amino group was found to depend on the sequence of the peptide, the 5′-terminal nucleotide of the dinucleotide and the RNA template. In all cases tested, highest yields were found for dinucleotides hybridizing next to the primer terminus. For the most reactive species, GlyPro-AA, anchoring yields ranged from 8–99%, depending on the template. When LeuLeu-AA, PhePhe-AA and GlyGly-AA were allowed to compete for anchoring on 3′-UUC-5′ as templating sequence, they gave a product ratio of 1 : 2 : 6, and this selectivity was almost independent of the terminal base of the primer. Our results show the control that a simple duplex context has over the covalent anchoring of peptido RNAs at a position known from peptidyl tRNAs. Processes of this type may have bridged the gap between untemplated condensation reactions and the highly specific processes of ribosomal protein synthesis.

The C-terminus of dipeptido dinucleotides reacts with the 3′-terminus of a primer strand in template directed fashion with a strong dependence on the structures of peptide and template.     

HO2 ELIMINATION FROM α-HYDROXYALKYLPEROXYL RADICALS IN AQUEOUS SOLUTION

Abstract— In aqueous solutions α-hydroxyalkylperoxyl radicals undergo a spontaneous and a base catalysed HO₂ elimination. From kinetic deuterium isotope effects, temperature dependence, and the influence of solvent polarity it was concluded that the spontaneous reaction occurs via an HO₂ elimination followed by the dissociation of the latter into H⁺ and O₂^-. The rate constant of the spontaneous HO₂ elimination increases with increasing methyl substitution in α-position ( k (CH₂(OH)O₂) < 10s^-1 k (CH₃CH(OH)O₂) = 52s^-1 k ((CH₃)₂C(OH)O₂) = 665 s^-1). The OH^- catalysed reaction is somewhat below diffusion controlled. The mixture of peroxyl radicals derived from polyhydric alcohols eliminate HO₂ at two different rates. Possible reasons for this behaviour are discussed. The mixture of the six peroxyl radicals derived from d -glucose are observed to eliminate HO₂ with at least three different rates. The fastest rate is attributed to the HO₂ elimination from the peroxyl radical at C-l ( k > 7000s^-1). Because of the HO₂ eliminations the peroxyl radicals derived from d -glucose do not undergo a chain reaction in contrast to peroxyl radicals not containing an α-OH group. In competition with the first order elimination reactions the α-hydroxylalkylperoxyl radicals undergo a bimolecular decay. These reactions are briefly discussed.     

On the effect of covalently appended quinolones on termini of DNA duplexes

Quinolones are gyrase inhibitors that are widely used as antibiotics in the clinic. When covalently attached to oligonucleotides as 5'-acylamido substituents, quinolones were found to stabilize duplexes of oligonucleotides against thermal denaturation. For short duplexes, such as qu-T*GCGCA, where qu is a quinolone residue and T is a 5'-amino-5'-deoxythymidine residue, an increase in the UV melting point of up to 27.8 degrees C was measured. The stabilizing effect was demonstrated for all quinolones tested, namely nalidixic acid, oxolinic acid, pipemidic acid, cinoxacin, norfloxacin, and ofloxacin. The three-dimensional structure of (oa-T*GCGCA)2, where oa is an oxolinic acid residue, was solved by two-dimensional NMR spectroscopy and restrained molecular dynamics. In this complex, the oxolinic acid residues disrupt the terminal T1:A6 base pairs and stack on the G2:C5 base pairs. The displaced adenosine residues bind in the minor groove of the core duplex, while the thymidine residues pack against the oxolinic acid residues. The "molecular cap" thus formed fits tightly on the G:C base pairs, resulting in increased base-pairing fidelity, as demonstrated in UV melting experiments with the sequence oa-T*GGTTGAC and target strands containing a mismatched nucleobase. The structure of the "molecular cap" with its disrupted terminal base pair may also be helpful for modeling how quinolones block re-ligation of DNA strands in the active site of gyrases.     

