Pyranosyl-RNA (‘p-RNA’): Base-pairing selectivity and potential to replicate. Preliminary communication

Base pairing in p-RNA (β-D -ribopyranosyl-(4′ → 2′)-oligonucleotides) is not only stronger than in DNA and RNA, but also more selective in the sense that it is strictly confined to the Watson-Crick mode. Homopurine sequences (tested up to decamers) exist as single strands under conditions where they undergo reverse-Hoogsteen self-pairing in homo-DNA or Hoogsteen self-pairing in DNA. This exceptional pairing selectivity is rationalized as hinging on two structural features of p-RNA: the large inclination between backbone axis and base-pair axes in p-RNA duplexes, and the higher rigidity of the p-RNA backbone compared with RNA, DNA, and homo-DNA. The most important consequence of the pairing selectivity refers to the potential of p-RNA to replicate. Replicative copying of sequence information by nonenzymatic template-controlled ligation is not hampered by self-pairing of guanine-rich templates, as it is known to be the case in the RNA series. We have demonstrated two replicative cycles in which G-rich p-RNA-octamer templates induce sequence-selective ligation of tetramer-2′-phosphate derivatives to complementary C-rich octamer sequences, and in which the latter, with comparable efficiency, induce corresponding ligation reactions back to the original G-rich octamers. Ligation is most satisfactorily achieved after pre-activation of the 2′-phosphate groups as 2′,3′-cyclophosphate derivatives; in this version, the process does not proceed as oligocondensation, but as a genuine oligomerization. This is of considerable promise for the search for potentially natural conditions under which homochiral p-RNA strands might self-assemble and self-replicate.     

Observations on the Hantzsch Reaction: Synthesis of N-tBoc-S-Dolaphenine

An understanding of the mechanism by which racemization occurs in the Hantzsch reaction preparation of 2-(1-aminoalkyl)thiazoles has enabled the development of a methodology to prevent racemization. N-^tBoc-S-dolaphenine (3) is then synthesized using this methodology.     

Why Pentose- and Not Hexose-Nucleic Acids??. Part VII. Pyranosyl-RNA (‘p-RNA’). Preliminary communication

Qualitative conformational analysis of the entirety of conceivable hexo- and pentopyranosyl oligonucleotide systems derived from the diastereoisomeric aldohexoses (CH₂O)₆ and aldopentoses (CH₂O)₅ predicts the existence of a variety of pairing systems which have not been experimentally investigated so far. In particular, the analysis foresees the existence of a ribopyranosyl isomer of RNA (‘p-RNA’), containing the phosphodiester linkage between the positions C(4′) and C(2′) of neighboring ribopyranosyl units. Double strands of p-RNA oligonucleotides are expected to have a linear structure and to show purine-pyrimidine and purine-purine (Watson-Crick) pairing comparable in strength to that observed in homo-DNA. Experimentally, synthetic β-D -ribopyranosyl (4′→2′)-oligonucleotides derived from adenine and uracil confirm this prognosis: adenine-uracil pairing in p-RNA duplexes is stronger than in the corresponding RNA duplexes. Importantly, adenine in p-Ribo(A₈) does not show (reverse-Hoogsteen) self-pairing, in sharp contrast to its behavior in the homo-DNA series. The sheer existence of strong and selective pairing in a system that is constitutionally isomeric to RNA and can be predicted to have a linear structure has implications for the problem of RNA's origin. In this context, a comprehensive experimental study of the pairing properties of p-RNA, of its potential for constitutional assembly, self-replication, and intra-duplex isomerization to RNA seems mandatory.     

Pyranosyl-RNA (‘p-RNA’): NMR and Molecular-Dynamics Study of the Duplex Formed by Self-pairing of Ribopyranosyl-(C-G-A-A-T-T-C-G)

The solution structure of the duplex formed by self-pairing of the p-RNA octamer β-D -ribopyranosyl-(2′→4′)-(CGAATTCG) was studied by NMR techniques and, independently, by molecular-dynamics calculations. The resonances of all non-exchanging protons, H-bearing C-atoms, P-atoms, and of most NH protons were assigned. Dihedral angle and distance constraints derived from coupling constants and NOESY spectra are consistent with a single dominant conformer and corroborate the main structural features predicted by qualitative conformational analysis. The duplex displays Watson-Crick pairing with antiparallel strand orientation. The dihedral angles β and ? in the phosphodiester linkages differ considerably from the idealized values. Model considerations indicate that these deviations from the idealized model allow better interstrand stacking and lessen unfavorable interactions in the backbone. The average base-pair axis forms an angle of ca. 40° with the backbone. The resulting interstrand π-π stacking between either two purines, or a purine and a pyrimidine, but not between two pyrimidines, constitutes a characteristic structural feature of the p-RNA duplex. A 1000-ps molecular-dynamics (MD) calculation with the AMBER force field resulted in an average structure of the same conformation type as derived by NMR. For the backbone torsion angle ?, dynamically averaged coupling constants from the MD calculation agree well with the experimental values, but for the angle β, a systematic difference of ca. 25° remains. The two base pairs at the ends of the duplex are calculated to be highly labile, which is consistent with the high exchange rate of the corresponding imino protons found by NMR.     

