title: Sequence-targeted cleavage of nucleic acids by oligo-alpha-thymidylate-phenanthroline conjugates: parallel and antiparallel double helices are formed with DNA and RNA, respectively.
abstract: Oligodeoxynucleotides can be synthesized by using the alpha anomers of nucleoside units. Oligo-alpha-deoxynucleotides are resistant to nucleases and could be used to regulate gene expression in vivo. Theoretical calculations were carried out to determine the conformational energy of an oligomeric alpha-beta duplex (dA)5.(dT)5 where the adenosine strand contains natural beta-deoxyribonucleotides and the thymidine strand contains synthetic alpha-deoxyribonucleotides. These calculations predict that in the more stable B-like conformation the two strands of the double helix should run parallel to each other whereas in the more stable A-like conformation the two strands should adopt an antiparallel orientation. In order to test these predictions 1,10-phenanthroline was covalently attached to the 5'-end of an alpha-octathymidylate. In the presence of copper ions and a reducing agent (beta-mercaptopropionic acid), the (phenanthroline)2-copper complex generates OH. radicals that cleave phosphodiester bonds in the complementary sequence to which the alpha-octathymidylate is bound. By use of a 27mer oligo-beta-deoxynucleotide containing an octadeoxyadenylate sequence as a target for the phenanthroline-substituted alpha-(dT)8, cleavage was observed on the 5'-side of the (dA)8 sequence, demonstrating that the alpha-beta DNA-DNA hybrid formed a double helix with parallel orientation of the two strands. The same result was obtained when alpha-(dT)8 was bound to beta-(dA)n with n = 8 or 10. When a beta-oligoriboadenylate was used as a target, cleavage occurred exclusively on the 3'-side of the (rA)8 or (rA)10 sequence, indicating that the alpha-beta DNA-RNA hybrid formed a double helix with an antiparallel orientation of the two strands. When a phenanthroline-substituted beta-octathymidylate was used instead of the alpha-octathymidylate, an antiparallel double helix was formed independently of whether the target beta sequence was a DNA or an RNA.
authors: Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U.201, CNRS UA.481, Paris, France.
authors: J S
authors: JS
authors: Sun
authors: J C
authors: JC
authors: François
authors: R
authors: R
authors: Lavery
authors: T
authors: T
authors: Saison-Behmoaras
authors: T
authors: T
authors: Montenay-Garestier
authors: N T
authors: NT
authors: Thuong
authors: C
authors: C
authors: Hélène
mesh_terms: D001483:Base Sequence; D004247:DNA; D004277:DNA, Single-Stranded; D009690:Nucleic Acid Conformation; D010618:Phenanthrolines; D012313:RNA; D013816:Thermodynamics; D013942:Thymine Nucleotides
chemical_list: D004277:DNA, Single-Stranded; D010618:Phenanthrolines; D013942:Thymine Nucleotides; D012313:RNA; D004247:DNA