In vitro selection of DNA aptamers which bind to cholic acid

DNA aptamers which bind to cholic acid have been identified by in vitro selection from a pool of approximately 9 X 10(14) DNA molecules. After 13 rounds of selection, 19 clones with 95-100 nucleotide length were sequenced. Deletion-mutant experiments and computational sequence analysis suggested that all clones contained cholic acid binding sequences which could fold into three-way junction structures. By comparing the sequences involved in the predicted three-way junction structure of these 19 clones, it was determined that the nucleotide sequences and lengths of three stem and loop regions have no similarity. The most, conserved structure seems to have three base pairs flanking the junction of the three stems and they may form a hydrophobic cavity in which they interact with cholic acid. (C) 2000 Elsevier Science B.V. All rights reserved.