CO2 Aggregation on Monoethanolamine: Observations from Rotational Spectroscopy

The initial stages of the gas-phase nucleation between CO₂ and monoethanolamine were investigated via broadband rotational spectroscopy with the aid of extensive theoretical structure sampling. Sub-nanometer-scale aggregation patterns of monoethanolamine-(CO₂)_n, n=1–4, were identified. An interesting competition between the monoethanolamine intramolecular hydrogen bond and the intermolecular interactions between monoethanolamine and CO₂ upon cluster growth was discovered, revealing an intriguing CO₂ binding priority to the hydroxyl group over the amine group. These findings are in sharp contrast to the general results for aqueous solutions. In the quinary complex, a cap-like CO₂ tetramer was observed cooperatively surrounding the monoethanolamine. As the cluster approaches the critical size of new particle formation, the contribution of CO₂ self-assembly to the overall stability increases.     

Replication of Micro- and Nanostructures on Polymer Surfaces

Summary : Via geometrical micro- and nanostructures new functionalities like controlled wetting properties, biological adhesive / dehesive properties or surface patterns for guided self assembly can be added to polymer surfaces. This is especially interesting for medical or biotechnological applications, because there is no new approval process necessary. The whole process from producing the structures via EUV-interference lithography to the injection moulding will be shown. How far the limits for the smallness of these structures on polymers are already pushed forward show the results from our latest injection moulded samples. Grooves of 18 nm width - this means world record! - could be reproduced in an industrial process and in an economical very interesting high-volume production.     

Further considerations on oxidative processes

Refuting recent criticisms by Russell, modification of the currently accepted mechanism of formation of benzyl chloride from toluene is introduced and current interpretation of the reactivity of carbonyl compounds is broadened. The results of the photochemical interaction of benzophenone, isopropyl alcohol, and nitric oxide are shown to accord with classical as against the hydrogen-abstraction theory of oxidation. Supplementary discussion of the behaviour of ethers, amines and paraffins is also contributed.     

Further studies on hydroxyperezone derivatives

Hydroxyperezone monoangelate (2c) was transformed into the mixture of α-(8) and β-perezols (9). Separation of these compounds permitted stereochemical assignments by NMR and ORD. The position of the angeloyl moiety in 2c was independently tested by its conversion to O-methylhydroxyperezone (1d) identified with a sample synthesised from perezone (1a). Several reactions distinguished the natural hydroxyperezone (2a) from the synthetic hydroxyperezone hydrate (3).     

Observations on some plasma-sprayed metal carbides

Results of a study into plasma-sprayed coatings of W and Cr- carbides are presented. The investigations comprised the assessment of phase composition, microstructure, carbon losses, hardness and scratch resistance of coatings obtained at the same spraying conditions. Of practical importance are the changes occurring in the carbides in the plasma stream, namely evaporation, melting, phase-changes, oxidation, and decomposition which bring about different microstructures and variations of the properties of the coatings. These changes have been evaluated on the basis of a detailed characterization of the starting powders and of the microstructure of the coatings.     

Observations on the permanganate-arsenious oxide titration

The reduction of permanganate and the oxidation of manganous ion have been studied in a variety of acid solutions. The product appears to be an unstable complex of trivalent manganese. The manganic sulfate complex is pink in solution and the manganic arsenate complex is green. Complexes prepared in hydrochloric acid were found to be highly unstable and decomposed rapidly with the formation of free chlorine. The results of this work shed some light on the mechanism of the permanganate-arsenious oxide titration.     

Further explorations on bridged 1,2,4-trioxanes

Three new bicyclo[3.2.1]-type 1,2,4-trioxanes have been designed and synthesized. One of them demonstrates better tolerance of the intramolecular hemiketals to steric crowding in hydroperoxidation. The other represents a prototype for possible manipulation of the transient radicals generated in cleavage reactions. A new substitution pattern in the bridged system is explored through synthesis of the third molecule. The configurations of all stereogenic centers in the bridged system can be effectively controlled by the chirality of the allyl alcohol as illustrated by the enantioselective synthesis of the fourth molecule. Finally, similar bicyclo[3.3.1]-type 1,2,4-trioxanes are shown very difficult to be synthesized because of the involvement of a conformer with two substituents at axial positions at the same time.     

Replication of a DNA microarray

A mechanical method for efficient replication of DNA microarrays is described. The approach consists of three steps. First, a master DNA microarray consisting of single-stranded DNA elements is exposed to a solution containing the biotin-functionalized complement of each array element. Following hybridization, a replica surface modified with streptavidin is brought into contact with the master. This results in linking of the biotin-functionalized complement with the replica surface. Next, the replica is separated from the master, and the complementary strands are transferred to the replica surface. The resulting complementary DNA microarray contains position-coded sequences that mirror the information contained on the master DNA microarray. Multiple replicas can be prepared from a single master, the replicas efficiently hybridize only their complement, and DNA not labeled with biotin is not transferred to the replica surface.     

Further synthetic studies on rifamycin s

Two new highly stereocontrolled syntheses of the optically active form of the aliphatic segment 2 of rifamycin S are described.     

Observations on Sampling Control Sera: Distributions of Chemistry Quality Control Values

Abstract

Data, obtained in quality control programs in automated clinical chemistry systems are often not normally distributed. Falsely assuming that the data is Gaussian produces errors in classifying patients, and in statistical inferences drawn from parametric tests.