RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information

Abstract

Aptamers are short single-stranded RNA/DNA molecules that bind to specific target molecules. Aptamers with high binding-affinity and target specificity are identified using an in vitro procedure called high throughput systematic evolution of ligands by exponential enrichment (HT-SELEX). However, the development of aptamer affinity reagents takes a considerable amount of time and is costly because HT-SELEX produces a large dataset of candidate sequences, some of which have insufficient binding-affinity. Here, we present RNA aptamer Ranker (RaptRanker), a novel in silico method for identifying high binding-affinity aptamers from HT-SELEX data by scoring and ranking. RaptRanker analyzes HT-SELEX data by evaluating the nucleotide sequence and secondary structure simultaneously, and by ranking according to scores reflecting local structure and sequence frequencies. To evaluate the performance of RaptRanker, we performed two new HT-SELEX experiments, and evaluated binding affinities of a part of sequences that include aptamers with low binding-affinity. In both datasets, the performance of RaptRanker was superior to Frequency, Enrichment and MPBind. We also confirmed that the consideration of secondary structures is effective in HT-SELEX data analysis, and that RaptRanker successfully predicted the essential subsequence motifs in each identified sequence.

RaptGen: A variational autoencoder with profile hidden Markov model for generative aptamer discovery

“…The continuous motif indicated that the sequences in the data had the preference for specific subsequences. The result was partly consistent with our previous research [20] that implied…”

“…The SPR assays were performed using a Biacore T200 instrument (GE Healthcare) as described previously with slight modifications [20]. BO uses both the search for sequences that have not been explored to a reasonable extent and the utility of utilizing sequences with known affinity to select the next sequence for evaluation.…”

Consistent Consideration of RNA Structural Alignments Improves Prediction Accuracy of RNA Secondary Structures

“…Conventional loop accessibilities on single structure succeeded in the analysis and prediction of RNA-binding proteins and the in silico RNA aptamer selection on HT-SELEX (79,80). There is a possibility that the loop accessibilities proposed in this study have a broader range of impactful applications, as with the conventional accessibilities.…”

Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology

“…RaptRanker [ 46 ] also carries out complex data analysis. In the first stage, it passes all sequences through a rough filter, however, they must exactly match in length and in the sequence of constant regions.…”

“…The extracted motifs can be further clustered to achieve more precise aptamer identification. No systematic comparison of different strategies and software solutions for candidate aptamer identification is available at the moment; however, in certain cases, research articles devoted to the development of particular bioinformatics tools describe a comparison to other similar instruments [ 23 , 24 , 46 ].…”