Base Pair Biotechnologies

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September 9, 2013 Issue

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With a Patented Multiplexed Approach, Base Pair Biotechnologies Develops Reagents for New Diagnostic Tests and Aptamers for Therapeutics at an Unprecedented Time and Cost

About Base Pair Biotechnologies

Scientists at Base Pair Biotechnologies have been studying aptamers and developing them on a research basis since 2004 and began recently offering these services commercially. With a patented multiplexed approach we can develop custom aptamers at unprecedented time and cost.

Dr. Bill Jackson


Bill Jackson serves as President and Chief Scientist of Base Pair Biotechnologies. Prior to formal spinout of aptamer discovery services under Base Pair, Bill guided numerous aptamer selections on both a service basis and for active research projects at parent company, BioTex, Inc. (also in Houston, TX).


Dr. Jackson is still partially employed by BioTex where he serves as a Senior Scientist on a number of synergistic research projects involving aptamers and biosensing. He joined BioTex in 2005 while concurrently finishing his Ph.D. in Chemical Engineering at nearby University of Houston. He has the somewhat rare distinction of funding his own doctoral dissertation while serving as Principal Investigator on a NASA-funded SBIR grant. At the University of Houston, his research focused primarily on the development of novel nucleic acid diagnostics using both mass spectrometry and nucleic acid microarrays. Since that time, Dr. Jackson has served as Principal Investigator on 11+ SBIR grants and co-investigator on several more. He has been issued 4 U.S. patents with 10+ pending.


In previous employment Bill has been involved in the development of a wide variety of analytical chemistry equipment including instruments still in service aboard the International Space Station. Dr. Jackson received the B.S. in biomedical engineering from Texas A&M University in 1997 and a B.A. in Spanish in 1998.


In 2010 Dr. Jackson co-authored, “Nucleic Acid Aptamers for Diagnostics and Therapeutics: Global Markets” for BCC Research.


Aptamer-Based Technologies


Base Pair Biotechnologies
8058 El Rio St.
Houston, TX 77054



Base Pair Biotechnologies

Print Version


Interview conducted by: Lynn Fosse, Senior Editor, CEOCFO Magazine, Published –  September 9, 2013


CEOCFO: Dr. Jackson, “Base Pair is the Aptamer Discovery Company.” Would you tell us what to company does?

Dr. Jackson: We develop reagents for new diagnostic tests. A small portion of our customers are interested in aptamers for therapeutics. In general an aptamer can be thought of as a placement for antibodies. Antibodies are what are typically used to bind to something else in a complicated biological mixture like a blood sample. Aptamers are an alternative comprising DNA or RNA rather than protein. This gives our aptamer reagents certain advantages over the status quo. We go through an entirely in vitro process in contrast to antibody production, which is done in animals. Once identified, an aptamer can be made by simple synthetic chemistry making them much easier to standardize and with more consistent performance. Aptamers are currently being incorporated in tests for cancer, pathogens, as well as carcinogens and other compounds in the environment.


CEOCFO: Are there many companies working in the same arena?

Dr. Jackson: I would say there are on the order of ten in the world. We are one of the few that focus solely on this as a service. Aptamers were first described in 1990, but the intellectual property was really concentrated in just one or two firms. Starting in about 2010 some of the intellectual property began to expire and that allowed us to offer this as a service to others. There are not really that many companies right now. We expect more to enter as competitors, but we are one of a very few, right now.


CEOCFO: What do you understand about aptamers that perhaps others do not?

Dr. Jackson: One aspect is that we can make them faster and cheaper. We have a patented process for multiplexing the technology. That means that we can make aptamers to multiple targets at the same time in parallel. At the end of any aptamer selection process the DNA or the RNA gets sequenced and we have a way for deciphering which aptamer belongs to which target so that we can do multiple targets in parallel. Therefore, for the last twenty years people have gone through the process called SELEX and that has been done against one target at a time. It could take weeks to months and you could come out with reagents that just bind one thing, whereas right now we can go through our process and have aptamers to thirty targets, simultaneously. So that is one aspect that is novel to Base Pair; we can make aptamers to many things and more efficiently. Then we have some “trade secret” know-how and a lot of experience, so we think we know what we are doing. Part of our service, which is somewhat unique, compared to our competitors, is that we also do a lot of characterization. We basically prove to the customer that these things work before we hand them over. Not all of our competitors do that.


CEOCFO: Is it because they do not always work?

Dr. Jackson: It takes some sophisticated equipment to do the necessary binding studies. There are several different types of instruments that can do these things. We have experience with most of them. Therefore, we can do a quantitative measurement of what is called the KD or Dissociation Constant of the aptamers before we hand them over. We do very basic but important characterization of all of our products before the customer begins to test them in their own system.


CEOCFO: When someone needs an aptamer is there anything else they could use or is it just a matter of which aptamer it would be? Is there even a choice about using an aptamer?

