New strategies for evaluation and analysis of SELEX experiments.
Aptamers are an interesting alternative to antibodies in pharmaceutics and biosensorics, because they are able to bind to a multitude of possible target molecules with high affinity. Therefore the process of finding such aptamers, which is commonly a SELEX screening process, becomes crucial. The standard SELEX procedure schedules the validation of certain found aptamers via binding experiments, which is not leading to any detailed specification of the aptamer enrichment during the screening. For the purpose of advanced analysis of the accrued enrichment within the SELEX library we used sequence information gathered by next generation sequencing techniques in addition to the standard SELEX procedure. As sequence motifs are one possibility of enrichment description, the need of finding those recurring sequence motifs corresponding to substructures within the aptamers, which are characteristically fitted to specific binding sites of the target, arises. In this paper a motif search algorithm is presented, which helps to describe the aptamers enrichment in more detail. The extensive characterization of target and binding aptamers may later reveal a functional connection between these molecules, which can be modeled and used to optimize future SELEX runs in case of the generation of target-specific starting libraries.
Bioinformatics Group, Department of Mathematics, Natural and Computer Sciences, University of Applied Sciences Mittweida, 09648 Mittweida, Germany.
Rico
0000-0003-3353-5039
R
Beier
Institute of Food Technology and Bioprocess Engineering, Department of Mechanical Engineering, Dresden University of Technology, 01062 Dresden, Germany.
Elke
E
Boschke
Bioinformatics Group, Department of Mathematics, Natural and Computer Sciences, University of Applied Sciences Mittweida, 09648 Mittweida, Germany.
Dirk
D
Labudde
D052157:Aptamers, Nucleotide / Q000235:genetics*; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D029322:Norovirus / Q000235:genetics / Q000302:isolation & purification; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics; D052156:SELEX Aptamer Technique / Q000379:methods*
D052157:Aptamers, Nucleotide; D036022:Capsid Proteins