Synthesis of [(MeCyt)2H]I-structure and stability of a dimeric threefold hydrogen-bonded 1-methylcytosinium 1-methylcytosine cation

Reaction of trimethylsilyl-protected cytosine with methyl iodide afforded N1-methylated product. Subsequent treatment with ethanol resulted in cleavage of the protection group forming [(MeCyt)2H]I (4). Identity of was confirmed by microanalysis, mass spectrometry, 1H and 13C NMR spectroscopy and by single-crystal X-ray diffraction analysis. Crystals of consist of dimeric [(MeCyt)2H]+ cations and I- anions. These ions are arranged in the crystal such that there is a strong base stacking (mean stacking distance 3,467 angstroms) and, furthermore, pi interactions between I- and cytosine rings (mean distance 3,737 angstroms). The dimeric [(MeCyt)2H]+ cations are centrosymmetric having three strong hydrogen bonds, namely two terminal N4-H...O' ones (N4...O' 2.815(4) angstroms) and a central N3-H...N3' (N3...N3' 2.813(4) angstroms) one. Quantum chemical calculations on the DFT level of theory show that the gas phase structure of the dimeric cation exhibits two different terminal N-HO hydrogen bonds, a stronger (N4...O' 2.722 angstroms) and a weaker one (N4'...O 2.960 angstroms). The central N3-HN3[prime or minute] hydrogen bond (N3...N3' 2.852 angstroms) was characterized to have an unsymmetrically located proton and a typical double minimum potential with a very low activation barrier. The interaction energy between [(MeCyt)H]+ and MeCyt yielding [(MeCyt)2H]+ was calculated to be -42.4 kcal mol(-1)(ZPE and BSSE corrected). Comparison with the interaction energy (calculated on the same level of the theory) between cytosine and guanine yielding the triply hydrogen-bonded Watson-Crick dimer (-24.2 kcal mol(-1)) revealed a much higher stability of the hydrogen bonds in [(MeCyt)2H]+.     

New Monoterpene-Substituted Dihydrochalcones from Piper aduncum

Five New unusual monoterpene-substituted dihydrochalcones, the adunctins A–E (1″S)-1-{2′-hydroxy-4′-methoxy-6′-[4″-methyl-1″-(1?-methylethyl)cyclohex-3″ -en-1″ -yloxy]phenyl}-3-phenylpropan-1-one ( 1 ), (5aR*,8R*,9aR*)-3-phenyl-1-[5′,8′,9′,9′a-tetrahydro-3′-hydroxy-1′-methoxy-8′-(1″-methylethyl)-5′-a-methyldibenzo-[b,d]furan-4′-yl]propan-1-one ( 2 ), (2′R*,4″S*)-1-{6′-hydroxy-4′-methoxy-4″-(1?-methylethyl)spiro[benzo[b]-furan-2′(3′H),1″ -cyclohex-2″ -en]-7′-yl}-3-phenylpropan-1-one ( 3 ), (2′R*,4″R*)-1-{6′-hydroxy-4′-methylethyl-4″-(1?-methylethyl)spiro[benzo[b]furan-2′(3′H),1″-cyclohex-2″-en]-7′-yl}-3-phenypropan-1-one ( 4 ), and (5′aR*,6′S*, 9′R*,9′aS*)-1-[5′a,6′,7′,8′,9′a-hexahydro-3′,6′-methoxy-6′-methyl-9′-(1″-methylethyl)dibenzo[b,d]-furan-4′-yl]-3-phenylpropan-1-one ( 5 ) were isolated from the leaves of Piper aduncum (Piperaceae) by preparative liquid chromatography. In addition, (?)-methyllindaretin ( 6 ), trans-phytol, and α-tocopherol ( = vitamin E) were also isolated and identified. The structures were elucidated by spectroscopic methods, including 1D- and 2D-NMR spectroscopy as well as single-crystal X-ray diffraction analysis. The antibacterial and cytotoxic potentials of the isolates were also investigated.     

