Combinatorial Chemistry & High Throughput Screening - Volume 5, Issue 4, 2002

In vitro selection can be used to generate nucleic acid binding species (aptamers) and catalysts (ribozymes) that can recognize a variety of molecules. Because nucleic acid function is largely derived from readily tabulated secondary structures, it has proven possible to engineer aptamers and ribozymes to function as biosensors. Labeling nucleic acids with reporter molecules has yielded simple antibody substitute Read More

Investigating ligand-DNA interactions using type IIS restriction enzymes (IISRE) as footprinting reagents is reviewed and contemplated. Ligand binding at a IISRE's cleavage but not sequence recognition site protects DNA from strand scission. This spatial arrangement has been exploited in the development of qualitative (combinatorial) and quantitative ligand-DNA investigative methods collectively termed Type IIS Restrictio Read More

While the in vitro selection of nucleic acid binding species (aptamers) requires numerous liquidhandling steps, these steps are relatively straightforward and the overall process is therefore amenable to automation. Here we demonstrate that automated selection techniques are capable of generating aptamers against a number of diverse protein targets. Automated selection techniques can be integrated with au Read More

Hammerhead ribozymes that are subject to allosteric control by small molecule and oligonucleotide effectors have been reported recently. Rational design has been an effective strategy for the creation of these ribozymes, which incorporate structurally interdependent hammerhead motifs and effector-binding sequences. In this paper we report the rational design of the first protein-responsive allosteric ribozymes that are regul Read More

In vitro selection with either DNA or RNA libraries was performed against the TAR RNA element of HIV-1. The role of the selection conditions on the outcome of the selection was evaluated by varying the magnesium concentration and the temperature. The selection stringency was demonstrated to determine i) the affinity of the best identified aptamers for the TAR target, and ii) the type of interaction between the two partners. S Read More

Metal ions play important roles in both the structure and function of catalytic DNA and RNA. While most natural catalytic RNA molecules (ribozymes) are active in solutions containing Mg2+, in vitro selection makes it possible to search for new catalytic DNA / RNA that are specific for other metal ions. However, previous studies have indicated that the in vitro selection protocols often resulted in catalytic DNA / RNA that Read More