Site‐specific cleavage reaction catalyzed by leadzyme is enhanced by combined effect of lead and rare earth ions

Sugimoto, Naoki; Ohmichi, Tatsuo

doi:10.1016/0014-5793(96)00860-5

Cited by 37 publications

(45 citation statements)

References 23 publications

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“…Firstly, the Pb 2 + -phos- [59,60] as well as Pb 2 + -dependent DNAzymes, [61] that is, RNA or DNA oligonucleotides with a structural motif that selectively binds Pb 2 + to promote hydrolytic cleavage of a second nucleic acid, could be selected by conducting in vitro selection experiments. Our results also explain why some leadzymes are strongly inhibited [62][63][64][65] by the presence of Mg 2 + and other divalent ions; such ions inhibit chelate formation of Pb 2 + . A difference in RNA binding between Pb 2 + and Mg 2 + has also been observed in hydrolytic cleavage experiments of a group II intron ribozyme [15] and other large RNAs.…”

Section: Discussionmentioning

confidence: 62%

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Knobloch

Suliga

Okruszek

et al. 2005

Chemistry A European J

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It is well known that Mg2+ and other divalent metal ions bind to the phosphate groups of nucleic acids. Subtle differences in the coordination properties of these metal ions to RNA, especially to ribozymes, determine whether they either promote or inhibit catalytic activity. The ability of metal ions to coordinate simultaneously with two neighboring phosphate groups is important for ribozyme structure and activity. However, such an interaction has not yet been quantified. Here, we have performed potentiometric pH titrations to determine the acidity constants of the protonated dinucleotide H2(pUpU)-, as well as the binding properties of pUpU3- towards Mg2+, Mn2+, Cd2+, Zn2+, and Pb2+. Whereas Mg2+, Mn2+, and Cd2+ only bind to the more basic 5'-terminal phosphate group, Pb2+, and to a certain extent also Zn2+, show a remarkably enhanced stability of the [M(pUpU)]- complex. This can be attributed to the formation of a macrochelate by bridging the two phosphate groups within this dinucleotide by these metal ions. Such a macrochelate is also possible in an oligonucleotide, because the basic structural units are the same, despite the difference in charge. The formation degrees of the macrochelated species of [Zn(pUpU)]- and [Pb(pUpU)]- amount to around 25 and 90 %, respectively. These findings are important in the context of ribozyme and DNAzyme catalysis, and explain, for example, why the leadzyme could be selected in the first place, and why this artificial ribozyme is inhibited by other divalent metal ions, such as Mg2+.

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Section: Discussionmentioning

confidence: 62%

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Knobloch

Suliga

Okruszek

et al. 2005

Chemistry A European J

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“…The total kinetics of combined 6-mers are in agreement with the buildup of 24-mer and the decay of the 30-mer ( Figure 1C). It is not clear, however, whether the same or a different bound Pb 2+ ion is involved in the two separate steps (3,4,8,10,21,22).The designed constructs showed a range of cleavage activity (Table S3 and Figure S3, Supporting Information), demonstrating various degrees of the influence of the functional group mutations that are highly context dependent. In particular, the P25 construct, where A25 is replaced by P, cleaves 3-fold (4 ( 0.1 min -1 ) faster than the WT.…”

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confidence: 94%

Conformational Distribution and Ultrafast Base Dynamics of Leadzyme

2009

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The dynamic nature of ribozymes represents a significant challenge in elucidating their structure-dynamics-function relationship. Here, using femtosecond time-resolved spectroscopy and other biophysical tools, we demonstrate that the active site of leadzyme does not have a unique structure, but rather samples an ensemble of conformations that undergo picosecond structural changes. Various base modifications have a profound context-dependent impact on the catalysis.

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“…18,19 Sugimoto and Ohmichi found that lanthanides in general can accelerates the enzyme rate, although Pb 2+ is still required for activity. Among the 11 lanthanides they tested, Nd 3+ produced the highest rate enhancement.…”

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confidence: 99%

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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Site‐specific cleavage reaction catalyzed by leadzyme is enhanced by combined effect of lead and rare earth ions

Cited by 37 publications

References 23 publications

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Conformational Distribution and Ultrafast Base Dynamics of Leadzyme

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

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Site‐specific cleavage reaction catalyzed by leadzyme is enhanced by combined effect of lead and rare earth ions

Cited by 37 publications

References 23 publications

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU3−)

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU3−)

Conformational Distribution and Ultrafast Base Dynamics of Leadzyme

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

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Product

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Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)