In This Issue:

  • What’s new at Base Pair? New Interns: Tiffany Bachner and Caitlin Bruns​ 
  • Aptamers in Artificial Extracellular Matrices (ECM) 
  • Base Pair Fibronectin Aptamer & ECM Functionalization


Tiffany Bachner and Caitlin Bruns begin internships at Base Pair

Born and raised in Germany, ​Tiffany moved to the U.S. for her higher education. She received a BS in Biology from the University of Houston Clear Lake (UHCL) where she worked on zip reporters in green peas.  As a graduate student, Tiffany worked as a teaching assistant in biochemistry and microbiology and explored the existence of a biochemical pathway within Barrel Clover and Chick Peas. Tiffany will be receiving her M.Sc. in Biology from UHCL in May.

​Caitlin received a BS in Biology from Angelo State University. Her undergraduate research included a seed bank study on Big Bend National Park cacti E. chisoensis and the monitoring of migration patterns of the endangered bat species L. nivalis. Caitlin is currently pursuing a masters degree in cell and molecular biology at the University of Houston Clear Lake.

Advancements in Aptamers: Aptamers in Artificial Extracellular Matrices

Artificial extracellular matrices are an important tool in the field of regenerative medicine. Natural extracellular matrices consist of insoluble macromolecules, growth factors, and adhesion ligands. These components send important biochemical signals that affect cell behavior and tissue growth and homeostasis. Permeable hydrogels allow
for the transport of cell nutrients and waste and for intercellular communication, but lack the growth factors and adhesion ligands found in natural ECMs. (3)

​Modifying the surfaces of matrices or scaffolds with chemical treatments can improve binding of certain functional groups, but covalent bonding limits protein mobility and can possibly generate toxic monomers. Studies involving the use of immobilized peptides to induce cell activation have yielded mixed results. Recent studies
have shown that aptamers to binding and signaling proteins may be good alternatives for the bioactivation of artificial scaffolds. (2) Aptamers are single-stranded oligonucleotides, typically 30 to 80 bases in length, that form secondary and tertiary structures that can selectively bind specific targets with high affinity. Aptamers tend to be non-toxic, non-immunogenic and are small enough to infiltrate tissues and sometimes cells. Aptamers are also easily modified at the
3′ and 5′ end to facilitate conjugation and signal generation, making them ideal candidates for the bioactivation of extracellular matrices. (1)

Researchers at the University of Parma, Italy, have explored the use of aptamers to fibronectin to improve cell adhesion. (4 – See article below) Researchers in the Dept. of Biomedical Engineering at Penn
State recently explored the use of a chimeric aptamer-gelatin hydrogel to bind HUVEC cells in the presence of vascular endothelial growth factor (VEGF). When VEGF was added to untreated hydrogel, about 90% was released after one day. In the aptamer hydrogel, only 28% of VEGF was released after 14 days. The remaining VEGF was shown to be bioactive. On day 14, fluorescence intensity for HUVEC cells stained with calcein AM was 8 times greater for the aptamer hydrogel. Use of the anti-VEGF aptamer improved VEGF availability and HUVEC
cell viability. (3) Aptamer-functionalized hydrogels are an exciting alternative for exploration in wound healing, tissue generation and cell implantation.

​​Product Highlights: Fibronectin Aptamer for ECM Functionalization
Fibronectin aptamer promotes fibronectin retention, cell attachment to scaffold, and cell proliferation

​Researchers at the University of Parma, Italy, studied the ability of anti-fibronectin aptamers to promote the attachment and growth of osteoblastic cells in an artificial extracellular matrix.

A single-strand DNA aptamer to bovine and human fibronectin, Base Pair# ATW0008, was modified with a thiol on the 3′ end and a biotin on the 5′ end. Selectivity for fibronectin was confirmed via Western
Blot.  Aptamers were bound to a hyaluronic acid/polyethyleneglycol-based hydrogel. A UV-fluorescence DNA
intercalating dye was used to confirm aptamer binding to the hydrogel. Osteoblastic cells were seeded on hydrogels at 5000 cells/well with varying concentrations of aptamer for ten days. Researchers studied cell density, cell viability and cell morphology in control hydrogels vs. hydrogels bound to anti-fibronectin aptamers. (2,4)

​In the presence of anti-fibronectin aptamers, human osteoblasts were more numerous, formed larger clusters, and migrated more deeply into the hydrogel. Cell morphology was also different, with cells exposed to aptamers being less elongated with broad podosomes. (4) This study shows the suitability of Base Pair aptamer ATW0008 for improved fibronectin and cell binding in extracellular matrices.

​Contact Base Pair to learn more about recent aptamer projects and aptamer opportunities.


​1. Jayasena, S., et al. Aptamers: An emerging class of molecules that rival antibodies in diagnostics. Clinical Chemistry. 1999. 45(9):1628-1650.

2.  Ludovica Parisi, Carlo Galli, Lisa Elviri, Annalisa Bianchera, Paola Lagonegro, Simone Lumetti, Edoardo Manfredi and Guido Maria Macaluso (2016). Aptamer-Mediated Selective Protein Affinity to Improve Scaffold Biocompatibility, Advanced Techniques in Bone Regeneration, Dr Alessandro Zorzi (Ed.), InTech, DOI: 10.5772/63265.

3. Zhang, X. et al. Chimeric aptamer-gelatin hydrogels as an extracellular matrix mimic for loading cells and growth factors. Biomacromolecules. Jan 2016. Accessed 2 Feb 2017 Doi/abs/10.1021/acs.biomac5b01511.

4.  Galli, C. et al. Improved scaffold biocompatibility through anti-Fibronectin aptamer functionalization. Acta Biomateriala. 15 Sept 2016.