SELEX: Critical factors and optimization strategies for successful aptamer selection.

Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.

Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies.

The monoclonal anti-CD20 IgG1 antibody rituximab is used as a first-line treatment for B cell lymphoma. Like all therapeutic antibodies, it is a complex protein for which both safety and efficacy heavily depend on the integrity of its three-dimensional structure. Aptamers, short oligonucleotides with a distinct fold, can be used to detect minor modifications or structural variations of a molecule or protein. To detect antibody molecules in a fold state occurring prior to protein precipitation, we generated DNA aptamers that were selected for extensively heat-treated rituximab. Using the magnetic bead-based systematic evolution of ligands by exponential enrichment (SELEX), we obtained six DNA aptamer sequences (40-mers) specific for 80°C heat-treated rituximab. In silico fold prediction and circular dichroism analysis revealed a G-quadruplex structure for one aptamer, while all others exhibited a B-DNA helix. Binding affinities ranging from 8.8-86.7 nM were determined by an enzyme-linked apta-sorbent assay (ELASA). Aptamers additionally detected structural changes in rituximab treated for 5 min at 70°C, although with lower binding activity. Notably, none of the aptamers recognized rituximab in its native state nor did they detect the antibody after it was exposed to lower temperatures or different physical stressors. Aptamers also reacted with the therapeutic antibody adalimumab incubated at 80°C suggesting similar aptamer binding motifs located on extensively heat-treated IgG1 antibodies. Within this work, we obtained the first aptamer panel, which is specific for an antibody fold state specifically present prior to protein aggregation. This study demonstrates the potential of aptamer selection for specific stress-based protein variants, which has potential impact for quality control of biopharmaceuticals.

Arabidopsis MAP-Kinase 3 Phosphorylates UDP-Glucose Dehydrogenase: a Key Enzyme Providing UDP-Sugar for Cell Wall Biosynthesis.

The enzyme UDP-glucose dehydrogenase (UGD) competes with sucrose-phosphate synthase for the common photosynthesis product UDP-glucose. Sucrose-phosphate synthase is part of a pathway for the export of sucrose from source leaves to neighboring cells or the phloem. UGD is a central enzyme in a pathway for many nucleotide sugars used in local cell wall biosynthesis. Here, we identify a highly conserved phosphorylation site in UGD which is readily phosphorylated by MAP-kinase 3 in Arabidopsis. Phosphorylation occurs at a surface-exposed extra loop in all plant UGDs that is absent in UGDs from bacteria or animals. Phosphorylated sucrose-phosphate synthase is shifted to an inactive form which we did not measure for phosphorylated UGD. Plant UGDs have an extra loop which is phosphorylated by AtMPK3. Phosphorylation is not causing a reduction of UGD activity as found for the competitor enzymes and thus sets a preference for maintaining UDP-sugars at a constant level to prioritize cell wall biosynthesis.