Poster abstracts

Poster number 160 submitted by Sineth G Kodikara

Single-Molecule Study of Telomeric Overhangs Using FRET Method

Sineth G Kodikara (Kent State University, Department of Physics ), Sajad Shiekh (Kent State University, Department of Physics ), Kylie Merkel (Kent State University, Department of Physics), Simon Haas (Kent State University, Department of Physics), Hamza Balci (Kent State University, Department of Physics)

Single-molecule FRET was used to analyze multiple telomeric overhang conformations and find the potassium chloride (KCl) dependence of binding frequency. This was accomplished by using surface-immobilized partial duplex DNA labeled with the donor fluorophore, Cy3, and a short Peptide Nucleic Acid (PNA) labeled with the acceptor fluorophore, Cy5. It was found that when the binding zones for the Cy5-PNA are increased, the width of the FRET energy transfer peak also increases. It was also found that the binding frequency of the Cy5-PNA increases as binding zones increase, unless three binding zones repeat in a row, then a possible triplex may form and prevent binding at higher salt concentrations. This was tested at varying KCl concentrations, and it was found that there appears to be an initial decrease in the binding frequency at low salt concentrations followed by an increase after about 20 mM KCl as higher salt concentrations possibly increase the binding affinity of PNA to DNA.

Keywords: Triplex