title: Assessing intermolecular RNA:RNA interactions within a ribonucleoprotein complex using heavy metal cleavage mapping.
abstract: Heavy metal cleavage mapping analysis of both assembling and fully mature ribonucleoprotein (RNP) complexes are informative techniques for assessing the intermolecular base pairing between small non-coding RNAs and their interacting target RNAs. Lead cleavage of the RNA in partially or fully assembled RNPs in the absence or presence of the interacting RNA can determine both the accessibility of the base pairing sequence within the RNP itself as well as its interaction with the target RNA. In this chapter, we detail how this technique was used to map the intermolecular RNA:RNA base pairing of a box C/D RNA with its target RNA within the assembling archaeal RNP complex.
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Medicine, Department of Chemistry and Biochemistry, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL, 62901-4413, USA, ktgagnon@siu.edu.
authors.forename: Keith T
authors.initials: KT
authors.lastname: Gagnon
authors.forename: E Stuart
authors.initials: ES
authors.lastname: Maxwell
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D007854:Lead / Q000378:metabolism*; D008967:Molecular Biology / Q000379:methods*; D008969:Molecular Sequence Data; D046912:Multiprotein Complexes / Q000378:metabolism*; D009691:Nucleic Acid Denaturation; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D046912:Multiprotein Complexes; D012261:Ribonucleoproteins; D007854:Lead; D012313:RNA