Separation of hydrophobically-modified nucleic acids in capillary electrophoresis

In this thesis, we present the use of hydrophobically modified nucleic acids for the sequence specific, and length dependent separation of DNA targets in capillary electrophoresis. The focus of the work has been the development of a methodology to enable the separation of nucleic acids in capillary electrophoresis in the absence of a gel or polymer matrix. This is accomplished through the alkylation of the DNA target followed by separation in micellar electrokinetic chromatography.; The method presented here relies on the transient attachment of a micelle to a DNA target. We promote this otherwise weak interaction with the micellar phase through attachment of an aliphatic tail to the DNA target. This attachment is conducted in one of two ways: For applications requiring the extension of the DNA target through enzymatic processes, such as DNA sequencing, the aliphatic group is covalently attached to the end of the molecule. For instances where biologically derived DNA is targeted, the aliphatic group is attached to the DNA target through the hybridization of a sequence specific Peptide Nucleic Acid Amphiphile probe. Following alkylation, electrophoretic separations are conducted in the presence of non-ionic micelles. Interactions the DNA has with the non-ionic micelles increases the hydrodynamic drag experienced by the DNA, leading to a decrease in its migrational velocity and a resultant separation of the alkylated-DNA from non-alkylated DNA present.; In this work, we will discuss the theoretical foundation for the mode of separation, both from a standpoint of the extent of hydrodynamic drag imposed by the micelle, and also in the degree of interaction the DNA has with the micellar phase. Experimental evidence will demonstrate the validity of the method for the separation of covalently attached and hybridized alkylated DNA. Application in DNA sequencing will also be investigated. The drag on the DNA target was originally intended to be induced by the micellar structure resulting from the self-assembly of the PNAA probe. Therefore, the characterization of the micellar size and morphology was also investigated.