AN RNA APTAMER TO THE XANTHINE GUANINE BASE WITH A DISTINCTIVE MODE OF PURINE RECOGNITION/

RNAs that bind to xanthine (2,6-dioxypurine) were isolated from a popu lation of 10(12) random sequences by in vitro selection. These xanthin e-binding RNAs were found to have a 10 nt consensus sequence at an int ernal loop in the most probable secondary structure. By trimming one o f the xanthine-binding RNAs, a representative xanthine-binding RNA (de signated as XBA) of 32 nt residues was prepared. The dissociation cons tant of this RNA for xanthine was determined to be 3.3 mu M by equilib rium filtration experiments. The XBA RNA can bind to guanine as well, whereas it hardly accommodates adenine,cytosine or uracil. The ltd val ues for various xanthine/guanine analogues were determined, and reveal ed that the N1H, N7 and O6 moieties of the ligand are involved in the binding with the XBA RNA. The ribonuclease sensitivities of some inter nal-loop residues changed upon the addition of xanthine, suggesting th at the internal loop of the XBA RNA is involved in the ligand binding. Interestingly, the consensus sequence of the xanthine/guanine-binding RNAs is the same as a sequence in one of the internal loops of the ha irpin ribozyme, except for a substitution that is neutral with respect to xanthine/guanine binding.