Tunneling spectroscopy analysis of hexachloro-fluorescein phosphoramidite fluorescent dye attached to deoxyribonucleic acid

Scanning tunneling microscopy (STM) was used to observe hexachloro-fluorescein phosphoramidite (HEX) attached to single-stranded deoxyribonucleic acid (ssDNA) with molecular resolution. Scanning tunneling spectroscopy (STS) was also used to study the electric properties of HEX in single-molecular spectroscopy. In the STM topographic images, the bright HEX molecule and each base subunit of DNA could be clearly observed, just as with fluorescein isothiocyanate (FITC) attached to ssDNA. In contrast to FITC, HEX molecules usually did not show a clear peak in their tunneling spectra. Two types of HEX molecules seemed to have different apparent heights, and only the HEX with the larger height in topographic images showed a peak at +0.6V. The conformation of the HEX seems to affect the measured spectra. Thus, we obtained another molecule marker in addition to FITC with different spectral features for STM.