PCR technology for screening and quantification of genetically modified organisms (GMOs)

Although PCR technology has obvious limitations, the potentially high degree of sensitivity and specificity explains why it has been the first choice of most analytical laboratories interested in detection of genetically modified (GM) organisms (GMOs) and derived materials. Because the products that laboratories receive for analysis are often processed and refined, the quality and quantity of target analyte (e.g. protein or DNA) frequently challenges the sensitivity of any detection method. Among the currently available methods, PCR methods are generally accepted as the most sensitive and reliable methods for detection of GM-derived material in routine applications.The choice of target sequence motif is the single most important factor controlling the specificity of the PCR method. The target sequence is normally a part of the modified gene construct, for example a promoter, a terminator, a gene, or a junction between two of these elements. However, the elements may originate from wildtype organisms, they may be present in more than one GMO, and their copy number may also vary from one GMO to another. They may even be combined in a similar way in more than one GMO. Thus, the choice of method should fit the purpose. Recent developments include event-specific methods, particularly useful for identification and quantification of GM content. Thresholds for labelling are now in place in many countries including those in the European Union. The success of the labelling schemes is dependent upon the efficiency with which GM-derived material can be detected. We will present an overview of currently available PCR methods for screening and quantification of GM-derived DNA, and discuss their applicability and limitations. In addition, we will discuss some of the major challenges related to determination of the limits of detection (LOD) and quantification (LOQ), and to validation of methods.     

Strategies for continuous on-line high performance liquid chromatography coupled with diode array detection and electrospray tandem mass spectrometry for process monitoring of sulphonated azo dyes and their intermediates in anaerobic-aerobic bioreactors

On-line HPLC with diode array detection (DAD) coupled to electrospray tandem mass spectrometry (ESI-MS/MS) is presented as an integrated quality control and process integrated optimisation tool for the continuous monitoring of sulphonated azo dyes (SADs) and their intermediates in anaerobic and aerobic bioprocesses. Ion-pair RP-HPLC is found out to be more suitable for simultaneous monitoring of aromatic amines (AAs), sulphonated aromatic amines (SAAs) and sulphonated azo dyes in comparison to RP-HPLC with polar embedded phases. Monitoring of the anaerobic degradation of the diazo Reactive Black 5 displays the dependency of a two stage azo group reduction mechanism on the redox potential of the bioreactor. An autoxidation sensitive intermediate released from the anaerobic reduction is characterised by ESI-MS/MS for the first time. The functionality of the method is demonstrated by the control and evaluation of selective adaptation of bacteria to certain pollutants and the identification of unknown intermediates causing re-gaining colour released from azo dye treatment.     

Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates,including Mechanistic Considerations

