title: Iron(II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: similar reactivity toward single- and double-stranded forms.
abstract: Fe(II)-EDTA catalyzes the cleavage of nucleic acids with little or no base-sequence specificity. We have now studied the preference of this reagent in catalyzing the cleavage of single- versus double-stranded nucleic acid structures. Three RNA and two DNA molecules, each expected to contain both single- and double-stranded regions, were synthesized and their structures characterized by enzymatic digestion using secondary structure specific nucleases. Fe(II)-EDTA catalyzed nearly uniform strand scission along the entire length of each molecule; no correlation with secondary structure was observed. The homopolymer sequence dA30:dT30, embedded in a mixed-sequence context to promote exact register of the homopolymer tract, was cleaved to an extent similar to that of flanking sequences. The reactions were relatively insensitive to K+, Na+, and Mg2+ in the range 10-100 mM and were quenched by Tris-HCl buffer. We conclude that the Fe(II)-EDTA-catalyzed strand scission reaction does not discriminate between typical single- and double-stranded regions, which simplifies the interpretation of experiments in which the reaction is used to probe the tertiary structure of RNA molecules [Latham, J. A., & Cech, T. R. (1989) Science 245, 276-282].
authors.affiliation: Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215.
authors.forename: D W
authors.initials: DW
authors.lastname: Celander
authors.forename: T R
authors.initials: TR
authors.lastname: Cech
mesh_terms: D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000378:metabolism*; D004492:Edetic Acid / Q000494:pharmacology*; D005296:Ferrous Compounds / Q000494:pharmacology*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000378:metabolism*; D009843:Oligoribonucleotides / Q000378:metabolism*; D012330:RNA, Double-Stranded / Q000378:metabolism*
chemical_list: D004277:DNA, Single-Stranded; D005296:Ferrous Compounds; D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D012330:RNA, Double-Stranded; C055526:Fe(II)-EDTA; D004492:Edetic Acid