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Analysis of aptamer discovery and technology

Abstract

Aptamers are nucleic acid molecules that mimic antibodies by folding into complex 3D shapes that bind to specific targets. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, most are generated in vitro and can be tailored for a specific target. Relative to antibodies, aptamers benefit from their ease of generation, low production cost, low batch-to-batch variability, reversible folding properties and low immunogenicity. However, the true value of aptamers lies in the simplicity by which these molecules can be engineered into sensors, actuators and other devices that are often central to emerging technologies. This Review examines changing trends in aptamer technology by analysing the first quarter century of aptamer data that is available in the scientific literature (1990–2015). We highlight specific examples that showcase the use of aptamers in key applications, discuss challenges that have impeded the success of aptamers in practical applications, provide suggestions for choosing chemical modifications that can lead to enhanced activity or stability, and propose standards for the characterization of aptamers in the scientific literature.

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Figure 1: Trends in aptamer publications.
Figure 2: Post-SELEX modifications.
Figure 3: Distribution of aptamer applications and targets.
Figure 4: Aptamer-based optical sensors.
Figure 5: L-RNA aptamers or spiegelmers.
Figure 6: Examples of aptamer applications and chemical modifications.
Figure 7: Chemical modifications used in aptamer selections.
Figure 8: Xenonucleic acids.

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Acknowledgements

The authors thank members of the Chaput laboratory for helpful comments and suggestions, and N. Chim for assistance with the figures. This work was supported by the Defense Advanced Research Projects Agency (DARPA) Folded Non-Natural Polymers with Biological Function (Fold Fx) Program (Award No.N66001-16-2-4061).

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Correspondence to John C. Chaput.

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Supplementary information

Supplementary information S1–S21 (tables)

Raw and normalized data for aptamer trends presented in Figure 1b. (XLSX 335 kb)

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Glossary

Phenotypes

Observable characteristics, such as binding or catalytic activity, that are encoded in the sequence of a nucleic acid or protein.

Genotypes

Genetic sequences that encode phenotypes.

Antibodies

Protein affinity reagents produced by the immune system that can be made to recognize a wide range of targets called antigens.

Aptagenic

A target that is known to produce an aptamer by in vitro selection.

Dissociation constant

The equilibrium constant for the dissociation of the target– aptamer complex (Kd = [target] [aptamer]/[target–aptamer]).

Lysate

The contents of a cell produced by cell lysis.

cDNA

The complementary DNA sequence that results when RNA (or xeno-nucleic acid (XNA)) is reverse transcribed into DNA.

Doped library

A nucleic acid library that contains variants of a single sequence, which feature a small fraction of non-wild type residues at each position. For example, if the wild-type residue is A, then the library would contain mostly A with a mixture of C with T and G.

Recombinant protein therapies

Therapies that are produced through recombinant DNA technology, which involves expressing and purifying a protein from bacterial or mammalian cells. Many biologics, such as monoclonal antibodies, are recombinant protein therapies.

Phosphodiester linkage

The chemical linkage, connecting the monomeric units in a nucleic acid polymer. In general, the linkage takes the form RO(O)P(O)OR′.

Induced-fit

A biochemistry model in which the initial interactions of an enzyme–substrate complex (or antibody–target complex) are strengthened by conformational changes that increase the strength of the intermolecular interactions involved in substrate or target recognition.

Fluorescent reporter

Molecules that elicit a fluorescent signal.

Fluorescence resonance energy transfer

A photophysical effect in which energy is transferred between fluorescent or light-sensitive moieties.

Mirror-image symmetry

Symmetry with respect to a reflection or plane of symmetry. Mirror-image molecules are non-superimposable. For example, your right hand cannot be superimposed on top of your left hand.

von Willebrand factor

A glycoprotein found in the blood that is involved in haemostasis (blood clotting).

Click chemistry

A general class of high-yielding cycloaddition reactions that occur between azide and alkyne functional groups. Click chemistry is often used to add new functional groups to biomolecules.

Primer extension

A DNA (or xeno-nucleic acid (XNA)) replication step in which a nucleic acid primer is extended by annealing the primer to a template and copying the template with a polymerase.

Fluorescence-activated cell sorting

A development of flow cytometry that enables sorting of a mixture of cells into two or more fractions based on the light scattering and fluorescence signal of each cell.

Enzyme-linked immunosorbent assay

A diagnostic test that uses affinity reagents, typically antibodies, to detect a substance.

Emulsion PCR

A variant of the polymerase chain reaction (PCR) that is performed in water-in-oil droplets.

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Dunn, M., Jimenez, R. & Chaput, J. Analysis of aptamer discovery and technology. Nat Rev Chem 1, 0076 (2017). https://doi.org/10.1038/s41570-017-0076

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