title: Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX.
abstract: Aptamers are structured macromolecules in vitro evolved to bind molecular targets, whereas in nature they form the ligand-binding domains of riboswitches. Adenosine aptamers of a single structural family were isolated several times from random pools, but they have not been identified in genomic sequences. We used two unbiased methods, structure-based bioinformatics and human genome-based in vitro selection, to identify aptamers that form the same adenosine-binding structure in a bacterium, and several vertebrates, including humans. Two of the human aptamers map to introns of RAB3C and FGD3 genes. The RAB3C aptamer binds ATP with dissociation constants about 10 times lower than physiological ATP concentration, while the minimal FGD3 aptamer binds ATP only cotranscriptionally.
authors.affiliation: Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA.
authors.forename: Michael M K
authors.initials: MM
authors.lastname: Vu
authors.forename: Nora E
authors.initials: NE
authors.lastname: Jameson
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Masuda
authors.forename: Dana
authors.initials: D
authors.lastname: Lin
authors.forename: Rosa
authors.initials: R
authors.lastname: Larralde-Ridaura
authors.forename: Andrej
authors.initials: A
authors.lastname: Lupták
mesh_terms: D000241:Adenosine / Q000737:chemistry* / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D001419:Bacteria / Q000378:metabolism*; D001483:Base Sequence; D019295:Computational Biology; D015894:Genome, Human; D020662:Guanine Nucleotide Exchange Factors / Q000737:chemistry / Q000235:genetics; D006801:Humans; D007438:Introns; D052156:SELEX Aptamer Technique; D020692:rab3 GTP-Binding Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D052157:Aptamers, Nucleotide; C549833:FGD3 protein, human; D020662:Guanine Nucleotide Exchange Factors; D000255:Adenosine Triphosphate; C116710:RAB3C protein, human; D020692:rab3 GTP-Binding Proteins; D000241:Adenosine