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DNA changes its conformation by combining a transcription factor or transcription factor complex on specific base sequences. We investigated the conformation changes by using local surface plasmon resonance of two gold nanoparticles linked to each other via the DNA, which compose a nano-dimer. Gap distance of the nano-dimer is reduced due to the DNA conformation change or bending, then the plasmon resonance shifts to longer wavelength. By measuring the plasmon resonant wavelength, gap distance is determined with a calibration curve prepared beforehand. Hence, conformation change of DNA bound with transcription factors is evaluated at nanoscale or sub-nanoscale. For example, a bending angle was determined to be 61.3º when SOX2, one of transcription factors, was bound on a double-stranded DNA having DC5 sequence and the DNA changes conformation. Binding SOX2 and PAX6 together on DC5 sequence, bending angles were evaluated to be 61.3º at SOX2 side and 5.7º at PAX6 side, respectively. When we used DNA having a DC5-con sequence which is a little different from DC5 sequence, bending angles were evaluated to be 61.1º at SOX2 side and 2.3º at PAX6 side. Such small difference in DNA conformations can be distinguished by using the local surface plasmon resonance. We also observed DNA conformation change by binding SOX2 on DC5 in real time and duration for conformation change was determined to be less than 100 msec. Such binding of DNA and transcription factors has possibility for a driving component for nano-machines.
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