Cr³⁺ Binding to DNA Backbone Phosphate and Bases: Slow Ligand Exchange Rates and Metal Hydrolysis

Abstract

The interaction between chromium ions and DNA is of great interest in inorganic chemistry, toxicology, and analytical chemistry. Most previous studies focused on in situ reduction of Cr(VI), producing Cr 3+ for DNA binding. Recently, Cr 3+ was reported to activate the Ce13d DNAzyme for RNA cleavage. Herein, the Ce13d is used to study two types of Cr 3+ and DNA interactions. First, Cr 3+ binds to the DNA phosphate backbone weakly through reversible electrostatic interactions, which is weakened by adding competing inorganic phosphate. On the other hand, Cr 3+ coordinates with DNA nucleobases forming stable crosslinks that can survive denaturing gel electrophoresis condition. The binding of Cr 3+ to different nucleobases was further studied in terms of binding kinetic and affinity by exploiting FAM-labeled DNA homopolymers. Once binding takes place, the stable Cr 3+ /DNA complex cannot be dissociated by EDTA, attributable to the ultra-slow ligand exchange rate of Cr 3+ . The binding rate follows the order of G > C >T ≈ A. Finally, Cr 3+ gradually loses its DNA binding ability after storing at neutral or high pH, attributable hydrolysis. This hydrolysis can be reversed by lowering the pH.This work provides a deeper insight into the bioinorganic chemistry of Cr 3+ coordination with DNA, clarifies some inconsistency in the previous literature, and offers practically useful information for generating reproducible results.3

Site‐Selective Labeling of Chromium(III) as a Quencher on DNA for Molecular Beacons

“…The binding of Cr 3+ ions to DNA bases is essentially irreversible (owing to inner‐sphere adduct formation), while its binding to the DNA phosphate backbone (electrostatic‐mediated binding) is much weaker and reversible . If ds‐DNA is formed, the bases are hidden, and the phosphate groups are exposed.…”

“…The Cr 3+ ion is another example that demonstrates an even slower ligand exchange rate (<10 −5 s −1 ) due to its d 3 electronic configuration in an octahedral ligand field . Compared to platinum, chromium is much more cost‐effective.…”

“…Compared to platinum, chromium is much more cost‐effective. The interaction between Cr 3+ and DNA has been extensively studied . Cr 3+ binds to DNA bases tightly, and no chelating or denaturing agents tested can sequester Cr 3+ from DNA .…”

“…The interaction between Cr 3+ and DNA has been extensively studied . Cr 3+ binds to DNA bases tightly, and no chelating or denaturing agents tested can sequester Cr 3+ from DNA . The Cr 3+ –DNA adduct is also a strong fluorescence quencher .…”

“…To achieve this goal, we needed to site‐specifically label Cr 3+ on DNA (e.g., at the end of a DNA strand) instead of relying on random reactions. Stable Cr 3+ adducts are formed only with DNA bases, which are available for reaction in ss‐DNA but are shielded in double‐stranded DNA (ds‐DNA). Therefore, we hypothesized that this selective labeling might be achieved by controlling the structure of DNA.…”