Dr. Jackson: There certainly is. That is a good question. The standard or de facto choice would normally be an antibody. That is the established technology. We have a challenge of convincing the customer to adopt a new technology. Aptamers have a number of potential advantages, but they are not as well understood in the marketplace. Therefore, there is a little bit of trepidation sometimes and we have to demonstrate that these things actually work. The advantages are that, unlike a protein based antibody, these nucleic acids can by synthesized, so it is more like a chemical; whereas the antibody has to come from an animal or expressed and purified from a cell line. Therefore, there is more variability and more steps involved in producing the antibody. Later in someone’s product commercialization program, aptamers offer the advantage of being simpler to produce and cheaper. The flip side is that it is a new technology for the most part; new to most people. Because the intellectual property was so concentrated, not many people have gone down a commercialization path with aptamers yet. Therefore, it is still relatively new to people. We are faced with all of the typical challenges of new technology adoption.                       


CEOCFO: How do you address the challenges?

Dr. Jackson: We spend a lot of time trying to get our message out and educate the community. We do a lot of trade shows. We have the domain of, where it is obviously related to our materials, but anyone can post there; even our competitors, education material, their posters and their publications. We do our best to publish posters and we have peer reviewed publications in the works, as do our customers. It can be a challenge, because many of our “for profit” customers do not really want to tell their competitors what they are doing or that they are considering aptamers. However, at least with our academic customers, we expect a number of publications to come out in the next year or so.


CEOCFO: Are you seeing a trend in general towards aptamers or towards a change in thinking that might lead to more use of aptamers?

Dr. Jackson: I certainly hope so. Our business has increased every month since we have been in business. Anecdotally, we see more and more new activity from others. In 2010 a colleague and I authored a market research report on aptamers for a company called BCC Research, and we put out an update of that report in 2012. A new independent market research report has come out this year. That would indicate that aptamers are starting to come up on people’s radar. I think that for the most part people are realizing that some of that priorintellectual property has fallen off. Therefore, I think that our timing for getting into this business was good and the activity will continue to increase.


CEOCFO: Is it difficult to find people for your company that are familiar with aptamers and with the process or are you pretty well set with the people you need right now?

Dr. Jackson: No, most of the skills that are required are standard molecular biology skills, so the talent pool is there. As is typical for many high tech industries, much of the talent pool is made up of international and graduate students. And we have a steady stream of people sending us resumes all of the time. I think that many people or students graduating from undergrad and graduate school see that this could be an industry of the future. Therefore, we get many excited cover letters on resumes. We generally take one or two interns every summer as well to help out. We have a very good talent base in Houston because of the Medical Center. It is one the largest Medical Centers in the world so .there is a large talent pool of people in molecular biology in the area. 


CEOCFO: When you are speaking with a prospective client do they understand the difference that Base Pair brings to the table or is there an “aha moment” when they get the fact that you are different and better?

Dr. Jackson: I think so. We are always honing our messaging. We do a lot of online marketing, but we also do scientific conferences and expos. There are sort of two tiers to that. There are people understanding the potential advantages over antibodies and there are people understanding Base Pair’s potential advantages over our aptamer competitors. I think those are two separate issues. In terms of Base Pair’s advantages over our competitors, our patent allows a quicker turn around, higher through put and it allows us to address more targets at the same time. Ourownershipmodel is different from most in that we stage the risk for the client. They do not necessarily pay a very large amount up front.  However, we either get involved with licensing deals for the aptamer sequences or lump some payments on the back end once their product is already working in their hands.    


CEOCFO: Getting off of the ground is always an expensive process. Are you funded for the next steps? Will you be seeking partnerships or additional funding?

Dr. Jackson: I believe we are well funded, at least for our initial foray into the market. We would always entertain additional capital under the right conditions. However, for the most part we are happy and we have a healthy runway. We are rare for a biotechnology company in that sometimes it takes years for a biotech company to establish any revenue at all, and we already have a decent revenue stream. Even on day one we had revenue coming in before taking on any funding. We also supplement a bit of our funding with grants mainly through the Small Business Innovation and Research program in the U.S., which is set-aside federal grant funding for small businesses doing various high tech projects.            


CEOCFO: What is ahead for the company?

Dr. Jackson: We are going to use our latest tranche of funding to continue to get the message out and do some more marketing. We have expanded our marketing presence through partnerships and consultancies in Europe. We just received a contract from the National Cancer Institute to make more aptamers to peptides; a small portion of the proteins that are potential markers for cancer. The aptamers will also be used in proteomic studies, which means understanding the proteins that are involved in various disease states. Then we will just continue to streamlineour operations and try to get more efficient so that we can make a better, faster and cheaper product.             


CEOCFO: Why should investors and people in the business community pay attention to Base Pair Biotechnologies? Why should Base Pair stand out?

Dr. Jackson: I think that, whether it is us or anyone else, aptamers are going to stay on the technology front as an important option in research and clinical diagnostics. I do not think that aptamers will completely replace antibodies. I think it should be viewed as another tool in the tool box. However, there is definitely going to be aptamer based diagnostics and further therapeutics based on aptamers in the near future. We are one of the early movers in this area. We are adding follow on intellectual property and know how, andwe want to be, as our tagline says, “The Aptamer Discovery Company”. Rather than people internally setting up their own capability to make aptamers, we think it is a wiser choice to outsource that function. We hope we stand out as the biggest and highest quality player in the aptamer discovery space.


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“… aptamers are going to stay on the technology front as an important option in research and clinical diagnostics … we want to be, as our tagline says, “The Aptamer Discovery Company”.- Dr. Bill Jackson


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