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"Peptide Nucleic Acid Surfactants for Sequence-Specific DNA Purification"

James Vernille (Advisor: Jim Schneider)


Development of sequence-specific DNA separation and purification techniques will continue to be critical to unlock the potential of biotechnology.  The ability to produce large amounts of plasmid DNA may contribute to the success and validity of many biochemical applications including gene therapy, a science currently moving from the laboratory to the clinic.  DNA purification kits based on anion exchange chromatography and cesium chloride gradients in the presence of ethidium bromide are widely used methods of purification, however, they are time consuming, require the use of hazardous materials, are expensive, and not sequence-specific.  Sequence-specific separation will ensure that plasmids used in gene delivery have the appropriate gene sequences needed for encoding proper products. 

This work involves development of a DNA purification technique based on sequence specific recognition of the target gene by specially designed surfactants.  The use of DNA-binding surfactants allows for the implementation of hydrophobically driven separation processes such as reverse phase and hydrophobic interaction chromatography.  The use of surfactants also gives rise to interesting solubility phenomena which can been tuned to promote controllable precipitation of the PNA/DNA complex allowing for two phase separations. 

DNA:

    

PNA:       

 

PNA, or peptide nucleic acid is a DNA analog capable of binding complementary single stranded (ss) DNA and even double stranded (ds) DNA.  With PNA, the entire sugar-phosphate backbone is replaced with neutral N-(2-aminoethyl)glycine units to which the nucleobases are attached.  ssDNA-ssPNA duplexes form a double helix structure very similar to the classical dsDNA double helix but with a greater thermal stability.     

We intend to modify a peptide nucleic acid with a lipid tail to create a surfactant capable of binding to DNA.  Due to the lipid tail attached to the PNA molecule, which can be tailored to desired length and architecture, the PNA-DNA complex exhibits different solubility characteristics and chromatographic behavior than that of the single DNA molecule.  With this design selective precipitation and/or chromatographic separation processes can be used for DNA purification.