For many years, researchers have been raising and modifying antibodies to detect specific circulating proteins and develop targeted therapeutic agents. While antibodies are highly effective for a wide range of applications, there are unique aptamer advantages that can overcome some difficult scientific challenges.
Target Small Molecules
Aptamers can be developed against molecules as small as 60 daltons, ten times smaller than the smallest antibody targets. Selective aptamers have been developed for a wide range of molecules including small molecule drugs, peptides, dyes, and viral particles.  Base Pair Biotechnologies has developed specific selection and characterization techniques for the development of aptamers to small molecules.
Pursue Toxic and Non-Immunogenic Targets
Because aptamer development/production does not involve animals or living cells, it is possible to select for aptamers to toxic compounds, including zootoxins and pathogenic bacteria. Unlike antibody development which requires an immune response, aptamer selection relies primarily on the “fit” of tertiary aptamer structures to target molecules. Aptamers can be developed to selectively bind molecules that are not very immunogenic, such as small molecule drugs. 
Design Stable Molecular “Sensors” and “Switches”
Allosteric aptamers undergo a conformational change upon ligand binding that either alters binding to a second effector or changes the enzymatic activity of the aptamer. Allosteric aptamers can be coupled with fluorescence quenching for direct detection assays, development of biosensors, or in vivo imaging. Direct detection eliminates wash steps and simplifies assay design. Aptamers that change conformation upon binding can be used to regulate protein expression or protein function in vivo, switching “On” and “Off” based on the availability of a particular ligand. 
Penetrate Tissues and Cells
Because aptamers are small (typically ~30–80 nucleotides), they are very efficient at penetrating tissues to reach specific targets. [1,2,3] Some aptamers are able to enter cells without external assistance. In a study involving aptamers to NSCLC cells, aptamers entered A549 cells and showed good nuclease resistance. Some also showed apoptotic activity. 
Perform Simple Chemical Modifications
Enhance affinity, stability, or solubility through sequence-specific modifications. Functional groups that increase nuclease resistance can extend survival time in biological fluids. Hydrophobic groups can be added to improve binding to hydrophobic targets. Easily conjugate to haptens, fluorophores, chromophores or enzymes for detection. 
Generate Enzymatic Aptamers
Aptazymes are allosteric aptamers that bind to a specific ligand then undergo a conformational change that affects upstream or downstream gene expression. Aptazymes have been developed for a growing number of ligands including adenosine triphosphate (ATP), flavin mononucleotide (FMN), cyclic nucleotide monophosphates, and thiamine pyrophosphate (TPP). Combining allosteric properties with selective ligand binding offers significant therapeutic potential. 
Reduce Manufacturing Time and Cost
Once optimal aptamer sequences have been selected, production of new batches of material is fast and inexpensive. Aptamers with fewer than ~75 bases can be chemically synthesized. Production is easily scalable to multi-gram batches.
Produce Stable Products
Aptamers can be stored long-term and transported at ambient temperature. Denaturation of aptamers at high temperature is reversible. Aptamers can re-form to their correct 3D configuration at room temperature. 
Improve Lot-to-Lot Reproducibility and Simplify Regulatory Procedures
Aptamers are chemically synthesized, simplifying scale-up and enabling a high degree of manufacturing control from batch to batch . No organisms (animals, cells) are involved in production, so regulatory procedures are reduced when compared to animal-based or cell-based production.
- Zhang, Y., et al. Tumor-Targeted Drug Delivery with Aptamers. Curr. Med. Chem. 2011. 18(27):4185-94.
- Sun, H. et al. Oligonucleotide Aptamers: New Tools for Targeted Cancer Therapy. Molecular Therapy – Nucleic Acids. 2014. 3, e182. Doi: 10.1038/mtna.2014.32.
- Jayasena, S. D. Aptamers: An emerging class of molecules that rival antibodies in diagnostics. Clinical Chemistry. 1999. 45(9):1628-50.
- Vinkenborg, J.L. , et al. Aptamers for allosteric regulation. Nature Chemical Biology. August 2011. 7;519-27. Doi: 10.1038/nchembio.609.
- Xu, Li, et al. Cellular Internalization and Cytotoxicity of Aptamers Selected from Lung Cancer Cell. American Journal of Biomedical Sciences. 24 December 2012.
- Kabori, S. et al. Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: Modeling of ligand-dependent and -independent expression. RNA. 2012. 18(8):1458-65. doi: 10.1261/ma.032748.112.