1,3,9‐Triaza‐2‐oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self‐Base Pairs with Three Ag<sup>I</sup> Ions in a Duplex

Fujii, Akane; Nakagawa, Osamu; Kishimoto, Yuki; Okuda, Tohru; Nakatsuji, Yusuke; Nozaki, Natsumi; Kasahara, Yuuya; Obika, Satoshi

doi:10.1002/chem.201900373

Cited by 31 publications

(35 citation statements)

References 87 publications

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“…Very recently, the T m values of duplexes containing fully matched and mismatched base pairs consisting of cytosine with each of the four natural bases in the presence or in the absence of Ag I ions were reported, but no detailed explanations on this matter were provided . The study indicated that the Δ T m values of duplexes containing a C‐C, a C‐A or a C‐T mismatch on addition of Ag I ions are +12, +9, and +3 to +6 °C, respectively.…”

Section: Resultsmentioning

confidence: 99%

Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

et al. 2019

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Spectroscopic characterization of AgI‐ion‐mediated C‐AgI‐A and C‐AgI‐T base pairs found in primer extension reactions catalyzed by DNA polymerases was conducted. UV melting experiments revealed that C‐A and C‐T mismatched base pairs in oligodeoxynucleotide duplexes are specifically stabilized by AgI ions in 1:1 stoichiometry in the same manner as a C‐C mismatched base pair. Although the stability of the mismatched base pairs in the absence of AgI ions is in the order C‐A≈C‐T>C‐C, the stabilizing effect of AgI ions follows the order C‐C>C‐A≈C‐T. However, the comparative susceptibility of dNTPs to AgI‐mediated enzymatic incorporation into the site opposite templating C is dATP>dTTP≫dCTP, as reported. The net charge, as well as the size and/or shape complementarity of the metal‐mediated base pairs, or the stabilities of mismatched base pairs in the absence of metal ions, would be more important than the stability of the metallo‐base pairs in the replicating reaction catalyzed by DNA polymerases.

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Section: Resultsmentioning

confidence: 99%

Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

et al. 2019

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“…We have previously reported that 9‐TAP showed fluorescence at 440 nm with excitation at 365 nm at pH 7.0 . The fluorescence quantum yields of the P and N nucleosides were 0.17 and 0.28, respectively.…”

Section: Resultsmentioning

confidence: 92%

“…TFOs (15‐mers) containing phenoxazine ( P ) and 9‐TAP ( N ) components were successfully synthesized according to our previous report (Figures S1 and S2 in the Supporting Information) …”

Section: Resultsmentioning

confidence: 99%

“…Synthesis of TFOs containing 9‐TAP : TFOs containing 9‐TAP ( N ) were synthesized according to our previous report …”

Section: Methodsmentioning

confidence: 99%

“…We recently developed a new phenoxazine analogue in the form of the 1,3,9‐triaza‐2‐oxophenoxazine (9‐TAP, N ; Scheme ) system . It displayed easy tautomerization between N1 and N10 thanks to the electron‐withdrawing effect of N9, and functioned as both a thymine (T) and a cytosine (C) analogue.…”

Section: Introductionmentioning

confidence: 99%

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Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex‐Forming Abilities and Fluorescence Properties

et al. 2019

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1,3‐Diaza‐2‐oxophenoxazine (“phenoxazine”), a tricyclic cytosine analogue, can strongly bind to guanine moieties and improve π–π stacking effects with adjacent bases in a duplex. Phenoxazine has been widely used for improving duplex‐forming abilities. In this study, we have investigated whether phenoxazine and its analogue, 1,3,9‐triaza‐2‐oxophenoxazine (9‐TAP), could improve triplex‐forming abilities. A triplex‐forming oligonucleotide (TFO) incorporating a phenoxazine component was found to show considerably decreased binding affinity with homopurine/homopyrimidine double‐stranded DNA, so the phenoxazine system was considered not to function as either a protonated cytosine or thymine analogue. Alternatively, a 9‐TAP‐containing artificial nucleobase developed by us earlier as a new phenoxazine analogue functioned as a thymine analogue with respect to AT base pairs in a parallel triplex DNA motif. The fluorescence of the 9‐TAP moiety was maintained even in triplex (9‐TAP:AT) formation, so 9‐TAP might be useful as an imaging tool for various oligonucleotide nanotechnologies requiring triplex formation.

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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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1,3,9‐Triaza‐2‐oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self‐Base Pairs with Three Ag^I Ions in a Duplex

Abstract: This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record.

Cited by 31 publications

References 87 publications

Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex‐Forming Abilities and Fluorescence Properties

Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden

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1,3,9‐Triaza‐2‐oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self‐Base Pairs with Three AgI Ions in a Duplex

Abstract: This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record.

Cited by 31 publications

References 87 publications

Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex‐Forming Abilities and Fluorescence Properties

Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden

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1,3,9‐Triaza‐2‐oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self‐Base Pairs with Three Ag^I Ions in a Duplex