The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical Study
The in vivo effectiveness of DNAzymes 10-23 (Dz10-23) is limited due to the low concentration of divalent cations. Modifications of the catalytic loop are being sought to increase the activity of Dz10-23 in physiological conditions. We investigated the effect of 5′S or 5′R 5′,8-cyclo-2′deoxyadenosin...
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MDPI AG
2024-02-01
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| author | Marcin Cieślak Bolesław T. Karwowski |
| author_facet | Marcin Cieślak Bolesław T. Karwowski |
| author_sort | Marcin Cieślak |
| collection | DOAJ |
| description | The in vivo effectiveness of DNAzymes 10-23 (Dz10-23) is limited due to the low concentration of divalent cations. Modifications of the catalytic loop are being sought to increase the activity of Dz10-23 in physiological conditions. We investigated the effect of 5′S or 5′R 5′,8-cyclo-2′deoxyadenosine (cdA) on the activity of Dz10-23. The activity of Dz10-23 was measured in a cleavage assay using radiolabeled RNA. The Density Functional Tight Binding methodology with the self-consistent redistribution of Mulliken charge modification was used to explain different activities of DNAzymes. The substitution of 2′-deoxyadenosine with cdA in the catalytic loop decreased the activity of DNAzymes. Inhibition was dependent on the position of cdA and its absolute configuration. The order of activity of DNAzymes was as follows: wt-Dz > <i>S</i>cdA5-Dz ≈ <i>R</i>cdA15-Dz ≈ <i>S</i>cdA15-Dz > <i>R</i>cdA5-Dz. Theoretical studies revealed that the distance between phosphate groups at position 5 in <i>R</i>cdA5-Dz was significantly increased compared to wt-Dz, while the distance between O4 of dT4 and nonbonding oxygen of PO<sub>2</sub> attached to 3′O of dG2 was much shorter. The strong inhibitory effect of RcdA5 may result from hampering the flexibility of the catalytic loop (increased rigidity), which is required for the proper positioning of Me<sup>2+</sup> and optimal activity. |
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| last_indexed | 2024-04-25T00:29:05Z |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-8249dc78f32849e6a70e3c87f1a89e412024-03-12T16:45:16ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-02-01255251910.3390/ijms25052519The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical StudyMarcin Cieślak0Bolesław T. Karwowski1Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, PolandFood Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, PolandThe in vivo effectiveness of DNAzymes 10-23 (Dz10-23) is limited due to the low concentration of divalent cations. Modifications of the catalytic loop are being sought to increase the activity of Dz10-23 in physiological conditions. We investigated the effect of 5′S or 5′R 5′,8-cyclo-2′deoxyadenosine (cdA) on the activity of Dz10-23. The activity of Dz10-23 was measured in a cleavage assay using radiolabeled RNA. The Density Functional Tight Binding methodology with the self-consistent redistribution of Mulliken charge modification was used to explain different activities of DNAzymes. The substitution of 2′-deoxyadenosine with cdA in the catalytic loop decreased the activity of DNAzymes. Inhibition was dependent on the position of cdA and its absolute configuration. The order of activity of DNAzymes was as follows: wt-Dz > <i>S</i>cdA5-Dz ≈ <i>R</i>cdA15-Dz ≈ <i>S</i>cdA15-Dz > <i>R</i>cdA5-Dz. Theoretical studies revealed that the distance between phosphate groups at position 5 in <i>R</i>cdA5-Dz was significantly increased compared to wt-Dz, while the distance between O4 of dT4 and nonbonding oxygen of PO<sub>2</sub> attached to 3′O of dG2 was much shorter. The strong inhibitory effect of RcdA5 may result from hampering the flexibility of the catalytic loop (increased rigidity), which is required for the proper positioning of Me<sup>2+</sup> and optimal activity.https://www.mdpi.com/1422-0067/25/5/25198,5′-cyclo 2′-deoxyadenosineDNAzyme 10-23catalytic DNAmolecular dynamicsDNA damage |
| spellingShingle | Marcin Cieślak Bolesław T. Karwowski The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical Study International Journal of Molecular Sciences 8,5′-cyclo 2′-deoxyadenosine DNAzyme 10-23 catalytic DNA molecular dynamics DNA damage |
| title | The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical Study |
| title_full | The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical Study |
| title_fullStr | The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical Study |
| title_full_unstemmed | The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical Study |
| title_short | The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical Study |
| title_sort | effect of 8 5 cyclo 2 deoxyadenosine on the activity of 10 23 dnazyme experimental and theoretical study |
| topic | 8,5′-cyclo 2′-deoxyadenosine DNAzyme 10-23 catalytic DNA molecular dynamics DNA damage |
| url | https://www.mdpi.com/1422-0067/25/5/2519 |
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