Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies

The human immunodeficiency virus type-1 (HIV-1) genome contains multiple, highly conserved structural RNA domains that play key roles in essential viral processes. Interference with the function of these RNA domains either by disrupting their structures or by blocking their interaction with viral or cellular factors may seriously compromise HIV-1 viability. RNA aptamers are amongst the most promising synthetic molecules able to interact with structural domains of viral genomes. However, aptamer shortening up to their minimal active domain is usually necessary for scaling up production, what requires very time-consuming, trial-and-error approaches. Here we report on the in vitro selection of 64 nt-long specific aptamers against the complete 5' -untranslated region of HIV-1 genome, which inhibit more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop. Based on this result, an in silico designed 16 nt-long RNA aptamer, termed RNApt16, was synthesized, with sequence 5'-CCCCGGCAAGGAGGGG-3-'. The HIV-1 inhibition efficiency of such an aptamer was close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication.

Aspects of the prevention and repair of chloride-induced corrosion of steel in concrete

Sodium formate, potassium acetate and a mixture of calcium and magnesium acetate (CMA) have all been identified as effective de-icing agents. In this project an attempt has been made to elucidate potentially deleterious effects of these substances on the durability of reinforced concrete. Aspects involving the corrosion behaviour of embedded steel along with the chemical and physical degradation of the cementitious matrix were studied. Ionic diffusion characteristics of deicer/pore solution systems in hardened cement paste were also studied since rates of ingress of deleterious agents into cement paste are commonly diffusion-controlled. It was found that all the compounds tested were generally non-corrosive to embedded steel, however, in a small number of cases potassium acetate did cause corrosion. Potassium acetate was also found to cause cracking in concrete and cement paste samples. CMA appeared to degrade hydrated cement paste although this was apparently less of a problem when commercial grade CMA was used in place of the reagent grade chemical. This was thought to be due to the insoluble material present in the commercial formulation forming a physical barrier between the concrete and the de-icing solution. With the test regimes used sodium formate was not seen to have any deleterious effect on the integrity of reinforced concrete. As a means of restoring the corrosion protective character of chloride-contaminated concrete the process of electrochemical chloride removal has been previously developed. Potential side-effects of this method and the effect of external electrolyte composition on chloride removal efficiency were investigated. It was seen that the composition of the external electrolyte has a significant effect on the amount of chloride removed. It was also found that, due to alterations to the composition of the C3A hydration reaction products, it was possible to remove bound chloride as well as that in the pore solution. The use of an external electrolyte containing lithium ions was also tried as a means of preventing cathodically-induced alkali-silica reaction in concretes containing potentially reactive aggregates. The results obtained were inconclusive and further practical development of this approach is needed.