Sephadex-binding RNA ligands (aptamers) were obtained through in vitro selection. They could be classified into
two groups based on their consensus sequences and the aptamers from
both groups showed strong binding to Sephadex G-100. One of the
highest affinity aptamers, D8, was chosen for further characterization.
Aptamer D8 bound to dextran B512, the soluble base material of Sephadex, but
not to isomaltose, isomaltotriose and isomaltotetraose,
suggesting that its optimal binding site might consist of more than
four glucose residues linked via α-1,6
linkages. The aptamer was very specific to the Sephadex matrix and
did not bind appreciably to other supporting matrices, such as Sepharose,
Sephacryl, cellulose or pustulan. Using Sephadex G-100, the aptamer
could be purified from a complex mixture of cellular RNA, giving
an enrichment of at least 60 000-fold, compared with a non-specific
control RNA. These RNA aptamers can be used as affinity tags for
RNAs or RNA subunits of ribonucleoproteins to allow rapid purification
from complex mixtures of RNA using only Sephadex.