Bifacial Base‐Pairing Behaviors of 5‐Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination

Abstract

A novel bifacial ligand-bearing nucleobase, 5-hydroxyuracil (U(OH) ), which forms both a hydrogen-bonded base pair (U(OH) -A) and a metal-mediated base pair (U(OH) -M-U(OH) ) has been developed. The U(OH) -M-U(OH) base pairs were quantitatively formed in the presence of lanthanide ions such as Gd(III) when U(OH) -U(OH) pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing U(OH) -A base pairs was destabilized by addition of Gd(III) ions. This observation suggests that the hybridization behaviors of the U(OH) -containing DNA strands are altered by metal complexation. Thus, the U(OH) nucleobase with a bifacial base-pairing property holds great promise as a component for metal-responsive DNA materials.

pH-Dependence of the thermal stability of metallo-DNA duplexes containing ligand-type 5-hydroxyuracil nucleobases

“…Our previous study revealed that most of the lanthanide ions and Zn(II) ions affected the thermal stability of the U OH -containing DNA duplexes [31]. Based on the results, Gd(III) and Zn(II) ions were chosen to investigate the pH dependence of metal complexation.…”

“…In addition, as it is well known that the U OH base forms a Watson-Crick-type hydrogenbonded base pair with adenine nucleobase (U OH -A) [32][33][34][35], it therefore shows bifacial base pairing behaviors. The U OH -Gd(III)-U OH base paring thermally stabilized the DNA duplexes, while addition of Gd(III) ions to the U OH -A base pairs caused a duplex destabilization [31]. Metal complexation of the U OH bases accompanied the deprotonation of the 5-OH group.…”

“…In this study, we have investigated pH dependence of a metalmediated base pair consisting of two 5-hydroxyuracil (U OH ) nucleobases [31]. The U OH nucleobase has a hard O,O-bidentate ligand, i.e.…”

Artificial DNA Base Pairing Mediated by Diverse Metal Ions

“…70 The carbonyl oxygen atom and the 5-hydroxy group offer a bidentate metal coordination site for metalmediated base pairing. Figure 10 for clarity).…”

“…Schematic representation of bifacial base pairing behaviors of U OH nucleobases, which form both metal-mediated U OH Gd III U OH base pairs and hydrogen-bonded U OH A base pairs. 70 Other possible coordinating ligands on the Gd 3+ ions are not shown for clarity. incorporated a dATP 107 or a dTTP 108 opposite a template C possibly through the formation of Ag(I)-mediated AAg I C or TAg I C base pairs (Figures 11b and 11c).…”