A thermodynamic approach for the targeting of nucleic acid structures using their complementary single strands

Area of Science:

• Biochemistry
• Molecular Biology
• Thermodynamics

Background:

• Understanding the physicochemical properties of nucleic acid structures is crucial.
• Intramolecular nucleic acid structures play significant roles in biological processes.
• Studying the interactions of these structures with complementary strands provides insights into their stability and function.

Purpose of the Study:

• To investigate the thermodynamic basis of interactions between various intramolecular nucleic acid structures and their complementary strands.
• To determine the standard thermodynamic profiles for these reactions.
• To explore the potential of these interactions for targeting nucleic acids for gene expression control.

Main Methods:

• Utilized isothermal titration calorimetry (ITC) to directly measure reaction enthalpies.
• Employed differential scanning calorimetry (DSC) to obtain unfolding data for thermodynamic analysis.
• Combined ITC and DSC data with spectroscopy techniques to establish comprehensive thermodynamic profiles.

Main Results:

• Investigated reactions involving triplex, G-quadruplex, hairpin loops, pseudoknot, and three-arm junctions.
• All studied reactions exhibited favorable free energy contributions, indicating strand invasion and disruption of intramolecular structures.
• Favorable free energy changes were found to be enthalpy-driven, resulting from a balance of exothermic and endothermic contributions.

Conclusions:

• Developed a thermodynamic approach to characterize nucleic acid structure interactions.
• Demonstrated that single strands can effectively invade and disrupt intramolecular DNA structures.
• The findings support the use of oligonucleotides targeting nucleic acid secondary structures, like mRNA, for gene expression regulation.