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

Abstract

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...

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

“…To avoid this artifact, we did not include the last two data points in our binding curve and the apparent dissociation constant (Kd) was determined to be 27.5  18 µM Ce 3+ for binding a single metal ion (inset of Figure 2C), which is comparable to the value obtained from the Tb 3+ luminescence study. 34 This result suggests two competing processes at high Ce 3+ concentrations: the DNAzyme can be either activated or inhibited by lanthanide ions. This is not surprising since Ln 3+ are trivalent 8 cations with strong affinity to the DNA phosphate and base.…”

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

“…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. 15 It is however still difficult to rationally design DNA sequences that can selectively bind lanthanides; many other metals also have high affinity for DNA.…”

Lanthanide-dependent RNA-cleaving DNAzymes as metal biosensors

“…Lanthanides are useful spectroscopic probes for understanding the binding with DNA. For example, we performed Tb 3+ luminescence spectroscopy and found an interesting lanthanide size-dependent interaction strength with DNA, 51 and guanine was found to be the critical base for lanthanide binding. Many lanthanide ions are strongly paramagnetic due to unpaired f electrons.…”

“…48,49 GT-rich DNA is effective in sensitized Tb 3+ luminescence. 50,51 All of these facts point towards a strong binding between lanthanides and DNA.…”