Poly(8-aminoguanylic acid): formation of ordered self-structures and interaction with poly(cytidylic acid)

Development of A Novel High Throughput Photo-catalyst Screening Procedure: UV-A Degradation of 17α-Ethinylestradiol with Doped TiO2-Based Photo-catalysts

The rising pollution of surface water by endocrine disruptive chemicals (EDCS) could lead to the persistent harm of aquatic wildlife. Addressing this concern, advanced waste water treatment techniques should be established in addition to the present sewage treatment. Therefore, the promising advanced oxidation process of photocatalysis is discussed. With the aim of establishing a novel high throughput screening approach for photocatalysts, a workflow resting upon the use of a self-constructed 60-fold parallel stirring UV-A LED photoreactor, followed by parallel sample extraction by SPE and sequential automated analysis by GC-MS, was developed, and is presented in this article. With the described system, TiO₂-based photocatalysts, doped with different amounts of zinc, and synthesised by a sol-gel-route, were tested regarding their activity in the photocatalytic degradation of the synthetic estrogen 17α-ethinylestradiol. Thereby, the functional behavior of the photoreactor system and its applicability in a high throughput process could be evaluated. As a result of the catalyst screening, TiO₂ catalysts with low amounts of zinc were found with a significantly higher activity, compared to undoped TiO₂. In conclusion, the presented system provides an easily accessible high throughput method for a variety of photocatalytic experiments.

Supramolecular hydrogels for environmental remediation: G4-quartet gels that selectively absorb anionic dyes from water

Binary mixtures of guanosine and 8-aminoguanosine form stable, transparent hydrogels with Ba²⁺ that selectively bind anionic dyes.

Evidence of strong hydrogen bonding by 8-aminoguanine

DNA oligonucleotides containing 8-aminodeoxyguanosine residues form a pH-dependent self-structure with strong hydrogen bonds.

Site-specifically located 8-amino-2'-deoxyguanosine: thermodynamic stability and mutagenic properties in Escherichia coli

2-Nitropropane (2-NP), an important industrial solvent and a component of cigarette smoke, is mutagenic in bacteria and carcinogenic in rats. 8-Amino-2'-deoxyguanosine (8-amino-dG) is one of the types of DNA damage found in liver, the target organ in 2-NP-treated rats. To investigate the thermodynamic properties of 8-amino-dG opposite each of the four DNA bases, we have synthesized an 11mer, d(CCATCG*CTACC), in which G* represents the modified base. By annealing a complementary DNA strand to this modified 11mer, four sets of duplexes were generated each containing one of the four DNA bases opposite the lesion. Circular dichroism studies indicated that 8-amino-dG did not alter the global helical properties of natural right-handed B-DNA. The thermal stability of each duplex was examined by UV melting measurements and compared with its unmodified counterpart. For the unmodified 11mer, the relative stability of the complementary DNA bases opposite G was in the order C > T > G > A, as determined from their -DeltaG degrees values. The free energy change of each modified duplex was lower than its unmodified counterpart, except for the G*:G pair that exhibited a higher melting transition and a larger -DeltaG degrees than the G:G duplex. Nevertheless, the stability of the modified 11mer duplex also followed the order C > T > G > A when placed opposite 8-amino-dG. To explore if 8-amino-dG opposite another 8-amino-dG has any advantage in base pairing, a G*:G* duplex was evaluated, which showed that the stability of this duplex was similar to the G*:G duplex. Mutagenesis of 8-amino-dG in this sequence context was studied in Escherichia coli, which showed that the lesion is weakly mutagenic (mutation frequency approximately 10(-3)) but still can induce a variety of targeted and semi-targeted mutations.

DNA-triplex stabilizing properties of 8-aminoguanine

A DNA-triplex stabilizing purine (8-aminoguanine) is designed based on molecular modeling and synthesized. The substitution of guanine by 8-aminoguanine largely stabilizes the triplex both at neutral and acidic pH, as suggested by molecular dynamics and thermodynamic integration calculations, and demonstrated by melting experiments. NMR experiments confirm the triplex-stabilizing properties of 8-aminoguanine and demonstrate that few changes are found in the structure of the triplex due to the presence of this modified base.

Triple helix stabilization properties of oligonucleotides containing 8-amino-2'-deoxyguanosine

Analysis of the Hoogsteen base pairs of guanine and 8-aminoguanine with cytosine in the gase phase shows a strong stabilization of the 8-aminoguanine.cytosine base pair due to the formation of an extra H-bond. Melting profiles of oligonucleotides carrying 8-amino-2'-deoxyguanosine confirm the triple helix stabilization properties of 8-aminoguanine.

Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomer DNA

The subject of four-stranded nucleic acid structures is reviewed. Studies on gels formed by guanosine and its analogues have provided appropriate models for the structures of poly(I) and poly(G). The stabilizing influence of certain cations, in particular K+, on Guo-5'-P gels and poly(I) is discussed in the light of recent data on selective K+ stabilization of telomeric DNA structures. The topological possibilities these dG containing sequences could adopt are discussed. In particular the role of the glycosidic linkage (anti/syn), the polarity of the strands and the orientation of the G-tetrad stacks is highlighted.

The properties of ATP-analogs in initiation of RNA synthesis catalyzed by RNA polymerase from E coli

Various base and sugar modified derivatives of ATP and UTP were used as substrate analogs for the steady state initiation reaction ATP+UTP=pppApU and the single step addition reaction ApC+ATP=ApCpA. These reactions were carried out by E. coli RNA polymerase on T7 DNA in the presence of rifampicin. The steady state kinetic parameters of the analogs, either as substrates or inhibitors, were determined. On the basis of the obtained results it is concluded that purine NTP s in initiation require anti-conformation about the glycosidic bonds as well as gauche-gauche conformation of the C(4')-C(5') bonds. The latter conformation is also a prerequisite for substrates in elongation, whereas strict anti-conformation of glycosidic bonds is not.

Infrared spectroscopy of polynucleotides in the carbonyl region in H2O solution: A.U systems

Strong absorbance of water at 1645 cm-1 has previously prevented dependable observation of infrared spectra of H2O solutions in the carbonyl region. We have obtained reliable spectra in pure water and in alcohol-water mixtures in this region and used them to study A.U polynucleotide interaction. Spectra in pure water were obtained by computer subtraction of solvent from that of solution measured in short path length cells. Mixed solvents, by diluting the water, permit use of longer cells and standard double-beam compensation methods. Poly(adenylic acid) in H20 solution has a strong NH2 deformation band at 1659 cm-1 coupled to an A ring vibration at 1605 cm-1. Poly(uridylic acid) has a broad band at approximately 1695 cm-1, predominantly C2 carbonyl stretch, an unresolved CR carbonyl band (probably near 1660 cm-1), and a ring vibration at approximately 1636 cm-1. The large changes these spectra undergo when helical structures are formed are discussed and compared with changes observed in D2O.

RNA structure

This review is concerned primarily with the physical structure and changes in the structure of RNA molecules. It will be evident that we have not attempted comprehensive coverage of what amounts to a vast literature. We have tried to stay away from particular areas that have been recently reviewed elsewhere. Citations to and information from them are included, however, so that access to the literature is available. Much of what we treat in depth deals with the crystal structures and solution behaviour of model RNA compounds, including synthetic polymers and molecular fragments such as dinucleoside phosphates. Sequence data on natural RNA are cited, but not in detail. Similarly, apart from tRNA, natural RNAs the structural determinations of which are presently not so far advanced, are not dwelt upon. We have tried to present in detail the available structural data with scaled drawings that permit facile comparisons of molecular geometries.

Poly(2-aminoadenylic acid): interaction with poly(uridylic acid)

Poly(2-aminoadenylic acid) forms both double and triple helices with poly(uridylic acid) [poly(U)]. The 2-amino group forms a third hydrogen bond, elevating the 2 leads to 1 transition temperature by 33 degrees C. The third strand, however, has about the same stability as poly(A)-2poly(U), as measured by Tm 3 leads to 2. This selective stabilization of the two-stranded helix results in a much greater resolution of the differnt thermal transitions than that observed in analogous polynucleotide systems. In contrast to other A, U systems 3 leads to 1 and 2 leads to 3 transitions are not observed under any conditions, and the triple helix always undergoes a 3 leads to 2 transition even at very high ionic strength. A 1:1 mixture of poly(2NH2A) and poly(U) exhibits no transient formation of 1:2 complex, unlike similar mixtures of poly(A) with poly(U) and poly(T). This difference is evidently due to a more rapid displacement reaction: [poly(2NH2A) + poly(2NH2A)-2poly(U) leads to 2 poly(2NH2A)-poly(U)] With poly(2NH2A) than with poly(A). We describe a method for establishing the combining ratios of polynucleotide complexes which used a computer to calculate the angles of intersection of mixing curves as explicit and continuous functions of the wavelength. The wavelength dispersions of the angles of intersection determine optimum wavelengths for establishing stoichiometry and can also provide reliable negative evidence that presumably plausible complexes are not formed. Analogous computer procedures have been developed to determine wavelengths which are selective for the formation of both 1:1 and 1:2 complexes. Infrared spectra of the 1:1 and 1:2 complexes resemble those of other A, U homoribopolynucleotide helices in having two and three strong bands, respectively, in the region of carbonyl stretching vibrations. CD spectra of the two complexes are unusual in having negative first extrema of moderate intensity. We attribute these extrema to intrastrand interactions of strong, well-resolved transitions at 278 nm (B2u) of the 2-aminoadenine residues. The CD spectra are correlated with those of other polynucleotide helices.