Self-assembling aptamer-protein hybrid systems binding biologically relevant ligands

Protein amyloid structures are well known as factors causing  diseases called amyloidoses, such as Alzheimer’s or Parkinson’s disease. However, a group of „functional amyloids“ has been identified which are fulfilling natural purposes in mostly lower eukaryotes, for example bacteria, fungi or spiders¹. Amyloids possess characteristic structural cross-β structure consisting of the β-sheets arranged perpendicularly along the fibril axis. Among the proteins which self-assemble into the fibrils, recombinant spider silk proteins have shown high potential for the use in biomedical as well as technological applications based on advantageous properties of the processed materials such as nanofibrils, particles, coatings, foams, fibers or hydrogels, showing biocompatibility, biodegradability and the absence of immune response of the living organisms². The purpose of this study was to prepare DNA-spider silk protein bioconjugates using recombinant spider protein eADF4(C16), which is derived from the natural dragline protein of the European garden spider Araneus diadematus fibroin 4 (ADF4). The recombinant protein provides the possibility of site-specific chemical modification with oligonucleotides^3,4. We used aptameric nucleic acids TBA15 and TBA29 which are known for binding of human thrombin. For the synthesis of these bioconjugates, the catalyst-free „click”-chemistry reaction was used after the modification of the protein N-terminus with azide (N₃) and the 5´-end of the oligonucelotides with dibenzocyclooctyne (DBCO). The accuracy of initial modifications and subsequent „click”-conjugation was verified using methods such as high-performance liquid chromatography (HPLC), mass spectrometry (MALDI-TOF) and native PAGE electrophoresis. Subsequently, our aim was to characterize the TBA15(29)-eADF4(C16) bioconjugates in terms of their ability to self-assembly kinetics in the presence of different ions using circular dichroism (CD) and atomic force microscopy (AFM). The experiments were carried out using different concentrations of phosphate ions (Pi), which is proved to promote fibril formation of the spider silk protein². The next step was various concentrations of Na⁺ and K⁺ ions to determine their impact on the aptamer secondary structure and the rate of the bioconjugate self-assembly. The data suggest that the bioconjugates TBA15(29)-eADF4(C16) retain their ability to self-assembly into higher structures while maintaining the same properties as naturally occurring protein cross-βfibrils. The kinetics of the self-assembly process appeared to be highly affected by the phosphate ions in the solution. Initial measurements of the kinetics at different conditions suggested that there was a more significant impact on the self-assembly caused by the Na⁺ ions in the solution than the K⁺ ions. Our observations indicate that there is a great potential for using the spider silk protein-DNA bioconjugates to prepare highly organized structures with the ability to bind biologically relevant agents, such as thrombin which could lead to the practical applications, for example as the drug delivery systems or biosensors.