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.