Sequence-Selective Cleavage of Oligoribonucleotides by 3d Transition Metal Complexes of 1,5,9-Triazacyclododecane-Functionalized 2‘-O-Methyl Oligoribonucleotides

Abstract

2'-O-Methyl oligoribonucleotides bearing a 3'-[2,6-dioxo-3,7-diaza-10-(1,5,9-triazacyclododec-3-yl)decyl phospate conjugate group have been shown to cleave in slight excess of Zn(2+) ions complementary oligoribonucleotides at the 5'-side of the last base-paired nucleotide. The cleavage obeys first-order kinetics and exhibits turnover. The acceleration compared to the monomeric Zn(2+) 1,5,9-triazacyclododecane chelate is more than 100-fold. In addition, 2'-O-methyl oligoribonucleotides having the 1,5,9-triazacyclododec-3-yl group tethered to the anomeric carbon of an intrachain 2-deoxy-beta-d-erythro-pentofuranosyl group via a 2-oxo-3-azahexyl, 2,6-dioxo-3,7-diazadecyl, or 2,9-dioxo-3,10-diazatridecyl linker have been studied as cleaving agents. These cleave as zinc chelates a tri- and pentaadenyl bulge opposite to the conjugate group approximately 50 times as fast as the monomeric chelate and show turnover. The cleavage rate is rather insensitive to the length of linker. Interestingly, a triuridyl bulge remains virtually intact in striking contrast to a triadenyl bulge. Evidently binding of the zinc chelate to a uracil base prevents its catalytic action. Replacement of Zn(2+) with Cu(2+) or Ni(2+) retards the cleaving activity of all the cleaving agents tested.

Artificial ribonucleases

“…55 The cleaving activity of both 3 -terminal (16,17) and intrastrand (18a-c) conjugates have been tested at pH 7.3 and 35 • C in 1 : 1 mixtures of the conjugate and target and in excess of the target. 29, 30 Both types of conjugates show turnover, in spite of the fact that the cleavage with 16-Zn 2+ and 17-Zn 2+ takes place outside the complementary region of the ORN target, viz. one nucleotide from the last base pair towards the 5 -end of the target.…”

“…one nucleotide from the last base pair towards the 5 -end of the target. 30 The cleavage efficiency is surprisingly sensitive to the structure of 3 -terminal linker. Although the linkers in conjugates 16 and 17 are approximately as long (10 and 12 atoms from the 3 -terminal phosphate, respectively), the disulfide linker (17) affords an 8 times higher cleavage rate than the b-peptide linker (16).…”

DNA-Dinucleotides Bearing a 3‘,3‘-Cobalt- or 3‘,3‘-Iron-1,2,1‘,2‘-dicarbollide Complex

“…Metal centers are usually attached to the nucleoside unit or to an internucleotide or a terminal phosphate group of DNA in the form of their metal complexes. In the majority of cases chelators are used as vectors for the metal ions. , One of the few exceptions is the metallocene type of complex, with the best known example being ferrocene. , The only other examples of nucleoside/metallocene type conjugate reported so far are nucleoside/metallacarborane modifications. , Recently we described a general method for the synthesis of conjugates of all four canonical nucleosidess, T, dC, dA, and dG, and metallacarboranes containing cobalt . Incorporation of thymidine conjugate into a DNA oligomer via the phosphoramidite method was also shown …”

DNA as Platform for New Biomaterials. Metal-Containing Nucleic Acids

“…Another class of sequenece-specific artificial chemical nucleases are 1,5,9-triazacyclodecane-functionalized 2'-Omethyl oligoribonucleotides [102]. It has been shown previously that azacrowns type of 1,5,9-triazacyclodecane bind 3d transition metal ions very tightly and promote efficient hydrolysis of RNA [103,104].…”