1 Introduction of Aptamer, SELEX, and Different SELEX Variants
25
analysis based on quantitative, ligand-dependent 2
acylation of solvent-accessible
regions of the selected RNA pools, followed by reverse transcription (SHAPE) and
deep sequencing (Fig. 1.17). The method reveals, in a single sequencing experiment,
the identity, structural features, and target dissociation constants for aptamers present
in the selected pool. Application of Apta-Seq to a human genomic pool enriched for
ATP-binding RNAs yielded three new aptamers, which together with previously
identified human aptamers suggest that ligand-binding RNAs may be common in
mammals.
Fig. 1.17 Apta-Seq scheme [80]. The pipeline consists of a an in vitro selection, b SHAPE analysis of selected pool, and c high-throughput sequencing for determination of sequence identity,
secondary structure, and d binding isotherms of individual aptamers
25
analysis based on quantitative, ligand-dependent 2
acylation of solvent-accessible
regions of the selected RNA pools, followed by reverse transcription (SHAPE) and
deep sequencing (Fig. 1.17). The method reveals, in a single sequencing experiment,
the identity, structural features, and target dissociation constants for aptamers present
in the selected pool. Application of Apta-Seq to a human genomic pool enriched for
ATP-binding RNAs yielded three new aptamers, which together with previously
identified human aptamers suggest that ligand-binding RNAs may be common in
mammals.
Fig. 1.17 Apta-Seq scheme [80]. The pipeline consists of a an in vitro selection, b SHAPE analysis of selected pool, and c high-throughput sequencing for determination of sequence identity,
secondary structure, and d binding isotherms of individual aptamers