Synthese und Charakterisierung von Aquapentachloroplatinaten(IV) – Struktur von [K(18-Krone-6)][PtCl5(H2O)]

Synthesis and Characterization of Aquapentachloroplatinates(IV) – Structure of [K(18-crown-6)][PtCl₅(H₂O)] The crown ether complex of the aquapentachloroplatinic acid of the composition [H₁₃O₆][PtCl₅(H₄O₂)] · 2(18-cr-6) ( 2 ) reacts with K₂CO₃ and [NⁿBu₄]OH in aqueous solution to give [K(18-cr-6)][PtCl₅(H₂O)] ( 5 a ) and [NⁿBu₄][PtCl₅(H₂O)] · ¹/₂ (18-cr-6) · H₂O ( 5 b ), respectively. Both compounds were characterized by microanalysis, vibrational (IR, Raman) and NMR (¹H, ¹³C, ¹⁹⁵Pt) spectroscopy. The X-ray structure analysis of 5 a (orthorhombic, pnma; a = 16,550(4), b = 18,044(3), c = 7,415(1) Å; Z = 4; R1 = 0,0183; wR2 = 0,0414) reveals that the crystal is threaded by chains built up of [PtCl₅(H₂O)]^? and [K(18-cr-6)]⁺ units. There are tight K …? Cl contacts (d(K? Cl1)) = 3,0881(9) Å and O_W? H? O_cr hydrogen bridges (d(O1 …? O2) = 2,806(3) Å) between these units. The coordination polyhedron [PtCl₅O] has approximately C_4v symmetry.     

Reductive electron transfer in phenothiazine-modified DNA is dependent on the base sequence

A new DNA assay has been designed, prepared and applied for the chemical investigation of reductive electron transfer through the DNA. It consists of 5-(10-methyl-phenothiazin-3-yl)-2'-deoxyuridine (Ptz-dU, 1) as the photoexcitable electron injector and 5-bromo-2'-deoxyuridine (Br-dU) as the electron trap. The Ptz-dU-modified oligonucleotides were synthesised by means of a Suzuki-Miyaura cross-coupling protocol and subsequent automated phosphoramidite chemistry. Br-dU represents a kinetic electron trap, since it undergoes a chemical modification after its one-electron reduction that can be analysed by piperidine-induced strand cleavage. The quantification of the strand cleavage yields from irradiation experiments reveals important information about the electron-transfer efficiency. The performed DNA studies focused on the base sequence dependence of the electron-transfer efficiency with respect to the proposal that C*- and T*- act as intermediate electron carriers during electron hopping. From our observations it became evident that excess-electron transfer is highly sequence dependent and occurs more efficiently over T-A base pairs than over C-G base pairs.     

Sizable concentration-dependent frequency shifts in solution NMR using sensitive probes

With the growing use of high fields and ultrasensitive probes, radiation damping emerges as a significant feedback interaction in modern solution NMR. Motivated by recent observations of mysterious concentration-dependent frequency shifts, experiments carried out on a cryoprobe at 600 MHz have revealed a time-averaged frequency shift of up to +83/-81 Hz. The sizable frequency shifts arise from deviations in the phase of the radiation damping field from perfect orthogonality relative to the net transverse magnetization. The frequency shift is shown to depend on the longitudinal magnetization and probe tuning conditions through experiments and numerical simulations. Such unexpected shifts in the solvent precession frequency provide a physical explanation for the empirical practice of adjusting the irradiation frequency of the saturating B1 field in solvent presaturation to achieve optimal suppression. Additional applications of the radiation damping induced frequency shift to solvent suppression and NMR methodology are discussed.     

Methyl methacrylate polymerization at samarium(II)-grafted MCM-41

Sm(II)-modified periodic mesoporous silica (PMS), Sm[N(SiHMe₂)₂]₂(THF)_x@MCM-41, was used for the synthesis of Sm(II) alkyl, alkoxide, and indenyl surface species via secondary ligand exchange. The performance of the novel Sm(II)-based organometallic–inorganic hybrid materials as initiators for the graft polymerization of methyl methacrylate (MMA) is reported. All of the Sm(II) hybrid materials including the new PMMA–PMS composites were characterized via N₂ physisorption, elemental analysis, FTIR spectroscopy, and scanning electron microscopy (SEM). The organic–inorganic composites revealed complete pore blockage as well as enrichment and strong adhesion of the polymer at the exterior of the porous silica material.