title: Adenosine is inherently favored as the branch-site RNA nucleotide in a structural context that resembles natural RNA splicing.
abstract: We previously used in vitro selection to identify the 7S11 deoxyribozyme, which catalyzes formation of 2',5'-branched RNA using a branch-site adenosine nucleophile and a 5'-triphosphate electrophile. An unanswered question is whether the use of branch-site adenosine is inherently preferred or a chance event during the particular selection experiment. Here we have found that deoxyribozymes newly selected to use uridine as the branch-site RNA nucleotide in a structural context that resembles natural RNA splicing instead prefer a branch-site adenosine, although adenosine was never available during the selection itself. Our results support a chemical basis for nature's choice of the branch-site nucleotide, which is almost always adenosine in group II introns and the spliceosome.
authors.affiliation: Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
authors.forename: Elena
authors.initials: E
authors.lastname: Zelin
authors.forename: Yangming
authors.initials: Y
authors.lastname: Wang
authors.forename: Scott K
authors.initials: SK
authors.lastname: Silverman
mesh_terms: D000241:Adenosine / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D021881:DNA, Catalytic / Q000737:chemistry / Q000378:metabolism; D008954:Models, Biological; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000737:chemistry*; D011687:Purines / Q000737:chemistry / Q000378:metabolism; D012313:RNA / Q000737:chemistry*; D012326:RNA Splicing; D013329:Structure-Activity Relationship; D014529:Uridine / Q000737:chemistry / Q000378:metabolism
chemical_list: D021881:DNA, Catalytic; D009711:Nucleotides; D011687:Purines; D012313:RNA; D000241:Adenosine; D014529:Uridine