Nanoparticles of Adaptive Supramolecular Networks Self-Assembled from Nucleotides and Lanthanide Ions

Nishiyabu, Ryuhei; Hashimoto, Nozomi; Cho, Ten; Watanabe, Kazuto; Yasunaga, Tomohide; Endo, Ayataka; Kaneko, Kenji; Niidome, Takuro; Murata, Masaru; Adachi, Chihaya; Katayama, Yoshiki; Hashizume, Makoto; Kimizuka, Nobuo

doi:10.1021/ja8058843

Cited by 324 publications

(281 citation statements)

References 42 publications

(53 reference statements)

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“…the hammerhead ribozyme, 32 HDV ribozyme, 33 [10][11][12][13][14][15][16][17][18][19][20][21][22][23] DNAzyme, 37 RNase P, 38 Group II intron, 39 ) use pro-Rp for metal binding (mostly Mg 2+ ). This study also indicates that the pro-Rp oxygen is more important for metal binding in the Ce13d DNAzyme.…”

Section: Resultsmentioning

confidence: 99%

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Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates

et al. 2015

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A trivalent lanthanide (Ln 3+ )-dependent RNAcleaving DNAzyme, Ce13d, was recently isolated via in vitro selection. Ce13d is active in the presence of all Ln 3+ ions. Via introduction of a single phosphorothioate (PS) modification at the cleavage site, its activity with Ln 3+ decreases while all thiophilic metals can activate this DNAzyme. This property is unique to Ce13d and is not found in many other tested DNAzymes. This suggests the presence of a well-defined but general metal binding site. Herein, a systematic study of Ce13d with the PO substrate (using Ce 3+ ) and the PS substrate (using Cd 2+ ) is performed. In both the PO and PS systems, the highest activity was with ∼10 μM metal ions. Higher concentrations of Ce 3+ completely inhibit the activity, while Cd 2+ only slows the activity. A comparison of different metal ions suggests that the role of metal is to neutralize the phosphate negative charge. Both systems follow a similar pH−rate profile with a single deprotonation step, indicating similar reaction mechanisms. The activity difference between the R p and S p form of the PS substrate is <10-fold, which is much smaller than most known RNA-cleaving enzymes. Mutation studies identified eight highly conserved purines, among which the two adenines play mainly structural roles, while the guanines are likely to be involved in metal binding. Ce13d can serve as a model system for further understanding of DNAzyme biochemistry and bioinorganic chemistry.

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Section: Resultsmentioning

confidence: 99%

“…8,[16][17][18] Ln 3+ are important probes for nucleic acids. [19][20][21][22][23] They are quite effective in hydrolyzing RNA, 24 and early examples can be traced back to the cleavage of tRNA. 25 Ln 3+ inhibit the hammerhead ribozyme and the 8-17 DNAzyme, 22,26 but accelerate the leadzyme and a Mg 2+ -dependent ligase.…”

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Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates

et al. 2015

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“…8 Lanthanides form complexes with nucleotides, especially with adenosine or guanosine phosphates. 9,10 GT rich DNA is effective in sensitized Tb 3+ luminescence. 11,12 Lanthanides have also been used as chemical and optical probes for DNA, 13,14 and can cleave RNA.…”

Section: Introductionmentioning

confidence: 99%

In Vitro Selection of a New Lanthanide-Dependent DNAzyme for Ratiometric Sensing Lanthanides

2014

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“…Finally, nucleotides and lanthanides can form coordination complexes with useful luminescence and DNA binding properties. [21][22][23][24] Given these progresses, few studies explored the binding of the whole lanthanide series with DNA or correlated metal binding with enzyme activity. Such studies are important for revealing the coordination chemistry of lanthanides, and for DNA bioinorganic chemistry in general.…”

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The group trend of lanthanides binding to DNA and DNAzymes with a complex but symmetric pattern

et al. 2014

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Using sensitized Tb 3+ luminescence spectroscopy as a tool, binding of 14 lanthanides to a lanthanide-dependent DNAzyme is studied, where the binding affinity is symmetric cross the series and the tightest binding occurs with Nd 3+ and Ho 3+ . This trend does not correlate with DNAzyme activity, suggesting that metal binding may not be the rate-limiting step of the DNAzyme catalysis.Lanthanides refer to the elements in the periodic table from La to Lu. Beyond their critical roles in modern technologies, lanthanides also emerge as important probes for biology and medicine. 1,2 In particular, they have been extensively used to study the structure and function of nucleic acids. These applications take advantage of a few of their unique properties. First, lanthanides and their complexes can efficiently cleave nucleic acids, 3 and thus are used as RNA structural probes 4 and DNA cleaving agents. 5 In addition, a number of in vitro selection experiments were carried out using lanthanides as metal cofactors to obtain DNA-based catalysts (so called DNAzymes 6-12 ) for RNA or DNA cleavage. 13,14 Second, a few lanthanides (especially Tb 3+ ) are luminescent and DNA can act as an antenna to increase their light absorption and thus emission intensity. This is useful for probing metal binding sites, 15 and for developing biosensors. 16 Third, lanthanides are hard Lewis acids and some have a similar size as Ca 2+ . Lanthanides can compete with other metal ions in enzymes and act as enzyme inhibitors. For example, both the 17E DNAzyme and the hammerhead ribozyme are inhibited by lanthanides. 15,17 On the other hand, the Leadzyme and a DNA-based ligase are accelerated by lanthanides. [18][19][20] All these examples suggest strong interactions between lanthanides and nucleic acids. Finally, nucleotides and lanthanides can form coordination complexes with useful luminescence and DNA binding properties. [21][22][23][24] Given these progresses, few studies explored the binding of the whole lanthanide series with DNA or correlated metal binding with enzyme activity. Such studies are important for revealing the coordination chemistry of lanthanides, and for DNA bioinorganic chemistry in general. 25,26 We recently performed an in vitro selection experiment using Ce 4+ as the intended metal cofactor. The selected DNAzyme (named Ce13d) was found to have similar activity with all trivalent lanthanides. 14 Therefore, Ce13d must bind all the lanthanides and this DNAzyme might provide a good scaffold for studying lanthanide binding. Herein, we employed Tb 3+ luminescence as a tool to study lanthanide binding to DNAzymes and its relation to catalytic activity. The secondary structure of the Ce13d DNAzyme complex is shown in Figure 1A. It consists of a substrate strand named Sub-rA with a single RNA linkage (rA, ribo-adenosine), and an enzyme strand named Ce13d. In the presence of a trivalent lanthanide, the substrate is cleaved into two fragments at the position pointed by the arrowhead. Lanthanides alone can catalyze the reaction and no div...

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Nanoparticles of Adaptive Supramolecular Networks Self-Assembled from Nucleotides and Lanthanide Ions

Cited by 324 publications

References 42 publications

Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates

Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates

In Vitro Selection of a New Lanthanide-Dependent DNAzyme for Ratiometric Sensing Lanthanides

The group trend of lanthanides binding to DNA and DNAzymes with a complex but symmetric pattern

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