RNA molecules that specifically bind @entity8728 (Rb) and @entity70210 ( @entity6532 ) have been isolated by in vitro selection. A simple structural motif containing intramolecular G-quartets was found to bind tightly to oxidized @entity8728 (Kd = 1-5 micromolar). DNA versions of the consensus sequence also bind, but with weaker affinity. DMS protection experiments show that the quartet structure of these aptamers is stabilized by interaction with the @entity1785 . As a measure of their redox specificity, the aptamers do not show significant differential binding between oxidized and reduced forms of a @entity70211 derivative that is a close structural analog of @entity8728 . In contrast to the lack of redox specificity of the @entity8728 aptamers, RNAs selected for binding to the @entity4571 portion of @entity2125 discriminate between @entity2125 and @entity2125 in solution by over an order of magnitude. A mutagenized pool based on one of the @entity6532 aptamer sequences was used to reselect for @entity6532 binding. Comparison of the reselected sequences led to the identification of the binding region of the aptamer. A complex secondary structure containing two interacting stem-loops is proposed for the minimal @entity6532 -binding RNA. The same mutagenized pool was used to select for increased discrimination between @entity6532 and NMNH. From these reselected sequences, a mutation within the binding region was identified that increases specificity for @entity6532 . These experiments show that RNA can bind these cofactors with low micromolar affinity and, in the case of @entity4571 cofactors, can discriminate between the two redox states. These cofactor binding motifs may provide a framework for generating new ribozymes that catalyze redox reactions similar to those found in basic metabolic pathways.

RNA aptamers that bind XXXX and @entity4571 redox cofactors.

@entity6532 :: ('CHEBI:14648', 'Chemical') :: ['NMN'] @entity2125 :: ('MESH:D009243', 'Chemical') :: ['NAD', 'NADH'] @entity1785 :: ('MESH:C024132', 'Chemical') :: ['flavin'] @entity70211 :: ('MESH:C007228', 'Chemical') :: ['5-deazariboflavin'] @entity70210 :: ('CHEBI:16171', 'Chemical') :: ['beta-nicotinamide mononucleotide'] @entity4571 :: ('MESH:D009536', 'Chemical') :: ['nicotinamide'] @entity8728 :: ('MESH:D012256', 'Chemical') :: ['riboflavin']
@entity1785 :: (MESH:C024132,Chemical) :: ['flavin']
