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We propose a method of in situ (in vitro) analysis of the chemical bonding state of DNA in aqueous solution by infrared absorption spectroscopy in the multiple internal reflection geometry (MIR-IRAS) in conjugation with electrophoresis. We demonstrate that MIR-IRAS is capable of detecting in vitro DNA hybridization. In our method, a Si prism, through which infrared lights penetrate and are also internally reflecting, also serves as the electrode for electrophoresis. We show that with a positive or negative potential being applied to the electrode (prism), DNA molecules are concentrated on or expelled from the electrode, respectively, leading to highly sensitive detection and manipulation of DNA in aqueous solution.