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Truncation of PDGF-BB Aptamer by Secondary Structural Analysis and Immunoassay

Cong Quang Vu1, Yuthana Tantirungrotechai1, Boonchoy Soontornworajit1, and Pichayanoot Rotkrua2
1 Department of Chemistry, Faculty of Science and Technology, Thammasat University, Pathumthani 12120, Thailand
2 Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, 12120, Thailand

Abstract—Aptamers demonstrate high binding affinity and specificity to their targets and contribute to a number of applications which require recognition molecules. Typically, original sequences of the aptamers comprised of 80 to 100 nucleotides (nt). Only certain nucleotides in each aptamer sequence play a key role in the binding functionality of the aptamers. Thus, each aptamer sequence comprised of two oligonucleotide regions: essential region and non-essential region. In many cases, the non-essential region causes a reduction of binding affinity of the parent aptamer sequence. It was, therefore, necessary to identify the essential region after aptamer screenings. This work aimed to truncate the PDGF-BB aptamer. The strategy relied on analyses of the secondary structure generated by RNAstructure and mfold. Then the truncated sequences were experimentally verified their bindings by enzyme-linked immunosorbent assay (ELISA). The results indicated that RNAstructure showed the high probability for predicting the secondary structure of aptamer and the truncated 36Apt exhibited an excellent binding capability to the target comparing to the binding capability of the full-length aptamer. Within the results, the secondary structural analysis was a promising strategy not only for aptamer truncation but also for the prediction of oligonucleotide structures.

Index Terms—secondary structure, PDGF-BB aptamer, ELISA

Cite: Cong Quang Vu, Yuthana Tantirungrotechai, Boonchoy Soontornworajit, and Pichayanoot Rotkrua, " Truncation of PDGF-BB Aptamer by Secondary Structural Analysis and Immunoassay," International Journal of Pharma Medicine and Biological Sciences, Vol. 5, No. 1, pp. 86-90, January 2016. doi: 10.18178/ijpmbs.5.1.86-90
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