In this Issue:

– What’s new at Base Pair – Chief Scientist receives $1.4M grant from NIH
– Gates Foundation recipient chooses Base Pair for detecting mosquito born disease
– Base Pair discovers a new aptamer to transgelin

Base Pair’s Chief Scientist receives grant from NIH to Detect Environmental Toxins in Blood

Base Pair Biotechnologies is pleased to announce that our Chief Scientist, Dr. George W. (Bill) Jackson, has just been awarded a new $1.4M SBIR Phase II grant from the National Institutes of Health, entitled “Portable nanofluidic aptamer-SERS instrument for measurement of chemical exposure.” Base Pair will collaborate on this project with BioTex, Inc., which will provide instrument design, development and engineering expertise.

Risk of exposure to hazardous chemicals in the environment is a reality of life today. This risk is present whether one lives in a city or a rural, agricultural region. While measuring the concentrations of these compounds in the environment provides a good indication of potential danger to humans, such a measurement does not provide any indication of the actual chemical dose that an individual might have experienced. Some of these compounds are readily taken up by living organisms and others are not. The goal of this grant project is to develop tests to determine the actual exposure that a given individual had to a particular compound. In collaboration with Professors Gerry Cote’ and Jun Kameoka of Texas A&M University’s department of biomedical engineering, we will develop new aptamer-based sensing chemistries and instruments to quantitatively measure the concentrations of certain small organic industrial compounds directly in blood.

Why aptamers are well suited for this purpose:

The immunogenicity of molecules smaller than a few thousand Daltons, such as hormones, antibiotics, pesticides, herbicides and other environmental pollutants (including most peptides) is low. Obtaining antibodies that recognize small molecules usually requires a carrier protein, such as keyhole limpet hemocyanin (KLH). The resulting KLH-conjugated target molecules may not be the strongest immunogen moiety in the resulting conjugates, requiring multiple screens and separation steps to remove linker-directed antibodies as well as carrier-directed antibodies from bleeds. In addition, even in conjugated form, many small molecules are not highly immunogenic. Finally, toxic and otherwise bioactive compounds can themselves adversely affect immune system function as well as the health and/or viability of the immunized animal, resulting in poor antibody titers and a diminished immune response.

Base Pair’s aptamers, which are highly specific and sensitive affinity agents derived from nucleic acids, are very well suited for detecting toxic compounds, since they are synthesized and selected entirely in vitro. Aptamers that bind botulinum toxin, cholera toxin, ricin and ochratoxin A have been reported [1–4]. Ultrasensitive detection of small, hazardous molecules using aptamers was described recently in the literature [5]. Joeng et al. [9] successfully isolated aptamers for the non-steroidal anti-inflammatory diclofenac and its structural analog 2-anilinophenylacetic acid (2-APA). Binding affinities (Kd values) for the best aptamer from this study reached 42.7 nM, and the aptamer was specific for DCF over the highly similar 2-APA. In another recent example, aptamers with Kd values in the nanomolar range that bound Bisphenol A (BPA, 228 Da) were described by Jo et al [10]. Those aptamers were highly specific for BPA, and did not bind to the highly related compounds Bisphenol B or 4,4’-Bisphenol. These examples emphasize one of the key advantages of Base Pair’s aptamer selection process: selection and counter-selection steps can be easily combined in a well-designed development project to obtain highly specific affinity agents.

Base Pair scientists routinely select aptamers to small molecules and are experts in their characterization. We also can help with the incorporation of aptamers into functional assays and biosensors. Please contact us for more information about these capabilities.

Gates Foundation Grant Recipient Chooses Base Pair to Discover New Aptamers to Chikungunya Virus

Mosquito-borne illness affects a large portion of the developing world. Malaria is endemic in many regions. Many mosquito-borne viruses also affect humans, including yellow fever, dengue, West Nile, Chikungunya, and the newly emerging Zika virus threat, which is dominating news channels today. There is no vaccine to prevent or medicine to treat Chikungunya infection. The most common symptoms of infection are fever and joint pain. Headache, muscle pain, joint swelling and/or rash may also occur. While previous outbreaks were in Africa, Asia, Europe and islands in the Pacific and Atlantic Oceans, the virus spread to the Americas in 2013. The only way to avoid infection is to avoid infected mosquitos. But how can one determine whether a mosquito is infected or not?

