Frequently Asked Questions (FAQs)

The Raptamer™ Advantage

What is a Raptamer™?

A Raptamer™ is a next-generation aptamer (similar in function to an antibody) that is comprised of a single strand of DNA with several chemical modifications attached to the DNA nucleobases and/or in the backbone. Raptamers™ are synthesized using a proprietary non-SELEX methodology.

What are these chemical modifications and what is their function?

The most common modifications used are amino acid functional groups such as indole (tryptophan), phenol (tyrosine), and amine (lysine). This unique chemistry significantly enhances interaction with a target for better binding affinity and better specificity than standard DNA or RNA aptamers that are not modified.

How can I use Raptamers™?

Raptamers™ can be used in any platform that does not denature the protein target: ELONA (ELISA using at least one oligonucleotide instead of an antibody), Luminex style assays, flow cytometry, immunohistochemistry, etc.

What are the benefits over standard aptamers?

  • Raptamers™improve on standard aptamers by having a significantly tighter binding affinity (Kd).
  • Raptamer™ selection is a two-step process involving one round of PCR, whereas standard aptamer discovery methods rely on SELEX, which is subject to PCR bias. PCR bias is a phenomenon whereby the repeated rounds of PCR, required by the SELEX method, result in selective enhancement of DNA/RNA sequences that are good amplifiers, but not necessarily good binders of your target. This also results in a less diverse set of candidate sequences as compared to the Raptamer™ selection process.
  • Standard aptamers are unmodified. As part of our proprietary process, custom modifications are added to the aptamers in our custom libraries. These modifications give our Raptamers™ more diversity, stronger binding, and greater hydrophobicity, thereby, increasing both specificity and antibody-like behavior.

What are the benefits over antibodies?

Raptamers™ can be discovered much more quickly than antibodies (weeks vs months) at a lower cost. Raptamers™ also have higher batch reproducibility, can be stored for longer (years vs. months), and do not require a freezer for storage.

What functional groups/chemical modifications enhance target interaction?

  • The phosphorodithioate (PS2) modification, which replaces the phosphate ester linker group in the DNA strand, has demonstrated extraordinary improvement in target interaction when used strategically. The replacement of just a single PS2 modification into an existing aptamer may enhance its binding affinity by 1000-fold.
  • PS2 modifications also imparts nuclease resistance, which can enhance serum stability.

What labels are available for Raptamers™?

Virtually any label, functional group, dye, linker, etc. can be attached. Commonly used labels include Fluorescein, Methylene Blue, Cy5, Thiol, and Biotin. RaptamersTM can also be functionalized to attach to virtually any material.

Raptamer™ Turnkey Service

What is the Turnkey Service and how does it work?

The Turnkey Service is a complete Raptamer™ development solution where we discover, characterize, and deliver Raptamers™ to you ready for use in your platform.

After a detailed discussion to learn about your Raptamer™ development needs and application, there are five distinct stages.

    1. Selection using a proprietary bead-based library.
    2. Next-generation sequencing and data analysis.
    3. Small-scale synthesis of candidate sequences.
    4. Binding studies using biolayer interferometry (BLI).
    5. Synthesis and delivery of top binding sequences at 1-μmol scale.

How long does the process take?

Once the target protein is received, the screen and initial selection of candidate aptamers will take approximately four weeks. Please inquire if you need a faster turnaround time.

What is the success rate?

For one selection using one library (we have various libraries to choose from), the success rate is about 60%. This compares favorably with SELEX, which has a published success rate of between 30% and 50%.

How many Raptamers™ will I get from the process?

A typical selection against a single target generates ~24 putative sequences, of which there are generally 1-4 sequences that have favorable binding study results. At your request, we can synthesize other putative sequences.

Targets

What targets work best with Raptamers™?

  • A purified sample is required. The exact amount depends on the target’s molecular mass.
  • Protein targets at least 2-3 kDa are ideal.
  • Small-molecule targets are possible, but pose greater technical challenges due to their much smaller size and difficulty tagging.
  • Whole-cell targets are also possible.
  • The target must be soluble in aqueous solution.

Does the target need to be the full-length protein, or can it be a truncated version of the protein?

It would be best to have the entire protein, however, having a reasonable portion of the targeted protein that has a good likelihood of folding into the native conformation or at least a folded domain of the targeted protein is sufficient.

Does the target need to be tagged for Raptamer™ selection?

Yes. Selection requires a way to isolate the target using magnetic particles.

This can be accomplished by biotinylating the target, by using a target expressed with a His tag, or by using an existing tagged antibody to the targeted protein.

You can provide a tagged target, or alternatively we can biotinylate the target for you.

Will a Raptamer™ bind to the same protein epitope as an antibody?

Generally, no. Raptamers™ and antibodies are different affinity molecule technologies and thus bind to proteins differently. Antibodies bind to convex surfaces of proteins while Raptamers™ often bind to clefts. While it is possible that a Raptamer™ will bind to the same protein epitope as an antibody, we have found that in the vast majority of cases Raptamers™ and antibodies bind to different protein epitopes.

Other

Can I use Raptamers™ in Western blots?

Raptamers™ and standard aptamers usually do not bind well to denatured proteins. They usually need the protein target (antigen) in its native conformation.

How can I get more of a particular Raptamer™ in the future?

Simply contact us and we can re-synthesize your Raptamer™ at your desired scale. The pricing will reflect only the cost of synthesis, as the sequence will already be known and characterized.

If you have a commercial license with us, which includes the sequence information, you can also have a separate oligonucleotide manufacturer perform the synthesis.

Do I need a license to use Raptamers™?

A customer can use the Raptamers™ provided for unlimited research use without a commercial license.

If you are interested in commercializing a Raptamer™, a commercial license must be obtained. Please contact us to discuss in more detail.

Will I get the sequence for the Raptamers™?

Sequence and modification information can be obtained upon purchase of a commercial license.
Academic institutions and non-profit organizations should inquire with us about potentially receiving the sequence information for inclusion in a scientific publication, if there is no intent to commercialize the Raptamers™.

Don’t see your question? Contact Raptamer Discovery Group below!

Raptamers™

NEXT-GENERATION APTAMERS

FASTER

4-6 Weeks from Target Receipt to Material Shipped

STRONGER

Higher Affinity Binding
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BETTER

Extensive Modifications Available

No PCR Bias

Raptamer Discovery Group’s mission is to help you find great binding molecules for your research or commercial application. Faster, stronger, better: the Raptamer™ way!

Let’s Discover a Raptamer™ Together!

Send us a message and our technical expert will get back to you!
Want to email us directly? Email: contact@raptamer.com