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Int. J. Mol. Sci. 2016, 17(6), 906; doi:10.3390/ijms17060906

The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase

Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Academic Editor: Eva Freisinger
Received: 12 May 2016 / Revised: 3 June 2016 / Accepted: 4 June 2016 / Published: 8 June 2016
(This article belongs to the Special Issue Applied Bioinorganic Chemistry and Selected Papers from 13th ISABC)
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Abstract

A metal-mediated base pair, composed of two ligand-bearing nucleotides and a bridging metal ion, is one of the most promising components for developing DNA-based functional molecules. We have recently reported an enzymatic method to synthesize hydroxypyridone (H)-type ligand-bearing artificial DNA strands. Terminal deoxynucleotidyl transferase (TdT), a template-independent DNA polymerase, was found to oligomerize H nucleotides to afford ligand-bearing DNAs, which were subsequently hybridized through copper-mediated base pairing (H–CuIIH). In this study, we investigated the effects of a metal cofactor, MgII ion, on the TdT-catalyzed polymerization of H nucleotides. At a high MgII concentration (10 mM), the reaction was halted after several H nucleotides were appended. In contrast, at lower MgII concentrations, H nucleotides were further appended to the H-tailed product to afford longer ligand-bearing DNA strands. An electrophoresis mobility shift assay revealed that the binding affinity of TdT to the H-tailed DNAs depends on the MgII concentration. In the presence of excess MgII ions, TdT did not bind to the H-tailed strands; thus, further elongation was impeded. This is possibly because the interaction with MgII ions caused folding of the H-tailed strands into unfavorable secondary structures. This finding provides an insight into the enzymatic synthesis of longer ligand-bearing DNA strands. View Full-Text
Keywords: artificial DNA; metal-mediated base pair; enzymatic synthesis; DNA polymerase; bioinorganic chemistry artificial DNA; metal-mediated base pair; enzymatic synthesis; DNA polymerase; bioinorganic chemistry
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Takezawa, Y.; Kobayashi, T.; Shionoya, M. The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase. Int. J. Mol. Sci. 2016, 17, 906.

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