Metal ion-directed dynamic splicing of DNA through global conformational change by intramolecular complexation

Ihara, Toshihiro; Ohura, Hiroyuki; Shirahama, Chisato; Furuzono, Tomohiro; Shimada, Hiroshi; Matsuura, Haruaki; Kitamura, Yusuke

doi:10.1038/ncomms7640

Cited by 19 publications

(6 citation statements)

References 60 publications

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“…Meanwhile, a variety of metal-mediated base pairs formed from artificial ligand-type nucleotides have been developed thus far and reported to show diverse metal selectivity . The use of metal ions that barely interfere with natural nucleotides (other than Hg II and Ag I ) is expected to contribute largely to the development of metal-responsive DNA materials, − especially in terms of the rational design. However, the application of such metallo-base pairs has been relatively poorly explored, mainly due to the cumbersome chemical synthesis required for DNA strands possessing artificial ligand-bearing nucleotides.…”

Section: Introductionmentioning

confidence: 99%

Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides

2019

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Metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, have shown promise as functional units to develop stimuli-responsive DNA materials. Although a variety of metal-mediated base pairs have been constructed with artificial ligand-type nucleotides and various metal ions, the application of such metal-mediated base pairs has been relatively poorly explored mainly due to the cumbersome chemical synthesis of artificial DNA strands. Herein we report a facile enzymatic method to synthesize DNA strands containing a ligand-type hydroxypyridone (H) nucleotide, which forms a Cu II -mediated base pair (H−Cu II −H). A two-step primer extension reaction using two commercially available polymerases enabled the incorporation of a H nucleotide at an internal position of oligonucleotides. The polymerase synthesis was subsequently applied to the development of metal-responsive deoxyribozymes (DNAzymes), whose catalytic activity was regulated by the formation of a single H−Cu II − H base pair in its stem region. The DNAzyme activity was reversibly switched by the alternate addition and the removal of Cu II ions. Furthermore, metal-dependent orthogonal activation of a Cu II -responsive H-DNAzyme and a Hg II -responsive T-DNAzyme was experimentally demonstrated by utilizing both H−Cu II −H as well as widely explored T−Hg II −T base pairs. These results suggest that the incorporation of H−Cu II −H base pairs would facilitate the rational design of metal-responsive functional DNAs. Accordingly, the facile enzymatic synthesis of artificial ligand-bearing DNAs developed in this study would significantly expand the toolbox of DNA-based supramolecular chemistry and DNA nanotechnology.

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Section: Introductionmentioning

confidence: 99%

Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides

2019

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“…Nevertheless, two sets of characteristic tpy signals spread out in a wide range (20–100 ppm) corresponding to the ⟨tpy–Co(II)–tpy⟩ connectivity were identified in the proton NMR, supporting formation of the proposed intermediate L·Co (Figure S24). We speculated that exclusive formation of the intermediate was energetically more favorable through intramolecular complexation rather than intermolecular complexation . In addition, those intermediates are reminiscent of folding in protein structures, resulting from conformational regulation .…”

Section: Resultsmentioning

confidence: 99%

Self-Assembly of Metallo-Supramolecules under Kinetic or Thermodynamic Control: Characterization of Positional Isomers Using Scanning Tunneling Spectroscopy

Wang

Song

et al. 2020

J. Am. Chem. Soc.

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Coordination-driven self-assembly has been extensively employed to construct a variety of discrete structures as a bottom-up strategy. However, mechanistic understanding regarding whether self-assembly is under kinetic or thermodynamic control is less explored. To date, such mechanistic investigation has been limited to distinct, assembled structures. It still remains a formidable challenge to study the kinetic and thermodynamic behavior of self-assembly systems with multiple assembled isomers due to the lack of characterization methods. Herein, we use a stepwise strategy which combined self-recognition and self-assembly processes to construct giant metallo-supramolecules with 8 positional isomers in solution. With the help of ultrahigh-vacuum, low-temperature scanning tunneling microscopy and scanning tunneling spectroscopy, we were able to unambiguously differentiate 14 isomers on the substrate which correspond to 8 isomers in solution. Through measurement of 162 structures, the experimental probability of each isomer was obtained and compared with the theoretical probability. Such a comparison along with density functional theory (DFT) calculation suggested that although both kinetic and thermodynamic control existed in this self-assembly, the increased experimental probabilities of isomers compared to theoretical probabilities should be attributed to thermodynamic control.

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“…By the specific formation of an intramolecular metal complex, a part of the sequence of the DNA in between the two terpyridine units was reversibly excluded, and the two flanking external DNA segments were directly connected with each other to form an Ω-shaped structure presenting a new sequence ( Figure 2 ). This can be regarded as a metal ion-directed reversible edition of the DNA sequence or dynamic DNA splicing [ 26 ].…”

Section: Metal Ion-directed Dynamic Splicing Of Dna Through Global Co...mentioning

confidence: 99%

“…Figure 3 b shows the time course of the reaction profiles. Equivalent concentrations of Fe 2+ and Ni 2+ ( r = 1) restored the activity of the split DNAzyme in the presence of terpy 2 DNA [ 26 ]. Cu 2+ and Zn 2+ also showed a moderate effect on the restoration of split DNAzyme activity.…”

Section: Metal Ion-directed Dynamic Splicing Of Dna Through Global Co...mentioning

confidence: 99%

Metal Ion-Directed Specific DNA Structures and Their Functions

Ihara

Kitamura

Katsuda

2022

Life

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Various DNA structures, including specific metal ion complexes, have been designed based on the knowledge of canonical base pairing as well as general coordination chemistry. The role of metal ions in these studies is quite broad and diverse. Metal ions can be targets themselves in analytical applications, essential building blocks of certain DNA structures that one wishes to construct, or they can be responsible for signal generation, such as luminescence or redox. Using DNA conjugates with metal chelators, one can more freely design DNA complexes with diverse structures and functions by following the simple HSAB rule. In this short review, the authors summarize a part of their DNA chemistries involving specific metal ion coordination. It consists of three topics: (1) significant stabilization of DNA triple helix by silver ion; (2) metal ion-directed dynamic sequence edition through global conformational change by intramolecular complexation; and (3) reconstruction of luminescent lanthanide complexes on DNA and their analytical applications.

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Metal ion-directed dynamic splicing of DNA through global conformational change by intramolecular complexation

Cited by 19 publications

References 60 publications

Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides

Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides

Self-Assembly of Metallo-Supramolecules under Kinetic or Thermodynamic Control: Characterization of Positional Isomers Using Scanning Tunneling Spectroscopy

Metal Ion-Directed Specific DNA Structures and Their Functions

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