Prof. Serap EVRAN
Ege University
Prof. Serap Evran is a distinguished academic at the Department of Biochemistry, Faculty of Science, Ege University. Her research encompasses a broad spectrum of scientific disciplines, including biochemistry, molecular biology and genetics, biotechnology, protein engineering, and biosensors. Her work spans from the structural and functional analysis of biomolecules to advancements in green chemistry and biotechnological applications.
Together with her research team, Prof. Evran employs cutting-edge scientific methodologies such as modern proteomics, transcriptomics, molecular biology, recombinant protein analysis, and biosensor technologies to investigate biochemical processes in depth. Her studies on DNA aptamers, enzyme engineering, and biotechnological sensor development contribute significantly to advancements in healthcare, environmental science, and industrial biotechnology.
In Vitro Selection of Aptamers for Proteins and Small Molecules: Applications in Biorecognition and Inhibition
Serap EVRAN
Ege University, Faculty of Science, Department of Biochemistry, 35100, Bornova-İzmir, Türkiye
serap.evran@ege.edu.tr
Nucleic acid aptamers are single-stranded DNA or RNA molecules that fold into specific three-dimensional structures and mimic the binding properties of antibodies.1 Aptamers confer superiority to antibodies in terms of small size, ease of chemical synthesis, and low cost. In recent years, aptamers have been widely employed as biorecognition elements in biosensors and diagnostic assays. Aptamers also hold promise for therapeutic applications, as they are non-immunogenic and selective for their targets. Aptamers are selected using an in vitro method called the Systematic Evolution of Ligands by Exponential Enrichment (SELEX), which enables the screening of a diverse aptamer library against proteins, cells, and small molecules.2 Since SELEX is performed in vitro, it is particularly advantageous for small-molecule targets, for which antibody production is challenging. Our studies have focused on the selection of DNA aptamers for proteins and small molecules3,4. One of the proteins we targeted was Yersinia outer protein M (YopM). We performed magnetic bead-based SELEX and identified an aptamer blocking the interaction between YopM and human DEAD-box helicase 3 (DDX3). In another study, we targeted histone deacetylase 10 (HDAC10). HDACs are emerging therapeutic targets for the treatment of cancer and inflammatory diseases. However, the lack of isoenzyme-specific inhibitors limits their application. Hence, we aimed to develop an isoenzyme-specific aptamer. For this aim, we performed counter-SELEX to eliminate the aptamers binding to the structurally similar HDAC6 isoenzyme. We showed that the aptamer could specifically inhibit HDAC10 enzyme activity, but not HDAC6 or other metalloenzymes. Our protein-SELEX studies also included the development of aptamers for the detection of food allergen proteins. In addition to proteins, we targeted small molecules that needed to be detected in biological samples. One of the targets was succinylacetone, a biomarker of tyrosinemia type 1. We performed graphene oxide SELEX (GO-SELEX) and obtained an aptamer for the detection of succinylacetone. The aptamer-based assay did not produce any signal against tyrosine, which is structurally similar to succinylacetone. We concluded that adjusting the in vitro selection conditions plays a major role in aptamer specificity.
We thank TÜBİTAK (project no: 120Z898 and 123Z076) and TÜSEB (project no:13234 and 33577) for the financial support.
References:
1. Ji, C.; Wei, J.; Zhang, L.; Hou, X.; Tan, J.; Yuan, Q.; Tan, W. Chem. Rev. 2023, 123, 12471–12506.
2. Ellington, A. D.; Szostak, J. W. Nature 1990, 346, 818–822.
3. Düzel, A.; Bora, B.; Özgen, G. Ö.; Evran, S. Int. J. Biol. Macromol. 2024, 257, 128540.
4. Erkocyigit, B.; Man, E.; Efecan, E.; Ozufuklar, O.; Devecioglu, D.; Bagci, B.; Aldemir, E.; Coskunol, H.; Evran, S.; Guler Celik, E. Biosensors 2025, 15, 31.
