A primer-free method that selects high-affinity single-stranded DNA aptamers using thermostable RNA ligase

Abstract

This article describes a method for selecting single-stranded DNA (ssDNA) molecules that bind with high-affinity aptamers to specific target proteins. This SELEX (systematic evolution of ligands by exponential enrichment) method is similar to other “primer-free” approaches where the random sequence ssDNA starting pool has no fixed sequences at the 5′ and 3′ termini. Therefore, there are no predetermined sequences that could bias selection. Like other SELEX methods, repeated cycles (typically 5–15) of selection and then amplification and reselection are used. The method differs from other primer-free approaches in that the key step for regenerating new material for subsequent rounds is ligation of the selected ssDNA to a defined sequence oligonucleotide using thermostable RNA ligase. Under specific conditions, this ligase ligated 30-nt random sequence ssDNA (5′-N 30-3′) to a specified 20-nt ssDNA with approximately 50% efficiency. Efficiency was improved to approximately 90% by the addition of a single T residue to the 3′ end (5′-N 29T-3′). High efficiency in this step is critical, especially early in the procedure because any selected material that is not ligated is lost. In this study, human immunodeficiency virus reverse transcriptase was used as the target protein, but the method could be applied to essentially any protein.