Organization of Inorganic Complexes in Supramolecular Structures Based on Peptides and Peptide Nucleic Acids

The research described in this thesis shows how the properties of PNA can be successfully leveraged to improve the functional and structural versatility of hybrid inorganic nanomaterials. Specifically, the thesis describes the synthesis and investigation of the properties of PNA triplex-metal complex, single stranded-PNA or PNA duplex-gold nanocluster (AuNC), PNA duplex-colloidal quantum dot (CQD) and peptide-metal complex assemblies. PNA triplexes were characterized as a nano-scaffold to organize four- or sixcoordinate metal complexes at predefined positions in the triplex. Binding of 3d metal ions (Fe²+, Ni²+, Cu²+ or Zn²+) to PNA triplexes modified with 2,2’-Bipyridine (Bpy) or 8-Hydroxyquinoline (Q) ligands were studied. UV-melting studies proved that the metal complexes function as alternative base triplets or pairs in that they increase the
thermal stability of the triplexes. The metal complexes coordinate two or three ligands although three bidentate ligands are in close proximity of each other within a triplex.
The specific stoichiometry can be understood based on the stability constants of the metal complexes determined by simulation of UV-Vis titration data using HypSpec
refinement program. Metal coordination to ligand-modified PNA triplexes was further studied by Electron Paramagnetic Resonance (EPR) spectroscopy and Circular
Dichroism (CD) spectroscopy. The metal-containing PNA triplexes contain a chiral LLysine and adopt a left-handed chiral structure in solution. The handedness of the PNA triplex determines that of the metal complexes formed with the Bpy-containing PNA triplexes. A method was developed to synthesize, purify and isolate PNA-AuNC
conjugates bearing a known number of single stranded PNAs per AuNC. Purification of the PNA-AuNC conjugates was achieved by gel-electrophoresis. UV-Vis spectroscopic analysis quantitatively proves that the discrete gel bands correspond to PNA-AuNC conjugates bearing a distinct number of ss-PNA per cluster. The PNAAuNC conjugates were characterized by UV-melting, CD Spectroscopy and
Fluorescence Spectroscopy. UV-melting analysis of PNA-AuNC conjugates shows that the AuNCs negatively affect the π-stacking of terminal nucleobases of the duplexes and
reduce the thermal stability of the PNA duplexes. The chiral properties of AuNCs are highly sensitive to the PNA modifications as revealed by CD spectroscopy. Fluorescence emission intensity and the maximum emission wavelength of AuNCs increases and blue-shifts, respectively, upon PNA modification. Scanning transmission
electron microscopy (STEM) proved that complementary PNA strands can “glue” two AuNCs into AuNC dimers.
The effect of the use of chiral y-PNA duplex as linkers that connect CQDs to random-shaped gold nanoislands on the extinction properties of a monolayer of CQDs was studied. A two-fold larger extinction enhancement in the visible spectrum was achieved when a monolayer of helical chiral y-PNA duplex molecules connects the CQDs to the gold nanoislands instead of when a monolayer of achiral molecules is used to connect the CQDs to the nanoislands. The increase in extinction was exploited to measure the differential absorption of right- and left-polarized light by the monolayer of chiral molecules. The effect of handedness on electron transfer through self-assembled monolayers of chiral helical peptides was studied by electrochemistry. A difference between the charge transfer rate constants for oxidation and reduction processes was observed. This observed asymmetry was reversed for left- and right-handed helical peptides. The result can be explained by invoking the spontaneous magnetization that occurs when chiral helical peptides are self-assembled on a gold substrate and the chiral induced spin selectivity of the electron transfer.