Interaction of aptamers to the target is based on the three Dimensional folding patterns. The complex 3 Dimensional structure of the single stranded oligonucleotide is due to the intramolecular hybridization, which causes the folding into particular shape. Due to this complex three dimensional shape, aptamers have high affinity and specificity towards the target molecules.

Aptamer Selection Process : Invitro Selection

The aptamers are selected by incubating the target molecule in a large pool of oligonucleotide (usually 40 to 60mers), the pool size of the oligonucleotide is from 10^10 to 10^20. The large pool size of the oligonucleotide ensures the selection and isolation of the specific aptamer. The structural and informational complexity of the oligonucleotide pool and its functional activity is an interesting and active area to develop an algorithm based development of nucleic acid ligands. Aptamers can distinguish between closely related but non-identical members of a protein family, or between different functional or conformational states of the same protein. In a striking example of specificity, an aptamer to the small molecule theophylline (1,3-dimethylxanthine) binds with 10,000-fold lower affinity to caffeine (1,3,7-trimethylxanthine) that differs from theophylline by a single methyl group. The protocol called systematic evolution of ligands by exponential enrichment (SELEX) is generally used with modification and variations for the selection of specific aptamers. Using this process, it is possible to develop new aptamers in as little as two weeks.

Different Aptamer Selection Methods

• Nitrocellulose Membrane Filtration-Based SELEX 

• Affinity Chromatography and Magnetic Bead-Based SELEX

SELEX for small molecules, as well as proteins, can be carried out using this method. Several aptamers were selected using this method by making an affinity column containing target-immobilized beads. However, the disadvantage of this method is that it cannot be applied if the target lacks the affinity tag or the functional group needed for coupling to the beads.

• Capillary Electrophoresis-Based SELEX

With the use of Capillary Electrophoresis-Based SELEX an aptamer can be selected by a mobility shift
among the mixture of a target, the library, and the target-library complex. In particular, the
greatest virtue of applying this method to SELEX is that the successful selection of the aptamer can be
achieved within very few rounds, generally 2–4 rounds, compared to other methods.

• Microfluidic-Based SELEX

Microfluidic Based SELEX method is mainly processed on a chip, it is able to enhance selection efficiency on a small scale. For example, the DNA aptamer-specific bound to neurotoxin type B wasobtained after a single round of selection using the Continuous-flow Magnetic Activated Chip-based Separation (CMACS) device.

• Cell-SELEX

Cell-SELEX is aimed at searching for an aptamer against a whole cell, whereas the primary targets of
other SELEX methods are single highly-purified proteins, where as the targets of Cell-SELEX
are extracellular proteins on the cell surface or unique structures of the cell.

• Other Method-Based SELEX

Aptamers Advantages:

While aptamers are analogous to antibodies in their range of target recognition and variety of applications, they possess several key advantages over their protein counterparts:

• Easier and more economical to produce. Aptamers are made through chemical synthesis, a process that is highly reproducible and can be readily scaled up. Their production does not depend on bacteria, cell cultures or animals.

• Compared to antibodies, toxicity and low immunogenicity of particular antigens do not interfere with the aptamer selection.

• Aptamers are capable of greater specificity and affinity than antibodies.

• Aptamers can easily be modified chemically to yield improved, custom tailored properties.

• Aptamers can specifically bound to either small molecules and complex multimeric structures.

• Small size of aptamers leads to a high number of moles of target bound per gram, and they may have improved transport properties allowing cell specific targeting and improved tissue penetration.

• Aptamers are much more stable at ambient temperature than antibodies yielding a much higher shelf life, and they can tolerate transportation without any special requirements for cooling, eliminating the need for a continuous cold chain.

• Ability to inactivate proteins, without altering genetic material.

Aptamers Disadavantages

• Lower levels of affinities than antibodies.

• Aptamers will not bind to some target molecules.

• Aptamers identification is expensive and labor intensive.

Review Articles: 

Aptamer-modified nanoparticles and their use in cancer diagnostics and treatment, Christine Reinemann, Beate Strehlitz- UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany.