This project aimed to manipulate DNA (deoxyribonucleic acid) aptamer AS1411, a short single-stranded oligonucleotide currently being developed to improve chemotherapy’s target cell specificity. As this aptamer binds explicitly to nucleolin, an overexpressed protein on the surface of cancer cells, chemotherapy damage to surrounding tissue may be lessened. This study modified the AS1411 DNA aptamer, which was named AS1411-N12, by adding 12 nucleotides to the 3’ and 5’ ends, forming a “flap” structure. The edition of said flap is attributed to theory that the increased mass will allow for tighter binding. This modification was hypothesized to further improve the DNA aptamer’s binding efficiency to the nucleolin protein expressed on cancer cells. Binding reactions occurred between DNA aptamers (AS1411 and AS1411-N12) and nucleolin samples. The resulting solutions were processed using micro-centrifugal filters, which separated small unbound single-stranded DNA aptamers from bigger unbound proteins and the DNA-Nucleolin complexes. Measured absorbance of the unbound filtered DNA aptamers were analyzed to compare binding efficiencies of the modified aptamer vs. the control. The average absorbance through 3 trials of the control AS1411 DNA aptamer was 1.907 at 260 nm, while the average absorbance through 3 trials was 1.364 at 260 nm. Through Beers Law, the unbound DNA control concentration was 146.6 µM while the modified DNA aptamers was 54.17 µM. This modification was highly effective as it yielded a 63% change in absorbance showing a drastic decrease in the amount of DNA aptamer left in solution. The modified DNA aptamer was significantly more effective in binding to its target protein. When attached to chemotherapy, AS1411-N12 will have a higher affinity to Nucleolin, improving cancer treatment.
Mayerfield et al. (Thu,) studied this question.