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Capillary electrophoresis with laser induced fluorescence (CE-LIF) detection is a powerful technique for the study of DNA conformational changes.We have studied the changes in the electrophoretic mobility of the complexes of 5 end labeled 6-FAM-T33 in the presence of Hg2+ using CE-LIF.Upon increasing the concentration of Hg2+, the electrophoretic mobility for 6-FAM-T33 increased, due to its conformation change from a random coil to a folded structure and a decrease in its charge-to-mass ratio.CE-LIF using 2% poly(ethylene oxide) solutions containing OliGreen (fluorophore) and 0.3 mM Hg2+ has been applied to the separation of T33, T5C28, T5C5T23, and T15C5T13.We have further employed CE-LIF using 2.7% PEO in the presence of EOF to detect and characterize dynamically metastable states in strand displacement reactions for bulge loop DNA conformations.The data from measurements of fluorescence polarization, circular dichroism, and melting points of the DNA samples have been further supported their conformation changes under the studied conditions.