Non-natural G-quadruplex in a non-natural environment

Area of Science:

• Biochemistry
• Supramolecular Chemistry
• Oligonucleotide Chemistry

Background:

• Deep eutectic solvents (DES) are sustainable and biocompatible, presenting an alternative to aqueous media for biomolecular studies.
• G-quadruplexes are crucial nucleic acid structures with applications in biology and nanotechnology.
• Understanding G-quadruplex behavior in various media is essential for their effective utilization.

Purpose of the Study:

• To synthesize and analyze the structural and stability changes of natural and non-natural G-rich oligonucleotides in aqueous and deep eutectic solvents.
• To investigate the impact of non-natural pyrene linkers on G-quadruplex conformation and thermal stability.
• To compare the conformational preferences of G-quadruplexes in buffer versus a choline chloride-urea deep eutectic solvent.

Main Methods:

• Synthesis of G-rich oligonucleotides (G3T3) and non-natural variants (Pyr1-Pyr3) with pyrene linkers.
• UV-Vis spectroscopy was used to monitor thermal denaturation and assess oligonucleotide stability.
• Circular dichroism spectroscopy was employed to determine G-quadruplex conformation (parallel vs. anti-parallel).

Main Results:

• Increased pyrene linker length enhanced thermal denaturation temperature in aqueous buffer, indicating greater stability.
• In aqueous buffer, G3T3 and Pyr1-Pyr3 predominantly formed anti-parallel G-quadruplex structures.
• G-rich oligonucleotides exhibited thermodynamic destabilization in the deep eutectic solvent (DES) with increasing loop modifications.
• G3T3 exclusively formed a parallel G-quadruplex in DES, while Pyr1-Pyr3 showed a mixed parallel/anti-parallel conformation.

Conclusions:

• Deep eutectic solvents influence G-quadruplex stability and conformation differently than aqueous media.
• Non-natural modifications, like pyrene linkers, can be used to tune G-quadruplex properties.
• The study provides insights into G-quadruplex behavior in sustainable solvents, relevant for nanodevice and biological applications.