Identification of a 14mer RNA that recognizes and binds flavin mononucleotide with high affinity.

ABSTRACT: Aptamers are nucleic acids developed by in vitro evolution techniques that bind to specific ligands with high affinity and selectivity. Despite such high affinity and selectivity, however, in vitro evolution does not necessarily reveal the minimum structure of the nucleic acid required for selective ligand binding. Here, we show that a 35mer RNA aptamer for the cofactor flavin mononucleotide (FMN) identified by in vitro evolution can be computationally evolved to a mere 14mer structure containing the original binding pocket and eight scaffolding nucleotides while maintaining its ability to bind in vitro selectively to FMN. Using experimental and computational methodologies, we found that the 14mer binds with higher affinity to FMN (K(D) approximately 4 microM) than to flavin adenine dinucl

SUBMITTER: Anderson PC 

PROVIDER: S-EPMC1322272 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature