Ab initio optical absorption spectra of size-expanded xDNA base assemblies.

Area of Science:

• Computational Chemistry
• Spectroscopy
• Biophysical Chemistry

Background:

• Synthetic nucleobases offer novel functionalities beyond natural DNA/RNA bases.
• Understanding their optical properties is crucial for applications in molecular recognition and diagnostics.
• Previous studies have explored structural modifications of nucleobases, but optical responses of size-expanded analogues require further investigation.

Purpose of the Study:

• To investigate the optical absorption spectra of size-expanded synthetic nucleobases (x-bases) and their base pairs.
• To elucidate the impact of a fused benzene ring on electronic structure and optical properties.
• To analyze the effects of hydrogen bonding and base stacking on spectral characteristics.

Main Methods:

• Time-dependent density functional theory (TD-DFT) calculations were employed.
• Optical absorption spectra were computed for individual x-bases (xA, xG, xT, xC) and their hydrogen-bonded and stacked pairs.
• Frontier molecular orbital analysis was performed to correlate electronic structure with spectral features.

Main Results:

• The benzene component of the highest occupied molecular orbital (HOMO) in x-bases dictates the absorption onset.
• Hydrogen-bonded base pairs exhibit a significant red shift in spectral peaks within the low-energy range.
• Stacked xG-C and xA-T pairs show enhanced hypochromicity compared to natural G-C and A-T pairs, indicating stronger stacking interactions.

Conclusions:

• Size-expanded nucleobases possess unique optical absorption properties influenced by their modified electronic structure.
• Hydrogen bonding and base stacking significantly alter the spectral profiles of these synthetic analogues.
• The enhanced stacking observed in x-base pairs suggests potential for novel supramolecular assemblies and biomaterials.