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No to Denaturation of Aptamers for Commercial Applications

    The phoenix of mythology arises from the ashes of its predecessor. This seems like a very intriguing phenomena, but strikes me as difficult to control in a commercial application. Yet, we keep getting asked whether this is necessary for aptamers to work. Do aptamers need to be denatured and then allowed to renature so that they will bind to a target? 

    Our answer at NeoVentures is that if this is necessary for a given aptamer, then this aptamer should be discarded and you should find one that does not require denaturation prior to use. This is simply impractical for a commercial product with the aptamer, either a therapeutic or diagnostic application. At NeoVentures we do denature our libraries during the selection process. We do this at this stage because there are a large assortment of different sequences present that could hybridize to each other. We then snap cool to enhance individual shapes. 

    In all  our binding assays we do not denature and renature. If an aptamer requires this then it will be observed as not working in our assays and discarded. Aptamers that require this are a non-starter for actual commercial use. 

    An aptamer that requires denaturation and renaturation in order to bind is a strong warning sign. Every aptamer is in flux among shapes at whatever temperature it is at (except 0 Kelvin). When we truncate and optimize aptamers we stabilize the shape that is responsible for binding, but still some flux is unavoidable. If an aptamer requires denaturation and renaturation to work this indicates that it is a sub-optimal shape (from a free energy point of view) that is responsible for the aptamer binding. The sub-optimal shape is likely more prevalent at an early stage of renaturation, and reduces in prevalence over time. We have observed aptamers that will work the first day that they are solubilized and then not work a few days or a week later (again, these would be discarded). For commercial applications (and really, why else are we doing this…) aptamers need to be able to stably perform for up to a year. 

    There are many beautiful concepts like the phoenix in mythology and I like to think that the aptamers we are producing for our clients are works of art, but works of art often only appreciate in value after the demise of the artist. The real beauty of a commercial aptamer application is robustness and simplicity. 

    Next week’s blog: an introduction to a new method of aptamer selection, “Neomers”.

     

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