Master Thesis Defense: Irena Roçi
  • FENS
  • Master Thesis Defense: Irena Roçi

You are here



Irena Roçi
 Biological Sciences and Bioengineering, MSc Program, 2012


Thesis Jury 

Asst. Prof. Javed H. Niazi Kolkar (Thesis Supervisor), Assoc. Prof. Uğur Osman Sezerman, Asst. Prof. Deniz Sezer, Prof. Dr.Yaşar Gürbüz, Asst. Prof. Alpay Taralp


Date &Time: August 6th, 2012 – 09:30

Place: FENS L063




There are ~71 different cancer types and most of them exhibit heterogenous phenotypic characteristics. For this reason, studying common physiological alterations in cancer cells can be a successful approach for cancer treatment. Molecules that serve as bottleneck in a certain pathway during cancer development are called biomarkers and their inhibition can cease the cancer progression. Sustaining proliferative signaling and inducing angiogenesis are two of the many acquired characteristics of cancer cells during cancer progression. Both HER2 and VEGF are overexpressed in each of the above conditions, respectively. Therefore, the aim of this study is to develop synthetic ssDNA molecules (aptamers) that can bind to HER2 and VEGF that inhibit their function, respectively. These aptamers are developed in our laboratory by using SELEX (Systematic Evolution of Ligands by EXponential enrichment) technology in which HER2/VEGF immobilized magnetic beads were employing for the selection of specific aptamers. The enriched ssDNA pool was cloned, sequenced and characterized. As a result, one aptamer for each biomarker was chosen among the candidates for binding and specificity assays.

We observed an interesting feature of anti-VEGF aptamer, a G-quartet structure which is predicted to provide the specific binding of VEGF. On the other hand, HER2 aptamer contained two stem-loops which may play a role in specific binding to HER2 protein. Equilibrium binding studies with anti-VEGF aptamer showed a dissociation constant (KD) of 270 nM indicating  that it had strong affinity for VEGF, whereas anti-HER2 aptamer had weak affinity with HER2 (KD=~4-8 µM). Our results demonstrate that  both the anti-VEGF and anti-HER2 aptamers in combination can potentially be applied as inhibitory drugs for cancer treatment.