IR study of base stacking interactions

Area of Science:

• Biophysical Chemistry
• Molecular Spectroscopy
• Nucleic Acid Chemistry

Background:

• Nucleic acids and related compounds exhibit complex interactions in solution.
• Infrared (IR) spectroscopy is a powerful tool for probing molecular structure and interactions.
• Distinguishing between different types of molecular associations, such as stacking and hydrogen bonding, is crucial for understanding biological systems.

Purpose of the Study:

• To investigate the concentration-dependent changes in IR spectra of nucleobases and related compounds in D2O solutions.
• To develop a method for determining thermodynamic parameters of association and molecular spectra of monomeric and associated forms.
• To differentiate stacking interactions from hydrogen bonding using IR spectral analysis.

Main Methods:

• Measurement of IR spectra (1800-1400 cm-1) for various compounds (1,3-dimethyluracil, cytidine, caffeine, inosine, 2'-deoxyadenosine) at different concentrations in D2O.
• Analysis of spectral changes to identify concentration-dependent effects indicative of association.
• Development of a method to extract thermodynamic parameters and molecular spectra from the concentration-dependent data.

Main Results:

• Concentration-dependent IR spectral changes were observed, reflecting stacking association of the studied compounds.
• A method was successfully developed to obtain thermodynamic parameters and molecular spectra for monomeric and associated forms.
• The homoassociation constant for 1,3-dimethyluracil was estimated at k=0.65.
• Stacking interactions significantly altered IR spectra, causing a high-frequency shift in carbonyl vibrations and reduced intensity of skeletal stretching bands.
• The spectral changes allowed for clear distinction between stacking interactions and hydrogen bonding.

Conclusions:

• Stacking interactions significantly influence the IR spectra of nucleobases and related compounds.
• The developed method provides a quantitative approach to study molecular association and its thermodynamic parameters.
• IR spectroscopy is a valuable tool for distinguishing stacking from hydrogen bonding.
• Stacking interactions play a considerable role in the IR spectral changes observed in DNA and polynucleotides during conformational transitions.