Aptamers vs. Antibodies

We are often asked, ‘what are the main differences between aptamers and antibodies?’ The following table highlights the contrasting characteristics which make aptamers a viable, and in some cases a better, alternative to antibodies for most applications.

 AptamersPeptide Ligands/ScaffoldsAntibodies
Target Range- Can be produced against almost any target including small molecules (e.g. toxins), peptides, proteins, viruses, cells, tissues and micro-organisms- Can be produced for small molecules (e.g. toxins), peptides and proteins- Limited to targets that produce an immune response like peptides, proteins and some small molecules (non-toxic)
Development Time- Several weeks- Several weeks - months- Several months - year(s)
Isolation, Synthesis & Manufacture- Isolated entirely in vitro
- Solid phase chemical synthesis (no animals or cells used)
- Low batch-to-batch variability
- Chemically synthesised. Excellent QC
- Isolated in vitro
- Produced through cell culture-based methods
- Batch-to-batch variation due to production in hybridoma / bacterial culture
- Isolated in animals
- Produced through recombinant / cell culture-based methods
- Expensive bioreactors required
- High batch-to-batch variability
Handling & Storage- Stable at ambient temperatures
- No cold-chain transport required
- Long term storage at -20°C
- Easily denatured
- Essential cold-chain transport
- Refrigeration / freezing needed
- Easily denatured
- Essential cold-chain transport
- Refrigeration / freezing needed
Stability- Can tolerate repeated cycles of denaturation, without loss of function
- Incorporation of modified nucleotides limits nuclease degradation
- Easily denatured
- Can refold and restore function in some applications
- Easily denatured losing structure/function under wide range of conditions.
- Cannot refold or restore function
Shelf Life- Very long (several years if frozen)
- Can be regenerated and reused in some applications
- Aptamer sequence is information - can be stored electronically
- Limited (several years when lyophilised)
- Can be reused in some applications
- Hybridoma / clones need special storage
- Limited (6 months)
Single use
- Hybridoma / clones need special storage
In vivo Complications- No intrinsic immune response- Can cause immune response if used as a drug- Can cause immune response if used as a drug
Size- 6.5-10KDa (20-30 nucleotide Optimer™)
- Low molecular weight gives high surface density for assays and excellent tissue penetration
- 12-14kDa- 150kDa
- High molecular weight gives low surface density for assays and poor tissue penetration
Down Stream Applications/ Assay Development- Functional under a broader range of conditions defined by the customer based upon the intended end use
- Controllable binding and release conditions
- Functional under a broader range of conditions
- Controllable binding and release conditions
- Work under near physiological conditions
- Difficult to adapt for other conditions
- Harsh release conditions required
Affinity & Specificity- High affinity and greater specificity due to tailored isolation process- High affinity and reasonable specificity - High affinity
- Cannot build in specificity so it is achieved through screening (if at all)