title: Molecular recognition of 6'-N-5-hexynoate kanamycin A and RNA 1x1 internal loops containing CA mismatches.
abstract: In our previous study to identify the RNA internal loops that bind an aminoglycoside derivative, we determined that 6'-N-5-hexynoate kanamycin A prefers to bind 1x1 nucleotide internal loops containing C·A mismatches. In this present study, the molecular recognition between a variety of RNAs that are mutated around the C·A loop and the ligand was investigated. Studies show that both loop nucleotides and loop closing pairs affect binding affinity. Most interestingly, it was shown that there is a correlation between the thermodynamic stability of the C·A internal loops and ligand affinity. Specifically, C·A loops that had relatively high or low stability bound the ligand most weakly whereas loops with intermediate stability bound the ligand most tightly. In contrast, there is no correlation between the likelihood that a loop forms a C-A(+) pair at lower pH and ligand affinity. It was also found that a 1x1 nucleotide C·A loop that bound to the ligand with the highest affinity is identical to the consensus site in RNAs that are edited by adenosine deaminases acting on RNA type 2 (ADAR2). These studies provide a detailed investigation of factors affecting small molecule recognition of internal loops containing C·A mismatches, which are present in a variety of RNAs that cause disease.
authors.affiliation: Department of Chemistry and The Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, Natural Sciences Complex, Buffalo, New York 14260, United States.
authors.forename: Tuan
authors.initials: T
authors.lastname: Tran
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Disney
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D001665:Binding Sites; D006868:Hydrolysis; D007612:Kanamycin / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000378:metabolism
chemical_list: C557457:6'-N-5-hexynoate kanamycin A; D008024:Ligands; D009711:Nucleotides; D007612:Kanamycin; D012313:RNA