Date of Award

2-2011

Embargo Period

5-10-2012

Degree Type

Dissertation/Thesis

Degree Name

Doctor of Philosophy (PhD)

Department

Chemistry

Advisor(s)

Catalina Achim

Second Advisor

Danith Ly

Third Advisor

Michael P. Hendrich

Abstract

The research in this dissertation is about investigation of steric effect on the
stablility of metal-containing peptide nucleic acid (PNA); thermodynamcs of metal
binding to ligand-modified PNA studied by Isothermal titration calorimetry (ITC);
incorporation of metal in 2,2’-bipyridine(Bpy) modified PNA triplexes and structural
characterization of copper complexed 8-hydroxyquinoline (Q) modified PNA. All these
research are necessary to further understand the coordination chemistry in PNA
context, in comparison with the corresponding coordination of metal and simple ligand
for the construction of hybrid inorganic-nucleic acid nanostructures.
The steric effect of ligand can be understood by using similar ligands that carry
the same metal binding site, namely 8-hydroxyquinoline, but are attached differently to
the PNA backbone and having incorporated them into PNA duplexes. We conclude that
the incorporation of a metal complex with high stability constant into a PNA duplex is
not a sufficient condition for the formation of stable hybrid metal-nucleic acid duplexes
and that the steric relationship between the complex and the duplex must be
considered in the design of metal-containing alternative base pairs.
Thermodynamic parameters of metal ions with ligand-containing PNA including
Cu2+ with Q-PNA, Ni2+ and Cu2+ with Bpy-PNA have been studied by ITC. This study
established that the previously proposed supramolecular chelate effect on metal binding
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
interaction between the metal complex and the PNA. In addition, the sequence of the
PNA, the base pair mismatches, and the position of ligands in the PNA also influence
the stability constants of metal complexes formed with ligand-modified PNAs.
The incorporation of metal ions in PNA triplexes is observed and confirmed by
spectroscopic methods and mass spectrometry. The formations of Ni-tsPNA and CotsPNA
are stable. Electron paramagnetic resonance(EPR) results show that in the PNA
triplex, the coordination environment of Cu2+ is similar to those of [Cu(Bpy)3]2+ or
trans-[Cu(Bpy)2]2+.
A crystal structure of a 9-base pair PNA with a central Q ligand modification is
obtained in the presence of excess Cu2+. Due to the unfavorable condition of
crystallization at pH 4.0 and with excess Cu2+, metal coordination is outside the PNA
duplex. An unusual Cu trinuclear cluster bridges two duplexes and excess Cu2+ is
coordinated to terminal nucleobases. The similarity between the EPR parameters for the
[CuQ2] complexes with 8-hydroxyquinoline and ipdq precluded us from distinguishing
between the possible cis- or trans-geometry of the complex formed by Cu2+ with Qmodified
PNA duplexes.
Future research includes investigation of thermodynamics by differential
scanning calorimetry (DSC); analysis of kinetics of ITC results and identification of the
intermediates; further characterization of the right-handed PNA induced by hydrogen
bonding and structural characterizations of metal-containing PNA.

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