title: The DNA strand of chimeric RNA/DNA oligonucleotides can direct gene repair/conversion activity in mammalian and plant cell-free extracts.
abstract: Chimeric oligonucleotides (chimeras), consisting of RNA and DNA bases folded by complementarity into a double hairpin conformation, have been shown to alter or repair single bases in plant and animal genomes. An uninterrupted stretch of DNA bases within the chimera is known to be active in the sequence alteration while RNA residues aid in complex stability. In this study, the two strands were separated in the hope of defining the role each plays in conversion. Using a series of single-stranded oligonucleotides, comprised of all RNA or DNA residues and various mixtures, several new structures have emerged as viable molecules in nucleotide conversion. When extracts from mammalian and plant cells and a genetic readout assay in bacteria are used, single-stranded oligonucleotides, containing a defined number of thioate backbone modifications, were found to be more active than the original chimera structure in the process of gene repair. Single-stranded oligonucleotides containing fully modified backbones were found to have low repair activity and in fact induce mutation. Molecules containing various lengths of modified RNA bases (2'-O-methyl) were also found to possess low activity. Taken together, these results confirm the directionality of nucleotide conversion by the DNA strand of the chimera and further present a novel, modified single-stranded DNA molecule that directs conversion in plant and animal cell-free extracts.
authors.affiliation: Department of Biological Sciences, University of Delaware, 105 Wolf Hall, Newark, DE 19716, USA.
authors.forename: H B
authors.initials: HB
authors.lastname: Gamper
authors.forename: H
authors.initials: H
authors.lastname: Parekh
authors.forename: M C
authors.initials: MC
authors.lastname: Rice
authors.forename: M
authors.initials: M
authors.lastname: Bruner
authors.forename: H
authors.initials: H
authors.lastname: Youkey
authors.forename: E B
authors.initials: EB
authors.lastname: Kmiec
mesh_terms: D000818:Animals; D001483:Base Sequence; D002457:Cell Extracts; D002460:Cell Line; D002474:Cell-Free System; D004260:DNA Repair / Q000235:genetics*; D004274:DNA, Recombinant / Q000235:genetics / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000502:physiology; D018274:Electroporation; D005785:Gene Conversion / Q000235:genetics*; D007613:Kanamycin Resistance / Q000235:genetics; D051379:Mice; D027425:ATP-Binding Cassette, Sub-Family C Proteins; D051718:MutS Homolog 2 Protein; D000074081:MutS Homolog 3 Protein; D009154:Mutation / Q000235:genetics; D009692:Nucleic Acid Heteroduplexes / Q000235:genetics / Q000378:metabolism; D009841:Oligonucleotides / Q000235:genetics / Q000378:metabolism; D059828:Plant Cells; D010944:Plants / Q000235:genetics; D010957:Plasmids / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000502:physiology; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D013753:Tetracycline Resistance / Q000235:genetics; D014169:Transformation, Bacterial
chemical_list: D002457:Cell Extracts; D004274:DNA, Recombinant; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D027425:ATP-Binding Cassette, Sub-Family C Proteins; D051718:MutS Homolog 2 Protein; D000074081:MutS Homolog 3 Protein; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D011518:Proto-Oncogene Proteins; D012313:RNA; C078444:MSH3 protein, human; C039919:RNA, recombinant; C497173:Msh2 protein, mouse; C421109:multidrug resistance-associated protein 1