title: Studies on Tris(2-aminobenzimidazole)-PNA Based Artificial Nucleases: A Comparison of Two Analytical Techniques.
abstract: A new peptide nucleic acid (PNA) construct carrying a tris(2-aminobenzimidazole) phosphodiester cleaver is presented. This non-metal-based artificial nuclease hydrolyzes RNA substrates that form a bulge upon binding to the PNA. Reaction rates depend on the bulge sequence. For conjugates of tris(2-aminobenzimidazole), substrate turnover is shown for the first time. Two methods of analysis for the kinetics are compared: IE-HPLC separation of oligonucleotide fragments and analysis of Cy5-labeled oligonucleotide fragments by denaturating PAGE on a DNA sequencer, respectively. The different methods give rates that are in the same range where, in general, the substrates for the sequencer method give slightly lower rates.
authors.affiliation: Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany.
authors.forename: Plamena
authors.initials: P
authors.lastname: Dogandzhiyski
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden.
authors.forename: Alice
authors.initials: A
authors.lastname: Ghidini
authors.affiliation: Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany.
authors.forename: Friederike
authors.initials: F
authors.lastname: Danneberg
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden.
authors.forename: Roger
authors.initials: R
authors.lastname: Strömberg
authors.affiliation: Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Göbel
mesh_terms: D001483:Base Sequence; D001562:Benzimidazoles / Q000737:chemistry*; D040761:Biomimetic Materials / Q000737:chemistry*; D004722:Endoribonucleases / Q000737:chemistry*; D006868:Hydrolysis; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*
chemical_list: D001562:Benzimidazoles; D020135:Peptide Nucleic Acids; D012313:RNA; C027391:2-aminobenzimidazole; D004722:Endoribonucleases