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Aptamer Structure Prediction

The relationship between structure and function is pretty obvious in a lot of engineering projects. Clearly the same is true for aptamers. The functionality of an aptamer is based entirely on it’s structure. In this series of blogs we are going to reveal how we perform meta-analysis of aptamer structures as a basis for identification of candidate sequences and as a means of improving selected sequences. 

Our ever improving ability to perform deep data analysis of aptamer structures is one of the keys that makes NeoVentures the top aptamer development company globally. 

How do we do this? 

Meta-analysis of aptamer sequences is relatively straightforward. Sequences are strings of information and as such thousands of sequences can be compared in a single run. The key to doing the same with structures is to reduce the structure information to strings of information. We have software that enables us to define the state of a nucleotide in terms of it’s structural status. This is entered as a code and rendered as a string. 

We then use a suite of in-house software that enables us to predict thousands of these structures from a data set and compare them for similarities. We overlay this analysis on the more traditional sequence analysis to develop an understanding of what effect a selection has had on aptamer structure. 

Our capacity for meta-analysis of aptamer structures in coupling with meta-analysis of sequences allows us to change the way we choose candidate sequences for further analysis. In the past we chose individual sequences based on the effect of selection of different targets on them. Now, we are able to consider the selected aptamers as a whole and determine what structures are being selected. We are then able to choose representatives of these selected choices. 

At NeoVentures, we perform this analysis on all of our aptamer projects. We are now ready to apply our capacity in this regard to your aptamer selection data and help you choose candidate sequences. Please contact us for a quote and a discussion of how this service could help you identify better aptamers.

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In the next blog we will discuss the power of structural analysis applied to our Neomer method for aptamer selection.