Dynamic interchange between DNA molecules plays important roles in controlling biological functions.Capillary electrophoresis with laser induced fluorescence (CE-LIF) detection has been utilized to investigate the metastable states of DNA bulge loops during strand displacement reactions.DNA samples consisting of 22-mer YX (X =GCTTCGGTGTG and Y =GCGTGCTCGTG and one of the X(CAG)nY (n =4-8, X =CACGAGCACGC and Y =CACACCGAAGC) were separated within 7 min by CE-LIF using 2.7% poly(ethylene oxide) (PEO) in the presence of EOF.Our CE data allowed calculation of the equilibrium constant (K) and rate constant (k) of the 34-mer X(CAG)4Y and 22-mer YX at 25 ℃ to be 6.3 × 106 M-1 and 4.5 × 102 M-1 S-1, respectively.The metastable DNAbulge loops and unbinding oligonucleotides were coexistent at room temperature, while they underwent heating at 95 ℃ and cooling at 25 ℃.Relative to CD and UV measurements, our CE-LIF approach for the study of DNA interactions provide high throughput and sensitivity.