I have been reading about aptamers, with the hope of working with them in our lab soon. As I understand, the three dimentional conformation taken up by an aptamer on binding to its target remains the same, through every batch of that aptamer synthesized. I could not however find an article about this. Could you help me with this please? -Swan

Dear Swan,

Thank you for your questions regarding aptamer conformation. Aptamer conformation is not straightforward, as a given sequence can take on multiple conformations. While some aptamers maintain one primary conformation, others do not. The secondary structure can depend on the actual sequence of the apatmer as well as external factors, including the pH and composition of the dilution buffer. In regards to whether aptamers can behave differently due to batch to batch variations, one can imagine a scenario where purity may influence structure and function. However, in general the synthesis should not affect aptamer conformation. Interestingly, we too were not able to easily find any online literature that specifically documents this phenomenon, though The Aptamer Handbook, edited by Sven Klussman presents a lot of useful information on aptamer activity, selection and design.

Please let me know if I can help you further.