Electrophoretic study of G-quadruplex aptamer interactions with different short single-strand complementary oligonucleotides

Abstract Aptamers are single-stranded nucleic acids, typically 20-80 nucleobases (nb) in length, which can bind different compounds with high affinity and selectively. Their ligand-binding properties be attenuated by adding short complementary strands. These interactions open new opportunities for aptamer-based assays. Strong dependence between the length electrophoretic mobility of acids makes polyacrylamide gel electrophoresis a powerful tool studying their complexes. The 36 nb DNA G-quadruplex aptamer (5’-GAT-CGG-GTG-TGG-GTG-GCG-TAA-AGG-GAG-CAT-CGG-ACA-3’) specific to ochratoxin A 9 (ssDNA) were studied. ssDNA varied from 5 nb. To maintain conformation aptamer, ionic strength buffer was used. best resolution its complex provided 15% monomer monomer/cross-linker ratio 15:1. Bands free observed all studied variants. If less than nb, position aptamer’s band remained unchanged, independent aptamer/ssDNA ratios, additional bands did not appear. longest (5’-CGC-CAC-CCA-3’) lead appearance band, but it slowed migration depending on concentration. Under 27-fold excess given ssDNA, relative changed 0.566 0.468. Thus, visualizes aptamer-ssDNA used development analytical systems.