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

Nishiyama, Kotaro; Takezawa, Yusuke; Shionoya, Mitsuhiko

doi:10.1016/j.ica.2016.04.040

Cited by 28 publications

(18 citation statements)

References 42 publications

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“…5-Hydroxyuracil ( OH U) is ap yrimidine derivative with fascinating base pairing properties.Inthe absence of suitable metal ions,itis amimic of thymine and uracil and hence forms stable Watson-Crick base pairs with ac omplementary adenine. [35] However,provided that coordinating metal ions are present and that the hydroxyl substituent is deprotonated for subsequent metalation, [35b] it prefers to engage in metalmediated base pairing (Figure 4g). This nucleobase has been used to generate the first metal-mediated base pairs involving lanthanides.A sh ydrogen bonding and metal coordination take place via different faces of the nucleobase,i th as been proposed for ametal-triggered hybridization of DNAstrands, possibly involving strand exchange reactions.…”

Section: Angewandte Chemiementioning

confidence: 99%

“…By incorporating pyridine nucleosides Pyr into the center of the triplex d(T 10 PyrT 10 )·d(A 10 PyrA 10 )*d(T 10 PyrT 10 ), as table triple helix was obtained. As its thermal stability was significantly increased in the presence of Ag I ions, [26,28] b) Im Phen-Hg II -T; [29] c) Im Phen-Ag I -C; [29] d) eA-Ag I 2 -eA; [32] e) eA-Hg II 2 -T; [33] f) COO Im-Cu II -COO Im; [34] g) OH U-M-OH U(M= for example, Gd III ,Z n II ); [35] h) C Hg -T; [36] i) Phe Py Pd -T. [37] R, R' = DNA backbone.…”

Section: Triple Helicesmentioning

confidence: 99%

“…In the absence of suitable metal ions, it is a mimic of thymine and uracil and hence forms stable Watson–Crick base pairs with a complementary adenine . However, provided that coordinating metal ions are present and that the hydroxyl substituent is deprotonated for subsequent metalation, it prefers to engage in metal‐mediated base pairing (Figure g). This nucleobase has been used to generate the first metal‐mediated base pairs involving lanthanides.…”

Section: Metal‐mediated Base Pairsmentioning

confidence: 99%

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Metal‐Modified Nucleic Acids: Metal‐Mediated Base Pairs, Triples, and Tetrads

2019

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The incorporation of metal ions into nucleic acids by means of metal‐mediated base pairs represents a promising and prominent strategy for the site‐specific decoration of these self‐assembling supramolecules with metal‐based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal‐binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI‐mediated base pairing, due to their expected compatibility with regular Watson–Crick base pairs. This minireview summarizes these advances in metal‐mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal‐modified nucleic acids, highlighting an expansion of the concept to metal‐mediated base triples (in triple helices and three‐way junctions) and metal‐mediated base tetrads (in quadruplexes). For all types of metal‐modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.

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Section: Angewandte Chemiementioning

confidence: 99%

Section: Triple Helicesmentioning

confidence: 99%

Section: Metal‐mediated Base Pairsmentioning

confidence: 99%

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Metal‐Modified Nucleic Acids: Metal‐Mediated Base Pairs, Triples, and Tetrads

2019

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“…We have so far developed several metal-mediated artificial base pairs [ 12 , 13 , 14 , 15 , 16 ] including Cu II -mediated hydroxypyridone self-base pair ( H –Cu II – H ). The H –Cu II – H base pair is composed of two bidentate hydoxypyridone-bearing nucleotides ( H ) and a Cu II ion [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

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

Takezawa

Kobayashi

Shionoya

2016

IJMS

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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–CuII–H). 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.

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“…In Abwesenheit geeigneter Metallionen verhält es sich wie Thymin und Uracil und bildet stabile Watson‐Crick‐Basenpaare mit einem komplementären Adenin aus . Sind jedoch koordinierende Metallionen vorhanden und ist die Hydroxygruppe für eine folgende Metallierung deprotoniert, so bevorzugt es die Ausbildung metallvermittelter Basenpaare (Abbildung g). Diese Nukleobase wurde eingesetzt, um das erste metallvermittelte Basenpaar mit Lanthanoiden zu erzeugen.…”

Section: Metallvermittelte Basenpaareunclassified

Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden

2019

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Das Einbringen von Metallionen in Nukleinsäuren mittels metallvermittelter Basenpaare stellt eine vielversprechende und weit verbreitete Methode zur ortsspezifischen Modifizierung dieser selbstassemblierenden Supramoleküle mit metallbasierter Funktionalität dar. In den vergangenen 20 Jahren wurden zahlreiche solcher Nukleosid‐Surrogate entwickelt, die die Bandbreite an Metallen durch perfekt zugeschnittene Metallbindungsstellen erweitert haben. In jüngster Vergangenheit rückten künstliche, von natürlichen Purin‐ und Pyrimidinbasen abgeleitete Nukleoside durch die erwartete Kompatibilität mit Watson‐Crick‐Basenpaaren in den Fokus AgI‐vermittelter Basenpaare. Dieser Kurzaufsatz fasst diese sowie weitere aktuelle Entwicklungen auf dem Gebiet metallvermittelter Basenpaare zusammen. Zudem befasst er sich mit weiteren Aspekten metallmodifizierter Nukleinsäuren, indem er eine Erweiterung des Konzepts auf metallvermittelte Basentripel (in Dreifachhelices und dreiarmigen DNA‐Kreuzungen) sowie ‐tetraden (in Quadruplexen) behandelt. Für alle Arten metallmodifizierter Nukleinsäuren werden darüber hinaus postulierte oder bereits erreichte Anwendungen kurz erwähnt.

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

Cited by 28 publications

References 42 publications

Metal‐Modified Nucleic Acids: Metal‐Mediated Base Pairs, Triples, and Tetrads

Metal‐Modified Nucleic Acids: Metal‐Mediated Base Pairs, Triples, and Tetrads

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

Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden

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