Nucleotide conjugated (ZnO)₃ cluster: Interaction and optical characteristics using TDDFT

Area of Science:

• Computational Chemistry
• Materials Science
• Biochemistry

Background:

• Understanding the interactions between nanomaterials and biological molecules is crucial for developing new biosensors and therapeutic agents.
• Zinc oxide (ZnO) clusters are of interest due to their unique electronic and optical properties.
• DNA nucleotides are the fundamental building blocks of genetic material.

Purpose of the Study:

• To investigate the binding mechanisms and stability of DNA nucleotide units with a zinc oxide (ZnO)₃ cluster in an aqueous environment.
• To analyze the electronic and photophysical properties of these hybrid systems.
• To explore the potential applications of these interactions in optical sensing.

Main Methods:

• Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) were employed for theoretical investigations.
• Analysis included molecular electrostatic potential (MEP) plots, hydrogen bonding, glycosidic torsion angles, and density of state (DOS) plots.
• Photophysical properties were studied using the TDDFT approach.

Main Results:

• A distinct stability order was predicted for (ZnO)₃-nucleotide systems: phosphate > cytosine (C) > adenine (A) > [sugars (S)] > thymine (T) ≈ guanine (G).
• The binding energy order for (ZnO)₃-nucleotide complexes was determined as: (ZnO)₃+nuc-C > (ZnO)₃+nuc-A > (ZnO)₃+nuc-G > (ZnO)₃+nuc-T.
• Absorption spectra of (ZnO)₃+nuc-A and (ZnO)₃+nuc-C complexes showed a red shift, indicating potential for optical sensing. Notably, the (ZnO)₃+nuc-T complex exhibited fluorescence.

Conclusions:

• The binding affinity of DNA nucleotides to (ZnO)₃ clusters varies, with phosphate and cytosine showing the strongest interactions.
• The electronic and structural analyses provide insights into the nature of these interactions.
• The observed photophysical changes, including red shifts and induced fluorescence, suggest that ZnO clusters could be utilized in fluorescent probes for DNA nucleotide detection.