Ludwig Mies van der Rohe, famously said of architecture that “Less is more”. This principle is based on the idea that removing superfluous elements enhances the clarity of the concept. It emphasizes functionality, clean aesthetics and simplicity. The German pavilion that he designed for the Barcelona world fair has been recreated and stands as clear testament to the truth of these words.
“Less is more” is definitely true for aptamer truncations.
In the picture above, the aptamer has long dangling ends on both the 5’ and 3’ sides. Why is this a problem? Single stranded DNA or RNA has a biphasic nature. The phosphate backbone has a positive charge and is strongly hydrophilic. The nucleotides on the other hand have mixed charges and are hydrophobic. This means that unhybridized single stranded oligonucleotide regions in the presence of water are driven to adhere to surfaces. This satisfies the hydrophobicity and hydrophilicity of both sides. Unfortunately, this also drives aspecific binding to other targets. The removal of such regions results in an increase in the specificity of binding.
Truncation of these regions also tends to lead to an increase in affinity as well. Why would that be?
The prediction of the structure shown above was performed with RNAFold. The colour coding corresponds to the probability of each nucleotide being in the position predicted, with red meaning highly probable and green to blue meaning improbable. This improbability is due to the potential for these regions to hybridize to other regions of the aptamer other than the ones in the predicted structure. In this case there are low probability prediction on the position of certain nucleotides in the dangling ends. This means that a certain amount of the time these nucleotides are hybridized to others resulting in a different overall structure. It is a safe assumption that only one of the aptamer structures binds to your favourite target. By removing the dangling ends the number of possible structures is reduced, thus the structure that binds to your target is present a higher proportion of the time. This is why aptamer truncation leads to higher affinity and specificity.
In subsequent blogs we will discuss how we use our Neomer library process to scientifically guide truncation. In keeping with Mies Van der Rohe, I will end this blog with one of his other sayings: “No design is possible until the materials with which you design are completely understood”.
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