title: Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.
abstract: LNA (locked nucleic acids, i.e. oligonucleotides with a methyl bridge between the 2' oxygen and 4' carbon of ribose) and 2,6-diaminopurine were incorporated into 2'-O-methyl RNA pentamer and hexamer probes to make a microarray that binds unpaired RNA approximately isoenergetically. That is, binding is roughly independent of target sequence if target is unfolded. The isoenergetic binding and short probe length simplify interpretation of binding to a structured RNA to provide insight into target RNA secondary structure. Microarray binding and chemical mapping were used to probe the secondary structure of a 323 nt segment of the 5' coding region of the R2 retrotransposon from Bombyx mori (R2Bm 5' RNA). This R2Bm 5' RNA orchestrates functioning of the R2 protein responsible for cleaving the second strand of DNA during insertion of the R2 sequence into the genome. The experimental results were used as constraints in a free energy minimization algorithm to provide an initial model for the secondary structure of the R2Bm 5' RNA.
authors.affiliation: Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627-0216, USA.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Kierzek
authors.forename: Ryszard
authors.initials: R
authors.lastname: Kierzek
authors.forename: Walter N
authors.initials: WN
authors.lastname: Moss
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Christensen
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Eickbush
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D000812:Anhydrides / Q000737:chemistry; D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics; D019476:Insect Proteins / Q000378:metabolism; D015636:Magnesium Chloride / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D015347:RNA Probes / Q000737:chemistry; D018626:Retroelements; D012965:Sodium Chloride / Q000737:chemistry; D013696:Temperature; D062367:ortho-Aminobenzoates / Q000737:chemistry
chemical_list: D000812:Anhydrides; D019476:Insect Proteins; D009841:Oligonucleotides; D015347:RNA Probes; D018626:Retroelements; C477371:locked nucleic acid; D062367:ortho-Aminobenzoates; D015636:Magnesium Chloride; C077537:N-methylisatoic anhydride; D012965:Sodium Chloride; D012313:RNA