Cartilage graft
Cartilage formed in vitro courtesy of Kate Chou: Case Western Reserve University

Artificial extracellular matrices are an important tool in the field of tissue engineering and regenerative medicine. Natural extracellular matrices (ECMs) consist of insoluble macromolecules, growth factors, and adhesion ligands. These components send important biochemical signals that affect cell behavior, 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). 

Aptamers in Extracellular Matrices

​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 without loss of affinity, making them ideal candidates for the bioactivation of extracellular matrices (1).

Fibronectin Aptamer-Activated Hydrogel

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. The researchers studied cell density, cell viability and cell morphology in control hydrogels vs. hydrogels bound to anti-fibronectin Aptamers (2,3). 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 (3). This study shows the suitability of Base Pair aptamer ATW0008 for improved fibronectin and cell binding in extracellular matrices.

Fibronectin Aptamer-Activated Chitosan Film

In a more recent study, the researchers tested the effects of the same anti-fibronectin aptamer on the colonization of chitosan films. Chitosan is a natural, biodegradable polymer with low immunogenicity and low toxicity that is produced by several marine species. It is increasingly being used in bandage fabrication for repair of a wide range of tissues (5). Chitosan can be formed into a wide range of shapes suitable for regeneration of periodontal tissue and exhibits natural activity against several common bacterial pathogens. In this study, binding of aptamer to chitosan film increased osteoblast cell (MC3T3-t1) growth in a dose-dependent manner. The presence of anti-fibronectin aptamer also increased cell viability and adhesion and improved osteoblast cell morphology (4).

Custom Aptamer Discovery

Base Pair has selected aptamers to collagen, fibrinogen, and fibronectin. Aptamers to specific cell surface markers, connective proteins, small molecules, growth factors, and other targets can be selected for specific applications, including regenerative medicine. Please contact Base Pair for more information on the use of aptamers in your application. We would love to learn more about your research.

Request a Free Aptamer Project Proposal


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

4. Parisi, L. et al. Anti-fibronectin aptamers improve the colonization of chitosan films modified with D-(+) Raffinose by murine osteoblastic cells. J. Mater. Sci.: Mater. Med. 2017. 28:136.

5. Frost, S.J., et al. Semitransparent bandages based on chitosan and extracellular matrix for photochemical tissue bonding. Biomedical Engineering Online. 2018. 17:7.