title: Core requirements of the adenine riboswitch aptamer for ligand binding.
abstract: The adenine riboswitch aptamer, the A box, positively regulates gene expression upon adenine binding. To provide insight into structure-function relationships, important for the adenine riboswitch aptamer, we have created alignments for six aptamer sequences that reveal the core requirements. In addition, 2-aminopurine (2AP) binding studies have been used to test the consensus sequence derived from the alignment. Overall, the consensus secondary structure is consistent with 2AP binding studies. However, a position in the core, previously identified as variable, shows restriction in nucleotide sequence. Furthermore, this restriction is found to be related with the ligand specificity of the riboswitch. The implications of this relationship for the riboswitch gene regulation mechanism are discussed.
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, Québec, Canada.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Lemay
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Lafontaine
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry; D000225:Adenine / Q000737:chemistry*; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D020029:Base Pairing; D001483:Base Sequence; D005453:Fluorescence; D005786:Gene Expression Regulation; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D038621:Regulatory Sequences, Ribonucleic Acid
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D038621:Regulatory Sequences, Ribonucleic Acid; D015075:2-Aminopurine; D000225:Adenine