Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom Phosphodiesterase
Antisense oligonucleotides conjugated with boron clusters (B-ASOs) have been described as potential gene expression inhibitors and carriers of boron for boron neutron capture therapy (BNCT), providing a dual-action therapeutic platform. In this study, we tested the nucleolytic stability of DNA oligo...
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MDPI AG
2020-05-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/10/5/718 |
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| author | Damian Kaniowski Katarzyna Kulik Katarzyna Ebenryter-Olbińska Ewelina Wielgus Zbigniew Lesnikowski Barbara Nawrot |
| author_facet | Damian Kaniowski Katarzyna Kulik Katarzyna Ebenryter-Olbińska Ewelina Wielgus Zbigniew Lesnikowski Barbara Nawrot |
| author_sort | Damian Kaniowski |
| collection | DOAJ |
| description | Antisense oligonucleotides conjugated with boron clusters (B-ASOs) have been described as potential gene expression inhibitors and carriers of boron for boron neutron capture therapy (BNCT), providing a dual-action therapeutic platform. In this study, we tested the nucleolytic stability of DNA oligonucleotides labeled with metallacarborane [(3,3’-iron-1,2,1’,2’-dicarbollide)(−1)]ate [Fe(C<sub>2</sub>B<sub>9</sub>H<sub>11</sub>)<sub>2</sub>] (FESAN) against snake venom phosphodiesterase (svPDE, 3’→5’-exonuclease). Contrary to the previously observed protective effect of carborane (C<sub>2</sub>B<sub>10</sub>H<sub>12</sub>) modifications, the B-ASOs containing a metallacarborane moiety at the 5’-end of the oligonucleotide chain were hydrolyzed faster than their parent nonmodified oligomers. Interestingly, an enhancement in the hydrolysis rate was also observed in the presence of free metallacarborane, and this reaction was dependent on the concentration of the metallacarborane. Microscale thermophoresis (MST) analysis confirmed the high affinity (<i>K</i><sub>d</sub> nM range) of the binding of the metallacarborane to the proteins of crude snake venom and the moderate affinity (<i>K</i><sub>d</sub> µM range) between the metallacarborane and the short single-stranded DNA. We hypothesize that the metallacarborane complex covalently bound to B-ASO holds DNA molecules close to the protein surface, facilitating enzymatic cleavage. The addition of metallacarborane alone to the ASO/svPDE reaction mixture provides the interface to attract freely floating DNA molecules. In both cases, the local DNA concentration around the enzymes increases, giving rise to faster hydrolysis. It was experimentally shown that an allosteric effect, possibly attributable to the observed boost in the 3’→5’-exonucleolytic activity of snake venom phosphodiesterase, is much less plausible. |
| first_indexed | 2024-03-10T20:01:15Z |
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| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T20:01:15Z |
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| spelling | doaj.art-5f873b141b914ea4a249834f6ef55d8c2023-11-19T23:33:04ZengMDPI AGBiomolecules2218-273X2020-05-0110571810.3390/biom10050718Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom PhosphodiesteraseDamian Kaniowski0Katarzyna Kulik1Katarzyna Ebenryter-Olbińska2Ewelina Wielgus3Zbigniew Lesnikowski4Barbara Nawrot5Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, PolandCentre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, PolandCentre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, PolandCentre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, PolandInstitute of Medical Biology, Polish Academy of Sciences, Laboratory of Medicinal Chemistry, 106 Lodowa St., 92-232 Lodz, PolandCentre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, PolandAntisense oligonucleotides conjugated with boron clusters (B-ASOs) have been described as potential gene expression inhibitors and carriers of boron for boron neutron capture therapy (BNCT), providing a dual-action therapeutic platform. In this study, we tested the nucleolytic stability of DNA oligonucleotides labeled with metallacarborane [(3,3’-iron-1,2,1’,2’-dicarbollide)(−1)]ate [Fe(C<sub>2</sub>B<sub>9</sub>H<sub>11</sub>)<sub>2</sub>] (FESAN) against snake venom phosphodiesterase (svPDE, 3’→5’-exonuclease). Contrary to the previously observed protective effect of carborane (C<sub>2</sub>B<sub>10</sub>H<sub>12</sub>) modifications, the B-ASOs containing a metallacarborane moiety at the 5’-end of the oligonucleotide chain were hydrolyzed faster than their parent nonmodified oligomers. Interestingly, an enhancement in the hydrolysis rate was also observed in the presence of free metallacarborane, and this reaction was dependent on the concentration of the metallacarborane. Microscale thermophoresis (MST) analysis confirmed the high affinity (<i>K</i><sub>d</sub> nM range) of the binding of the metallacarborane to the proteins of crude snake venom and the moderate affinity (<i>K</i><sub>d</sub> µM range) between the metallacarborane and the short single-stranded DNA. We hypothesize that the metallacarborane complex covalently bound to B-ASO holds DNA molecules close to the protein surface, facilitating enzymatic cleavage. The addition of metallacarborane alone to the ASO/svPDE reaction mixture provides the interface to attract freely floating DNA molecules. In both cases, the local DNA concentration around the enzymes increases, giving rise to faster hydrolysis. It was experimentally shown that an allosteric effect, possibly attributable to the observed boost in the 3’→5’-exonucleolytic activity of snake venom phosphodiesterase, is much less plausible.https://www.mdpi.com/2218-273X/10/5/718antisense oligonucleotidemetallacarboraneboron clustersnake venomphosphodiesteraseexonuclease |
| spellingShingle | Damian Kaniowski Katarzyna Kulik Katarzyna Ebenryter-Olbińska Ewelina Wielgus Zbigniew Lesnikowski Barbara Nawrot Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom Phosphodiesterase Biomolecules antisense oligonucleotide metallacarborane boron cluster snake venom phosphodiesterase exonuclease |
| title | Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom Phosphodiesterase |
| title_full | Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom Phosphodiesterase |
| title_fullStr | Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom Phosphodiesterase |
| title_full_unstemmed | Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom Phosphodiesterase |
| title_short | Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom Phosphodiesterase |
| title_sort | metallacarborane complex boosts the rate of dna oligonucleotide hydrolysis in the reaction catalyzed by snake venom phosphodiesterase |
| topic | antisense oligonucleotide metallacarborane boron cluster snake venom phosphodiesterase exonuclease |
| url | https://www.mdpi.com/2218-273X/10/5/718 |
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