Mapping the binding region of aptamer targeting small molecule: Dabigatran etexilate, an anti-coagulant

Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions

“…Six different aptamers were studied, and it was found that two aptamers fold into a G-quadruplex, while the other four adopt a structure similar to B-DNA helices. More recently, Aljohani et al [144] used the change in the intensity of the ellipticity as a measure of the conformational change and strength of the binding. They studied an aptamer against dabigatran etexilate, an anti-coagulant, together with a truncated form and found that upon addition of the target the truncated form has a more sensitive response.…”

Aptamer–Protein Interactions: From Regulation to Biomolecular Detection

“…Generally, full-length aptamers derived from the SELEX process are 70–130 nucleotides (nt) in length, consisting of a random region (30–50 nt) and two fixed primer regions. − Only a small fraction of nucleotides in a full-length aptamer, known as essential and supporting nucleotides, play critical roles in the interactions with target protein. , The remaining nucleotides that do not support aptamer–protein interactions are regarded as nonessential nucleotides . These nonessential nucleotides not only produce unnecessary steric hindrance but also increase nonspecific interactions, affecting the affinity and specificity of aptamers to a certain extent. − Therefore, appropriately truncating aptamers to eliminate nonessential nucleotides is one of the important strategies to regulate aptamer–protein interactions. To determine which nucleotides can be deleted, analyzing the sequence and structure of aptamers is first required. , In general, some available software algorithms, such as ClustalW and Mfold, are applied to conduct multiple sequence alignments or predict the secondary structure of aptamers, thereby deducing the essential sequences for interactions between aptamers and target proteins. ,, Subsequently, the aptamers are rationally truncated on the principle of preserving the required sequence.…”