Figure 1

Schematic representation of the polarization-modulation imaging method. (a) The spinning QWP and a wedge prism in a hollow motor generate the rotating, linearly polarized light and the incident angle for the total internal reflection, respectively. The linear polarization of the resulting evanescent wave rotates parallel to the sample plane. (b) When the polarization of the excitation light is perpendicular to the transition dipole, the emission signal of one of the fluorophores is turned off, which allows the position of the remaining fluorophore to be determined. (c) By measuring the angle ($\alpha$) between the two incident polarizations perpendicular to each transition dipole, the angle ($\phi$) between the transition dipoles is determined. (d) The centroid position of the PSF is the sum of the intensity profile of each fluorophore and therefore shifts to the fluorophore with the higher intensity as the incident polarization rotates in a period of 180°.Reuse & Permissions

Figure 2

The application of the polarization-modulation imaging method to DNA Holliday junctions. (a) The geometry of a four-way junction (Holliday junction) consisting of 93-bp double-stranded DNA branches (left) and a representative time trace of the Cy3 emission signal (right). (b) The time trace of the emission signal was converted to the centroid position ($x$, $y$) of the emission intensity and the direction of the incident beam polarization. (c) The position and direction of the ten points in (b) $R_{cm}$ and ${\theta }_{cm}$ indicate the position and angle, respectively, of the two centers, each of which consists of 5 points. (d) The geometry of a Holliday junction consisting of 43- and 45-bp branches was determined.Reuse & Permissions

Figure 3

The end-to-end distance ($D$) as a function of the angle ($\varphi$) of the 93–93-bp (blue points) and the 43-45-bp Holliday junctions (red points). The measured data correlate well with the calculated $D$ and $\varphi$ (solid lines), with Pearsons correlation coefficients of $r_{93-93}=0.85$ and $r_{43-45}=0.85$. The error bars indicate the s.d.Reuse & Permissions