Considering that practically all reactions that involve nucleotides also involve metal ions, it is evident that the coordination chemistry of nucleotides and their derivatives is an essential corner stone of biological inorganic chemistry. Nucleotides are either directly or indirectly involved in all processes occurring in Nature. It is therefore no surprise that the constituents of nucleotides have been chemically altered—that is, at the nucleobase residue, the sugar moiety, and also at the phosphate group, often with the aim of discovering medically useful compounds. Among such derivatives are acyclic nucleoside phosphonates (ANPs), where the sugar moiety has been replaced by an aliphatic chain (often also containing an ether oxygen atom) and the phosphate group has been replaced by a phosphonate carrying a carbon–phosphorus bond to make the compounds less hydrolysis-sensitive. Several of these ANPs show antiviral activity, and some of them are nowadays used as drugs. The antiviral activity results from the incorporation of the ANPs into the growing nucleic acid chain—i.e., polymerases accept the ANPs as substrates, leading to chain termination because of the missing 3′-hydroxyl group. We have tried in this review to describe the coordination chemistry (mainly) of the adenine nucleotides AMP and ATP and whenever possible to compare it with that of the dianion of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA²⁻ = adenine(N9)-CH₂-CH₂-O-CH₂-PO32) [or its diphosphate (PMEApp⁴⁻)] as a representative of the ANPs. Why is PMEApp⁴⁻ a better substrate for polymerases than ATP⁴⁻? There are three reasons: (i) PMEA²⁻ with its anti-like conformation (like AMP²⁻) fits well into the active site of the enzyme. (ii) The phosphonate group has an enhanced metal ion affinity because of its increased basicity. (iii) The ether oxygen forms a 5-membered chelate with the neighboring phosphonate and favors thus coordination at the P_α group. Research on ANPs containing a purine residue revealed that the kind and position of the substituent at C2 or C6 has a significant influence on the biological activity. For example, the shift of the (C6)NH₂ group in PMEA to the C2 position leads to 9-[2-(phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer with only a moderate antiviral activity. Removal of (C6)NH₂ favors N7 coordination, e.g., of Cu²⁺, whereas the ether O atom binding of Cu²⁺ in PMEA facilitates N3 coordination via adjacent 5- and 7-membered chelates, giving rise to a Cu(PMEA)_cl/O/N3 isomer. If the metal ions (M²⁺) are M(α,β)-M(γ)-coordinated at a triphosphate chain, transphosphorylation occurs (kinases, etc.), whereas metal ion binding in a M(α)-M(β,γ)-type fashion is relevant for polymerases. It may be noted that with diphosphorylated PMEA, (PMEApp⁴⁻), the M(α)-M(β,γ) binding is favored because of the formation of the 5-membered chelate involving the ether O atom (see above). The self-association tendency of purines leads to the formation of dimeric [M₂(ATP)]₂(OH)⁻ stacks, which occur in low concentration and where one half of the molecule undergoes the dephosphorylation reaction and the other half stabilizes the structure—i.e., acts as the “enzyme” by bridging the two ATPs. In accord herewith, one may enhance the reaction rate by adding AMP²⁻ to the [Cu₂(ATP)]₂(OH)⁻ solution, as this leads to the formation of mixed stacked Cu₃(ATP)(AMP)(OH)⁻ species, in which AMP²⁻ takes over the structuring role, while the other “half” of the molecule undergoes dephosphorylation. It may be added that Cu₃(ATP)(PMEA) or better Cu₃(ATP)(PMEA)(OH)⁻ is even a more reactive species than Cu₃(ATP)(AMP)(OH)⁻. – The matrix-assisted self-association and its significance for cell organelles with high ATP concentrations is summarized and discussed, as is, e.g., the effect of tryptophanate (Trp⁻), which leads to the formation of intramolecular stacks in M(ATP)(Trp)³⁻ complexes (formation degree about 75%). Furthermore, it is well-known that in the active-site cavities of enzymes the dielectric constant, compared with bulk water, is reduced; therefore, we have summarized and discussed the effect of a change in solvent polarity on the stability and structure of binary and ternary complexes: Opposite effects on charged O sites and neutral N sites are observed, and this leads to interesting insights.     

A Novel Sensor Based on Carbon Paste Electrode Modified with Polypyrrole/Multi-walled Carbon Nanotubes for the Electrochemical Detection of Cytostatic Drug Rapamycin

The electrocatalytic oxidation of rapamycin, one of the most studied immunosuppressant, cancer-preventing drug, is investigated for the first time on the surface of the modified carbon paste electrode prepared by incorporating multi-walled carbon nanotubes (MWCNTs) and conductive polymer pyrrole using differential pulse voltammetry (DPV). Rapamycin exhibited a well-defined oxidation peak at +1.1 V (versus Ag/AgCl) in Briton Robinson buffer solution with a pH 4.0. Effect of the most important experimental parameters was optimized and obtained signals are linear to the concentration of rapamycin in the range from 0.1 to 20 μM with 0.06 μM limit of detection. The repeatability is calculated as ±2 % and the reproducibility as ±5 %. The possible interfering compounds were tested showing negligible effect and the sensor was successfully applied for the determination of rapamycin in commercial pharmaceutical formulations with obtained recoveries in the range from 98 % to 102 %.     

Shape transformation of poly(butadiene)‐b‐poly(ethyleneoxide) plus DTAB compound micelles in aqueous solutions

The micellar shape of Poly(butadiene)‐b‐poly(ethyleneoxide) (PB‐PEO) plus Dodecyltrimethylammoniumbromide (DTAB) compound micelles was investigated by light scattering, small‐angle X‐ray scattering and small‐angle neutron scattering in dependence of the molar ratio between block copolymer and surfactant. The given block copolymer forms cylindrical micelles in binary aqueous solution, which transform to spherical aggregates upon the addition of a sufficiently high amount of DTAB. It is interesting to note that the micellar shape seems to be a bistable feature, in the sense that it depends not only on the molar ratio of BCP and DTAB but also in a predictable manner on the preparation procedure of the solution.