Predicting motifs and secondary structure of steroid aptamers using APTANI

Aptamers are synthetic oligonucleotides that fold into flexible structures and bind to a variety of targets. Aptamers are selected using a biochemistry method called Systematic Evolution of Ligands by Exponential enrichment (SELEX), which can identify specific aptamers capable to bind to target from the pool of billions of random sequences. However, this iterative SELEX process is time consuming and requires specialized lab equipment. APTANI is an existing computational tool that can process the billions of random sequences generated from SELEX and generate secondary structure of the selected aptamer sequence. This can significantly reduce the complexity of SELEX and increase accuracy and throughput in lesser time and resources. Here, APTANI is used to analyze existing steroid aptamers (17ß-estradiol, deoxycortisol, estradiol, testosterone) and to identify sequence motifs/patterns and predict their secondary structure. Graphical Abstract Systematic Evolution of Ligands by Exponential enrichment: SELEX begins with an initial library of random sequences in the scale of 10e20 molecules. The library contains a variable region that is flanked by two fixed sequences. The oligonucleotide library is exposed to a desired target. A washing step will remove oligonucleotides that are weakly or unbound to the target. The remaining oligonucleotide-target complex will be separated with an elution step to recover the oligonucleotide sequence and amplified using PCR to regenerate a new pool for the next cycle. The goal of each new cycle is to enrich the high affinity sequences by modifying the binding conditions. The result is high affinity sequences for the target.