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New insight into the aptamer conformation and aptamer/protein interaction by surface-enhanced Raman scattering and
Wafa Safar1, Andra-Sorina Tatar, Aymeric Leray
1IMMM - UMR 6283 CNRS, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, Cedex 9, France. marc.lamydelachapelle@univ-lemans.fr.
Nanoscale
|July 12, 2021
Summary
This study reveals how aptamer structure and flexibility change when interacting with the MnSOD protein. Aptamer orientation and flexibility depend on experimental conditions and a thymine spacer, with binding freezing its structure.
Area of Science:
- Biophysical Chemistry
- Molecular Biology
- Analytical Chemistry
Background:
- Aptamers are crucial in molecular recognition and diagnostics.
- Understanding aptamer-protein interactions is key for developing biosensors.
- Surface-enhanced Raman scattering (SERS) offers label-free detection of molecular interactions.
Purpose of the Study:
- To investigate the structural dynamics of an aptamer interacting with its target, manganese superoxide dismutase (MnSOD) protein.
- To elucidate the role of experimental conditions and aptamer design (e.g., thymine spacer) on aptamer conformation and flexibility.
- To characterize the structural changes in the aptamer upon binding to MnSOD.
Main Methods:
- Utilizing surface-enhanced Raman scattering (SERS) spectroscopy to obtain detailed structural information.
- Applying multivariate statistical analysis, specifically principal component analysis (PCA), to interpret complex SERS spectral data.
- Examining aptamer behavior under varying conditions, including in air and in buffer, to understand environmental influences.
Main Results:
- Aptamer conformation and orientation were found to be dependent on the presence of a 15-thymine spacer and experimental environment (lying flat in air, standing in buffer).
- Principal component analysis of SERS data enabled probing of aptamer conformations and surface orientations.
- The interaction with MnSOD significantly reduced aptamer flexibility, locking it into a single conformation.
Conclusions:
- Aptamer structural flexibility is significantly influenced by flanking sequences and the surrounding medium.
- The binding event with MnSOD induces a conformational "freeze," highlighting the specificity and impact of the aptamer-analyte interaction.
- This study provides novel insights into aptamer-protein complex formation at the molecular level using advanced spectroscopic and analytical techniques.
