Thermodynamics of Metal Binding to Ligand-Modified PNA
Creators: name: Zhijie  Ma
Publisher: name: Carnegie Mellon University
Year: 2011
Subjects: subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences

description: The research in this dissertation is about investigation of steric effect on the<br>stablility of metal-containing peptide nucleic acid (PNA); thermodynamcs of metal<br>binding to ligand-modified PNA studied by Isothermal titration calorimetry (ITC);<br>incorporation of metal in 2,2’-bipyridine(Bpy) modified PNA triplexes and structural<br>characterization of copper complexed 8-hydroxyquinoline (Q) modified PNA. All these<br>research are necessary to further understand the coordination chemistry in PNA<br>context, in comparison with the corresponding coordination of metal and simple ligand<br>for the construction of hybrid inorganic-nucleic acid nanostructures.<br>The steric effect of ligand can be understood by using similar ligands that carry<br>the same metal binding site, namely 8-hydroxyquinoline, but are attached differently to<br>the PNA backbone and having incorporated them into PNA duplexes. We conclude that<br>the incorporation of a metal complex with high stability constant into a PNA duplex is<br>not a sufficient condition for the formation of stable hybrid metal-nucleic acid duplexes<br>and that the steric relationship between the complex and the duplex must be<br>considered in the design of metal-containing alternative base pairs.<br>Thermodynamic parameters of metal ions with ligand-containing PNA including<br>Cu<sup>2+</sup> with Q-PNA, Ni<sup>2+</sup> and Cu<sup>2+</sup> with Bpy-PNA have been studied by ITC. This study<br>established that the previously proposed supramolecular chelate effect on metal binding<br>to PNA duplexes exists and it is entropy-driven. Another major factor that influences the binding affinity of ligand-containing PNA for transition metal ions is the steric<br>interaction between the metal complex and the PNA. In addition, the sequence of the<br>PNA, the base pair mismatches, and the position of ligands in the PNA also influence<br>the stability constants of metal complexes formed with ligand-modified PNAs.<br>The incorporation of metal ions in PNA triplexes is observed and confirmed by<br>spectroscopic methods and mass spectrometry. The formations of Ni-tsPNA and CotsPNA<br>are stable. Electron paramagnetic resonance(EPR) results show that in the PNA<br>triplex, the coordination environment of Cu2+ is similar to those of [Cu(Bpy)3]2+ or<br>trans-[Cu(Bpy)2]2+.<br>A crystal structure of a 9-base pair PNA with a central Q ligand modification is<br>obtained in the presence of excess Cu2+. Due to the unfavorable condition of<br>crystallization at pH 4.0 and with excess Cu2+, metal coordination is outside the PNA<br>duplex. An unusual Cu trinuclear cluster bridges two duplexes and excess Cu<sup>2+</sup> is<br>coordinated to terminal nucleobases. The similarity between the EPR parameters for the<br>[CuQ<sub>2</sub>] complexes with 8-hydroxyquinoline and ipdq precluded us from distinguishing<br>between the possible cis- or trans-geometry of the complex formed by Cu<sup>2+</sup> with Qmodified<br>PNA duplexes.<br>Future research includes investigation of thermodynamics by differential<br>scanning calorimetry (DSC); analysis of kinetics of ITC results and identification of the<br>intermediates; further characterization of the right-handed PNA induced by hydrogen<br>bonding and structural characterizations of metal-containing PNA.