Frequently Asked Questions (FAQs)

Raptamer™ Basics

What is a Raptamer™?

A Raptamer™ is a binding agent (similar in function to an antibody) that is comprised of a single strand of DNA with several, randomly placed chemical modifications attached to the DNA nucleobases and/or backbone.

What do these randomly placed chemical modifications do?

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 unmodified DNA or RNA aptamers.

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), ELISA, Luminex style assays, flow cytometry, immunohistochemistry, etc.

Can I use Raptamers™ in Western blots?

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

What are the benefits over standard aptamers?

RaptamersTM improve on standard aptamers by having tighter binding affinity (Kd). In addition, RaptamerTM selection is a single-cycle process, whereas standard aptamers rely on SELEX that leads to PCR bias.

PCR bias is a phenomenon whereby the repeated rounds of PCR required of SELEX result in enhancement of DNA/RNA sequences that are good amplifiers, but not necessarily good binders of your target. This also results in a less diverse library of enhanced sequences as compared to the RaptamerTM selection process.

What are the benefits over antibodies?

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

Raptamer™ Turnkey Service

What is the Turnkey Service and how does it work?

The Turnkey Service is a complete RaptamerTM development solution where we discover, characterize, and delivers RaptamersTM to you ready for use in your platform.

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

    1. Selection using a proprietary bead-based library.
    2. Next-gen sequencing and Data Analysis.
    3. Small scale synthesis of candidate sequences.
    4. Binding studies using biolayer interferometry.
    5. Synthesis of top binding sequences at 2 μmol scale and shipment.

How long does the process take?

The Turnkey Service takes approximately four weeks from receipt of the tagged target. Please inquire if you need a faster turnaround time.

What is the success rate?

For one selection using one library, the success rate is about 60%. This compares favorably with SELEX, which has a published success rate of between 30% and 50%. We also have additional libraries.

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.

Raptamer™ Modifications

What functional groups/chemical modifications enhance target interaction?

  • 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 modification also imparts nuclease resistance, which can enhance serum stability.

What labels are available for Raptamer™?

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

Targets

What targets work best with Raptamers™?

  • A purified sample is required. The exact amount depends on the target molecular mass.
  • Protein targets at least 2-3 kDaltons in molecular mass 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.

Do I need the antigen used to develop the antibody that I have?

It would be best to have the entire protein that the antibody recognizes (many recognized antigens are only a portion of the amino acid sequence of the targeted 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 chemically 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 tag the target yourself or we may be able to tag the target for you.

Other

Won’t a Raptamer™ just bind to the same protein epitope as an antibody?

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

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

Simply contact us and we can re-synthesize your RaptamerTM at your desired scale. The cost will reflect only the synthesis portion, 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 organization perform the synthesis.

Do I need a license to use Raptamers™?

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

If you are interested in commercializing with a RaptamerTM, a commercial license must be obtained. A typical license includes a low yearly maintenance fee and a single-digit royalty.

Will I get the sequence for the Raptamers™?

Sequence and modification information can be obtained upon purchase of a commercial license.

Universities and non-profit organizations can receive the sequence and modification information, if required, for acceptance of a publication in a scientific journal. However, if the university or non-profit does not submit a patent application for the RaptamerTM sequence, then Raptamer Discover Group will ask for performance data in return, as well as the non-exclusive rights to commercialize the RaptamerTM.

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!