X-Aptamer Selection and Validation

Methods Mol Biol. 2017;1632:151-174. doi: 10.1007/978-1-4939-7138-1_10.

Abstract

Aptamers and second generation analogs, such as X-Aptamers (XAs), SOMAmers, locked nucleic acids (LNAs), and others are increasingly being used for molecular pathway targeting, biomarker discovery, or disease diagnosis by interacting with protein targets on the surface of cells or in solution. Such targeting is being used for imaging, diagnostic evaluation, interference of protein function, or delivery of therapeutic agents. Selection of aptamers using the original SELEX method is cumbersome and time-consuming, often requiring 10-15 rounds of selection, and provides aptamers with a limited number of functional groups, namely four bases of DNA or RNA, although newer SELEX methods have increased this diversity. In contrast, X-Aptamers provide an unlimited number of functional groups and thus are superior targeting agents. Here, we discuss the X-Aptamer selection process.

Keywords: Aptamer; Aptamer nanoparticle conjugation; Aptamer siRNA chimeras; Bead-based selection; Biotin labeling; Chemical cross-linking; Drug aptamer conjugation; Dye labeling; Molecular targeting; Proteomics; Split-pool synthesis; X-Aptamer.

MeSH terms

  • Aptamers, Nucleotide / chemistry*
  • Aptamers, Nucleotide / genetics*
  • Gene Targeting
  • High-Throughput Nucleotide Sequencing
  • Magnetite Nanoparticles
  • Polymerase Chain Reaction
  • RNA / chemistry
  • RNA / genetics
  • Reproducibility of Results
  • SELEX Aptamer Technique*
  • Staining and Labeling

Substances

  • Aptamers, Nucleotide
  • Magnetite Nanoparticles
  • RNA