New insight into the aptamer conformation and aptamer/protein interaction by surface-enhanced Raman scattering and multivariate statistical analysis

We study the interaction between one aptamer and its analyte (the MnSOD protein) by the combination of surface-enhanced Raman scattering and multivariate statistical analysis. We observe the aptamer structure and its evolution during the interaction under different experimental conditions (in air or in buffer). Through the spectral treatment by principal component analysis of a large set of SERS data, we were able to probe the aptamer conformations and orientations relative to the surface assuming that the in-plane nucleoside modes are selectively enhanced. We demonstrate that the aptamer orientation and thus its flexibility rely strongly on the presence of a spacer of 15 thymines and on the experimental conditions with the aptamer lying on the surface in air and standing in the buffer. We reveal for the first time that the interaction with MnSOD induces a large loss of flexibility and freezes the aptamer structure in a single conformation.

Automated summary

By utilizing surface-enhanced Raman scattering and multivariate statistical analysis, we studied the interaction between an aptamer and its analyte, observing the structural changes of the aptamer under different experimental conditions and revealing the impact of the interaction with MnSOD. The data from principal component analysis of SERS spectra allowed us to probe the conformation and orientation of the aptamer relative to the surface, showing that the flexibility of the aptamer is greatly affected by the presence of a 15-thymine spacer and the experimental conditions.