What is an aptamer?

Aptamers are short, single strands of DNA or RNA that form unique tertiary structures and can be used to selectively bind specific targets, including peptides, proteins, small molecules, toxins, and nucleic acids. Learn more about the history and selection of aptamers.

Do you have previously-selected aptamers available for evaluation?

We have generated multiple aptamers to a wide range of target types, including small molecules, toxins, secreted proteins, and trans-membrane proteins. These aptamers are available for feasibility testing in various assays. Some are available for commercial exploration as well.  For a minimal cost these aptamers can be purchased for testing. A current list of catalog aptamers can be found here.

Can you select aptamers to small molecules?

Base Pair has been able to generate successful aptamers to several small molecules, including ampicillin, epirubicin, epinephrine, and tenofovir. Several of our current customers have contracts for development of aptamers to other small molecules.  Perhaps the most important aspect of selecting aptamers is target presentation.  Base Pair has the expertise to identify the best small molecules and small molecule derivatives for aptamer targeting and unique methods for small molecule target presentation, bioconjugation, and sensor development.

Are peptides viable targets for aptamer selection?

This is a valid point and one that has been cited when peptides fail as successful antigens for antibody development.  As such, a similar risk exists when using a peptide as an “antigen” for aptamer development. Selecting peptides as subsequences/surrogates for whole proteins is a difficult process involving sophisticated bioinformatics programs. It is up to the customer to provide the peptide target. While we cannot guarantee aptamer binding in the context of the larger protein, we generally can arrive at tightly binding aptamers to the peptides themselves and provide multiple clonal candidates for testing purposes.

Are DNA aptamers or RNA aptamers better?

Both DNA aptamers and RNA aptamers offer unique advantages, including detection of difficult targets (toxic, non-immunogenic), low immunogenicity,  improved access to tissues/cells (vs. larger molecules), robust chemical synthesis, and good batch-to-batch reproducibility. Is it better to select for DNA aptamers or RNA aptamers? The answer will depend on your specific end-use application. At Base Pair, we work with both DNA and RNA. Deciding whether to select for DNA or RNA aptamers is part of the initial project design phase. While DNA selection is a faster and simpler process and typically yields stable aptamers, certain applications (riboswitches and in vivo imaging) require RNA. Download the full article on DNA Aptamers or RNA Aptamers? to learn more.

Can you provide aptamer sandwich pairs?

Depending on the target, Base Pair can design a program with the best chance of establishing a sandwich pair (a pair of aptamers that bind the same target at complementary locations). This may involve screening a larger number of aptamer candidates. Aptamer pair testing is typically conducted in an ELASA configuration.

Do thiolated aptamers need to be reduced prior to each use?

To ensure optimal performance, thiolated Aptamers should be reduced prior to each use. The procedure for thiol reduction can be found on page two of the Aptamer Best Practices guide.

What does the KD or dissociation constant mean?

The dissociation constant (KD) is a measure of the binding strength between the aptamer and target. A low value for the dissociation constant (KD) means a low concentration of aptamer and target are required for binding to occur and indicates high affinity or binding strength. http://chemistry.tutorvista.com/inorganic-chemistry/dissociation-constant.html. Accessed 19 Jan 2017.

We’re planning an in vivo (or cell culture) application. Will my DNA aptamer remain stable?

The use of aptamers in vivo or in cell culture is generally challenged by the susceptibility of unmodified nucleic acids to degradation by nucleases.  In particular, 3’-exonuclease activity has been found to be the most prevalent nuclease activity both in calf and human serum1.  Synthesis with a 3’-inverted thymidine can extend DNA stability in the bloodstream to approximately 72 hours2.  For many in vivo or cell culture applications, simple 3’-terminal modifications are likely to confer acceptable resistance to nuclease degradation. Immobilization of an aptamer, on beads for example, is likely to further extend serum half-life, and the free-solution end of the aptamer can be readily modified as well, often by pegylation.

  1. Shaw JP, Kent K, Bird J, Fishback J, Froehler B: Modified deoxyoligonucleotides stable to exonuclease degradation in serum. Nucleic acids research 1991, 19:747-50.
  2. Takei Y, Kadomatsu K, Itoh H, Sato W, Nakazawa K, Kubota S, Muramatsu T: 5′-,3′-Inverted Thymidine-modified Antisense Oligodeoxynucleotide Targeting Midkine. Journal of Biological Chemistry 2002, 277:23800 -23806.

Custom Aptamer Discovery Questions

How will I know the status of my project?

Base Pair offers a proprietary project management portal, the AptaTracker. Researchers join a project-specific, confidential chat and data sharing environment to interact with Base Pair scientists and track progress.

What do I need to provide for a custom aptamer discovery project?

Targets such as proteins, peptides, small molecules, and cells of interest are provided by researchers as targets for our SELEX process. The amount of target required will vary depending on the type of molecule and the scope / design of the project. In general, a basic aptamer discovery project for a secreted protein (a cytokine, for example) would require a minimum of 5 mg of recombinant protein at 90%+ purity. Base Pair is available to assist with sourcing and selection of target material, when possible.

How many aptamers will we get to evaluate?

While our process typically yields multiple aptamer sequences per target as valid aptamer candidates, for basic discovery programs we can only provide KD determination on a few aptamer sequences validated to bind. The number of aptamers to be supplied will be clearly defined in the project proposal. Additional aptamers can be evaluated at an additional cost.

What affinity can we expect for our custom aptamers?

Every target is different. We have a publicly available list of aptamers in our catalogs with a range of binding constants. These lists reflect aptamers developed under a variety of projects over a considerable period of time and is intended to represent KD values for a range of target classes. Several aptamer clones (sequences) may need to be validated for very small or very large targets (such as small molecules or very large proteins, respectively) to identify an aptamer with the best KD. Through feedback during the selection process, we can verify that enrichment of “good” binders is occurring for your target.  Finally, we should emphasize that a small KD may not be the only determinant for success depending on your application, especially in the case of competitive binding or reversible sensing applications.

Who owns the aptamer clones, or sequences, at the end of the aptamer discovery project?

Base Pair owns the aptamers at the end of the discovery process, unless agreed otherwise.  We are glad to discuss commercial use terms, which can include exclusive or non-exclusive rights.  Please contact us to get more information about commercial use.

Don’t see your question? Contact Base Pair Technical Support for more information at +1-832-230-5518 or support@basepairbio.com.