Answers by Dr. Gregory Penner

Should I consider using modified nucleotides?

For diagnostic applications I have yet to see data that demonstrates that modified nucleotides leads to lower binding affinity than is possible with natural nucleotides. Our use of next generation sequencing in the discovery process enables us to identify the best natural nucleotide sequences available.
If you are serious about developing a commercial diagnostic platform with the aptamer you develop, your first considerations should be business considerations. With natural nucleotides you will have a lower cost of synthesis and you will have the freedom to have your aptamer synthesized by anyone without a royalty. For therapeutic applications you need to use modified nucleotides at all positions in the selection process and this will result in lower synthesis costs on your final commercial aptamer than with a mixture of nucleotides and will provide the level of nuclease protection necessary. You will also need to add mass to the aptamer to avoid it being flushed through the body too quickly.
Should I use an RNA or DNA aptamer?

I am not convinced that DNA aptamers do not work as well as RNA aptamers. The theory is that RNA aptamers are more flexible, and there has been considerable work done with RNA sequences to model tertiary structures. I think we are just beginning to scratch the surface regarding what tertiary structures single stranded DNA molecules are capable of forming. G-quartet structures make excellent aptamers with binding affinities similar to RNA aptamers.
For diagnostic applications an RNA aptamer will cost you more to synthesize commercially and will have less shelf life than an antibody based product. A natural nucleotide DNA aptamer will have a shelf life of a year at room temperature.
For therapeutic applications, I worry that the passage of modified nucleotides through the three enzymes used for RNA aptamer selection has the potential to cause significant bias. Bias in selection constrains our ability to identify the best aptamer possible.

Why are there not more aptamer based products commercialized?

The key reason is not technical performance but rather legal constraints. Until recently the use of oligonucleotides as ligands has been covered by broad patents. The expiration of these patents has led to the boom of aptamer development that we are experiencing now.

Is it true that NeoVentures does not take an Intellectual Property position on aptamers that are developed for clients?

Yes, we think our competition is with antibody providers. Antibody providers do not take an IP position on antibodies that are custom developed for you. We do however invent the aptamers that we provide you with. As such, it is necessary that we be listed as inventors on patents that you file regarding these aptamers. As part of our supplier service agreement we provide clients with a royalty free, exclusive, global, irrevocable license to the aptamers that we provide them with for the application intended.

What is our success rate with aptamer development?

This is not a fair question as we cheat on the answer. We structure projects to share risk with clients. Part of your payment structure is based on our delivery of aptamers that meet agreed upon specifications. As such, we will not attempt to develop aptamers where we think that the risk of failure is too high. We reserve the right to decline projects that we consider too risky.

Can we order synthesized aptamers from NeoVentures?

Yes, we do provide an aptamer synthesis service. There is nothing special about natural oligonucleotides aptamer synthesis. This is the same as primer synthesis for PCR applications.  In most cases it makes more sense for clients to have aptamers synthesized locally to avoid shipping and customs costs. We do not require clients to be committed to us for their supply of aptamers that we develop for them.

Are my aptamers ready for commercialization following a project with NeoVentures?

Yes. We perform binding assays under the conditions that you indicate the aptamer will be used commercially. You may wish to contract us to trim the aptamer to a shorter length to reduce production costs. We often find that trimming aptamers improves their performance.
We are prepared to provide you with technical support to your commercial development process. We also offer a full service package where we will do all aspects of aptamer based diagnostic kit development including regulatory approvals. Costs on this service are higher than our cost for aptamer development.

Why does it take NeoVentures four months to develop an aptamer?

We wish we could do it faster, but our commitment to the development of the best possible aptamer for clients prevents us from doing so. We do not use automated selection processes. All selections are done by hand, results from each selection round are discussed, and dynamic adjustments are made to ensure that we are maintaining appropriate stringency on affinity and often more importantly on specificity. For next generation sequencing we are currently relying on the use of an Illumina HiSeq 2500 at the Hospital for Sick Children in Toronto. Errors and bias in the next generation sequencing process are poorly understood, especially for aptamer discovery. We do not have a genomic template to compare sequences against. We have developed a database of sequences across a broad array of projects. This enables us to perform meta-analysis to remove NGS bias and to identify what sequences are special to your project.At the end of a project with us you have an aptamer that you can synthesize on a commercial scale in a week, locally. There is no need to clone genes, and develop recombinant expression systems. Aptamer development from project initiation to commercialization is faster than antibody development.

Do aptamers work in the same applications as antibodies?

Anything that an antibody can do an aptamer can do. You will note, I did not say necessarily better. Aptamers can be applied to a broader range of targets than antibodies. We develop aptamers for targets that are too large for antibodies, such as membrane proteins in situ within cells, and targets that are too small for antibodies. It is also possible to develop aptamers for targets that are too toxic for antibody production, where the injection of the target molecule would kill the animal it is being injected into.
Does NeoVentures provide sequence information from the apatmers they develop for clients?

We consider all of the information that we develop within a project as the property of the client. As such we provide sequence as soon as it is available, even before we perform binding assays. With the next generation sequencing that we provide there can be as many as thirty million sequences. We are prepared to share all of these with clients if they desire. Most of our clients prefer to receive a report describing all of the sequences that bind to the target.

Please send your questions to us. We recognize that there is a need to provide information regarding aptamers openly and broadly. Maybe aptamers are not the solution for you, by asking us though at least you will be able to make an informed decision regarding aptamers as an alternative.