Base Pair is excited to announce that University of Central Florida researcher, Dr. Bradley Willenberg, has received a “Grand Challenges Exploration” grant from the Bill & Melinda Gates Foundation to develop a novel method to detect the Chikungunya virus in live mosquitos and has chosen Base Pair to develop the aptamers for this project. Dr. Willenberg will employ a novel trap and feeding solution containing aptamer-functionalized gold nanoparticles to label the mosquitoes. Mosquitoes that are infected with the Chikungunya virus and consume the aptamers will turn blue due to aggregation of the gold particles in their digestive tract.

Base Pair is pleased and honored to be associated with this project, which will involve performing Base Pair’s proprietary aptamer development process in saliva isolated from living mosquitos – a new challenge even for Base Pair, adding to our experience in using a variety of sample types, including racehorse urine, human urine, human saliva, blood, serum, stool samples, and the like.

Please contact us if you have an unusual detection matrix for your desired binding assay – we can generally design a screen that will allow us to develop an aptamer that meets your needs, even under relatively unusual conditions.

New Products

Base Pair scientists have recently developed an aptamer that specifically binds the C-terminal domain of transgelin. Transgelin is a transformation and shape-change sensitive actin cross-linking/gelling protein found in fibroblasts and smooth muscle. Its expression is down-regulated in many cell lines, and this down-regulation may be an early and sensitive marker for the onset of transformation [6]. Recent evidence suggests that transgelin acts as a tumour suppressor. Its expression is reduced or absent in certain prostate, breast and colon cancers. This result is consistent with suppression of the metallo matrix protease-9 (MMP-9) activity or expression by transgelin, since MMP-9 is upregulated in those cancers [7].

In order to create an affinity reagent to this important protein, Base Pair scientists performed an aptamer selection against the unique C-terminal peptide, MTGYGRPRIQIIS. Characterization of the aptamer binding curve was performed by microscale thermophoresis (MST) as shown below. The equilibrium binding constant was found to be 24 nM. Such an aptamer could form the basis for a new diagnostic test for oncogenesis as well as providing a useful research tool.

This transgelin aptamer is available for purchase as a custom aptamer in its unlabeled form or a labeled format.

Figure 1. Binding of Base Pair’s novel DNA aptamer to the peptide, MTGYGRPRIQIIS, the C-terminus of transgelin.


1. Bruno JG, Kiel JL: Use of magnetic beads in selection and detection of biotoxin aptamers by electrochemiluminescence and enzymatic methods. BioTechniques 2002, 32:178–80, 182–3.

2. Ding S, Gao C, Gu LQ: Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore. Analytical chemistry 2009, 81:6649–55.

3. Kuang H, Chen W, Xu D, Xu L, Zhu Y, Liu L, Chu H, Peng C, Xu C, Zhu S: Fabricated aptamer-based electrochemical “signal-off” sensor of ochratoxin A. Biosensors & bioelectronics 2010, 26:710–6.

4. Wei F, Ho CM: Aptamer-based electrochemical biosensor for Botulinum neurotoxin. Analytical and bioanalytical chemistry 2009, 393:1943–8.

5. McKeague M, Giamberardino A, DeRosa MC: Advances in Aptamer-Based Biosensors for Food Safety. In Environmental Biosensors. Edited by Somerset V. Rijeka, Croatia: InTech; 2011:17–41.

6. TAGLN. Wikipedia, the free encyclopedia 2015.

7. Assinder SJ, Stanton J-AL, Prasad PD: Transgelin: An actin-binding protein and tumour suppressor. The International Journal of Biochemistry & Cell Biology 2009, 41:482–486.