Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles

Abstract

The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.

Identification of a novel DNA aptamer that selectively targets lung cancer serum

“…The predicted secondary structures of the candidate aptamers had abundant secondary structures, which were mainly based on the typical stable loop-stem and bulge structures. The results indicate that the stem-loop structures 30,31 could play a major role in their binding to target serum. The predicted secondary structures of aptamers Ap-LC-2, Ap-LC-3, Ap-LC-6 and Ap-LC-19 with minimum free energies (Δ G ) of −20.20 and −22.80 kcal mol −1 , respectively, are shown in Fig.…”

The Evolution and Application of a Novel DNA Aptamer Targeting Bone Morphogenetic Protein 2 for Bone Regeneration

“…Given the adenine-rich property of BA1, it is possible that BA1 was Unlike general DNA aptamers, BA1 unusually has a high density of adenine residues. Adenine-rich aptamers were reported in prior studies to target gold surfaces and immobilized nickel ions (Ni 2+ ) [25,26]. Since nickel magnetic beads were used as the target support in this study, we examined the affinity of BA1 to nickel beads to confirm its binding specificity.…”