Surface-Enhanced Fourier Transform Raman Scattering Study on the Adsorption Structure of an RNA Triple Helix at a Silver Electrode

Abstract

In this research, we studied the adsorption structure of an RNA triplex, poly[rU]poly[rA]poly[rU], at a silver electrode by surface-enhanced Fourier transform Raman scattering (FT-SERS) spectroscopy and compared it to those of the corresponding single-stranded poly[rA] and duplex poly[rA] · poly[rU]. Some interesting phenomena have been observed. At the ex situ electrochemically roughened silver electrode, the SERS behavior of the duplex RNA is close to that of the single-stranded poly[rA], thereby indicating that the duplex RNA adsorbed at the electrode might be partly destabilized. However, on the highly positively charged surfaces, the SERS spectra revealed that the triplex was predominantly adsorbed at the electrode via the phosphate-moiety-directed mechanism, and thus the helical structure of the triplex molecules was well preserved; furthermore, since the electrode potential was set to approach the potential of zero charge (pzc) of the silver metal, in the spectral region between 1800 and 600 cm−1 the triplex gives rise to SERS spectra similar to those of the corresponding duplex, and also yields only two enhanced signals at 734 and 1382 cm−1, due to the ring-breathing and ring-vibration modes of the adsorbed adenine residues, respectively, along with the disappearance of some bands originating from the corresponding rU residues and phosphate groups. In fact, a dramatic transition of the SERS spectra of the triplex at the electrode was found to occur between −0.2 and −0.4 V. On the basis of the structural characteristics of triple-helical nucleic acids, we concluded that in this case there are two types of competitive adsorbed species—the triplex itself and the unpaired adenine residues in the incomplete region of the triplex RNA—which might be responsible for the unique potential-dependent transition.