The nonlinear optical technique, second harmonic generation (SHG), is applied here for the first time to probe single and double strand DNA (ssDNA and dsDNA) chemically attached to fused quartz/water interfaces. DNA interfaces are often a critical functional component of biodetection, thus, the development of molecular biosensors requires a thorough investigation of the physical and chemical properties of interfacial DNA. This work advances our understanding of DNA on a molecular level, as well as predicts and quantifies macromolecular interactions, improving and optimizing biodiagnostic capabilities, and understanding life processes.
Specifically, we use the SHG [special characters omitted] technique to study the thermodynamic parameters of ssDNA bound to an insulator surface by probing the interfacial potentials set up by the phosphate charges along the nucleotide backbone. Using the Gouy-Chapman-Stern model, we calculate surface charge densities between 9×10-3 C/m2 to 3×10-2 C/m2 for T15-T35 oligonucleotides, which correspond to DNA densities of approximately 5×1011 strands/cm2. We also calculate the interfacial potentials and interfacial free energy densities of the charged DNA interfaces. We then take advantage of the π-π* transitions of the oligonucleotide bases to probe the electronic structure of ssDNA and dsDNA with resonantly enhanced SHG. We find the SH signal of the DNA is maximum at 260 nm, the same as that of DNA in the bulk.
We demonstrate that a strong nonlinear optical linear dichroism response is obtained when surface-bound DNA hybridizes with solution phase complementary strands, and, therefore, we use polarization-resolved SHG-LD to differentiate between the chiral properties of ssDNA and dsDNA. We track the chiral duplex formation of surface-bound DNA oligonucleotides in situ and in real time, and determine that hybridization occurs within 2 hours, which we confirm with fluorescence measurements. We also use vibrational sum frequency generation (SFG) to track changes in the ordering of the DNA duplex, as well as changes in local and supramolecular chirality when oligonucleotide strands hybridize. Therefore, we sense the four significant intrinsic characteristics of native DNA, namely electronic resonance, charge, vibrational transitions, and chirality.
|Advisor:||Geiger, Franz M.|
|Commitee:||Barron, Annelise E., Geiger, Franz M., Van Duyne, Richard P.|
|School Location:||United States -- Illinois|
|Source:||DAI-B 69/11, Dissertation Abstracts International|
|Keywords:||DNA-functionalized, Second harmonic generation|
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