In The April Issue

  • Now Hiring! at Base Pair
  • Aptamer Technology Articles
  • Aptamers in Vaccine Development and Monitoring


Now Hiring! at Base Pair

Base Pair is currently seeking an experienced aptamer development Scientist and an Associate Scientist with molecular biology / PCR experience to join our fast-based aptamer discovery and aptamer applications development team in Pearland, Texas. Visit the Careers page to learn more.

Aptamer Technology Articles

Have you missed one of our recent aptamer technology articles? The latest articles are now available online.

What is an Aptamer? 
DNA Aptamers or RNA Aptamers?
Importance of Negative Aptamer Selection

Aptamers in Vaccine Development and Monitoring

Antibodies are frequently used in vaccine development and monitoring. They are used as adjuvants to enhance the effectiveness of vaccines, in tests to confirm vaccine concentration, and assays to determine antibody titer following administration. More commonly, antibodies are used to detect outbreaks of infectious disease. While antibody-based adjuvants and assays have worked well, there are some concerns. Antibodies can be unstable at high temperatures, affecting product performance in tropical areas hit hardest by infectious disease. Bioproduction is costly, highly regulated, and susceptible to batch-to-batch issues. Maintaining effective cell lines throughout the life of a vaccine for quality control can also be a concern. (7).

Aptamers, small strands of DNA or RNA with selective binding to a specific molecule, are chemically synthesized and can be produced consistently from batch to batch throughout the life of a vaccine at a lower cost than antibody bioproduction. They are also stable at high temperatures, making them ideal affinity reagents for use in tropical climates. Small aptamer size typically renders them non-immunogenic, an ideal characteristic for an injectable adjuvant (7).

Aptamers as Adjuvants for Enhanced Immunity

Several groups have begun exploring the use of aptamers as adjuvants in vaccines. Researchers in Spain led a study involving the selection of RNA aptamers to CD28, a costimulatory factor involved in the activation of T lymphocytes. While the original and truncated aptamers to CD28 inhibited binding to CD28, production of an aptamer dimer generated agonistic activity. The CD28 aptamer dimer exhibited a costimulatory effect, eliciting an enhanced cellular response when administered with vaccine. Co-administration of the CD28 aptamer dimer with an anti-tumor vaccine in a mouse model resulted in delayed tumor growth and extended survival when compared with vaccine alone and vaccine administered with CD28 antibody (4).

Researchers at Duke University developed DNA aptamers to OK40, a costimulatory receptor expressed on activated T lymphocytes. OX40 ligand (OX40-L) binding to the OX40 receptor increases cell proliferation and cytokine production and extends T lymphocyte survival. The DNA aptamer selected demonstrated binding to the OX40-L binding site. As in the CD28 example above, an OX40 aptamer multimer was required for agonistic activity. Co-administration of the OX40 aptamer multimer with CD3/CD28 antibodies increased IFNγ production 2.4-fold (5). Aptamers to costimulatory receptors are promising vaccine adjuvants, offering enhanced immunity along with simplified production, improved lot-to-lot reproducibility, and increased stability at room temperature.

Aptamers for Prevention of Infection

In recent years, we have experienced worrisome outbreaks of the flu coupled with flu vaccines with limited effectiveness. Aptamer research conducted a decade ago in Israel resulted in DNA aptamers to viral hemagglutinin (HA) that block influenza A virus binding to host cell receptors and prevent uptake into host cells. When the HA aptamer was co-administered with the virus in a mouse model, there was a 90-99% reduction of viral infection in the lungs. Unfortunately, pre-treatment with aptamer 24 hours prior to virus administration did not protect the mice, indicating potential instability of the aptamer (2).

A more recent study in China involved the development of selective aptamers to bovine herpesvirus1 (BoHV-1), a common virus in cattle. In this study, aptamers were selected against the purified virus. The best candidates were tested in a plate-based assay. Aptamer IBRV-A4 had the greatest selectivity and affinity for the boHV-1 virus. Based on time course studies, it was determined that the aptamer blocked binding to and entry into host cells. MDBK (bovine kidney) cells inoculated with aptamer IBRV-A4 just prior to inoculation with virus exhibited a 100-fold reduction in viral titer. Aptamer administered up to 1.5 hours following inoculation with virus showed protective effects. At the 2 hour time point, the aptamer had reduced effect, as the virus had already entered cells, indicating the need for early intervention to prevent the spread of viral infection. Interesting, the aptamer also showed selective binding to boHV-1 -infected MDBK cells, indicating diagnostic potential. (8) Similar aptamer-induced viral protection has been demonstrated with the Singapore grouper iridovirus (SGIV) (3) and dengue viruses (1).

Modifications to extend the stability of aptamers that block viral infection could enable the development of more effective vaccines. Extending aptamer life from hours to days or weeks to generate short-term vaccines could prevent the spread of viral infection following early detection of an outbreak and prevent infection when administered prior to travel to high-risk areas.

Aptamers for Vaccine Potency Assays and Assessment of Antibody Titer

As selective affinity reagents, aptamers can be utilized in almost any antibody-based application. Traditional enzyme-linked immunosorbent assays (ELISA) utilizing antibodies to determine the concentration of antigen and other key components in vaccines can be replaced with aptamer-based (ELASA) assays, simplifying production, improving long-term supply, and increasing batch to batch consistency. Likewise, antibody-based tests to determine anti-viral antibody titers following vaccination can be replaced with aptamer-based assays, yielding assays that are more cost-effective, consistent, and stable. (7, 6)

Custom Aptamer Selection for Vaccine Development and Monitoring

A growing number of researchers are looking to utilize aptamers for vaccines. The wide range of options for aptamer selection and labeling offer the potential to utilize aptamer affinity reagents in vaccine development, quality control, and evaluation of antibody titers.
Contact Base Pair today for more information on selection of aptamers to viral antigens, vaccine components, co-stimulatory receptors, and antibodies.


1. Chen, H., et al. Selection and characterization of DNA aptamers targeting all four serotypes of dengue viruses. PLoS ONE. 2015. 10(6): e0131240.
2. Jeon, S.H., et al. Aptamer prevents influenza infection by blocking the receptor binding region of the viral hemagglutinin. Journal of Biological Chemistry. 279(46):48410-48419.
3. Ling, P., et al. Isolation and characterization of a new class of DNA aptamers specific binding to Singapore grouper iridovirus (SGIV) with antiviral activities. Virus Research. 2014. 188:146-154.
4. Pastor, F. et al., Aptamers as Powerful Immune Response Modulators. Molecular Therapy: Nucleic Acids. 2013. 2(6):e98.
5. Pratico, E.D., et al. Identification and characterization of an agonistic aptamer against the T cell costimulatory receptor, OX40. Nucleic Acid Therapeutics. 2013. 23(1):35-43.
6. Toh, S.Y., et al. Aptamers as a replacement for antibodies in enzyme-linked immunosorbent assay. 2015. 64:392-403.
7. Yoon, S.Y., et al. Application of aptamers for assessment of vaccine efficacy. Clinical and Experimental Vaccine Research 2017. 6(2):160-163.
8. Xu, J., et al. A DNA aptamer efficiently inhibits the infectivity of bovine herpesvirus 1 by blocking viral entry. Scientific Reports. 2017. 7:11796.