Deciphering Structural Dynamics of DNA-Surfactant Interactions Using the Isomorphic Nucleobase Analogue

Area of Science:

• Biophysical Chemistry
• Materials Science
• Nanotechnology

Background:

• DNA-surfactant interactions are crucial for gene regulation, drug delivery, and nanotechnology.
• The precise conformational changes induced by cationic surfactants like CTAB in DNA remain largely uncharacterized.

Purpose of the Study:

• To investigate the structural and dynamic effects of CTAB on both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA).
• To elucidate the molecular mechanisms underlying DNA compaction and condensation mediated by CTAB.

Main Methods:

• Utilized photophysical properties of 2-aminopurine (2Ap)-labeled ssDNA and dsDNA.
• Employed Scanning Electron Microscopy (SEM) and X-ray Diffraction (XRD) for aggregate analysis.
• Conducted Circular Dichroism (CD) spectroscopy and computational methods (molecular docking, MD simulations, MM/PBSA).

Main Results:

• CTAB induced cooperative compaction in 2Ap-ssDNA, forming aligned lamellar aggregates.
• CTAB caused compaction/condensation and structural denaturation in 2Ap-dsDNA, forming mixed lamellar and hexagonal aggregates.
• Computational studies confirmed CTAB binding to both DNA forms via electrostatic and hydrophobic interactions.

Conclusions:

• ssDNA and dsDNA exhibit differential structural responses to CTAB binding.
• Findings provide insights into DNA-surfactant interactions for designing DNA-based nanostructures and drug delivery systems.