Electrostatic effects in DNA triple helices

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Electrostatic interactions are crucial for nucleic acid behavior.
• Sequence-specific electrostatic effects arise from protonated cytosines in polypyrimidine third strands binding to DNA.
• These effects depend on the number (global) and position (local) of cytosines.

Purpose of the Study:

• To investigate the influence of local and global electrostatic effects of protonated cytosines on nucleic acid binding affinity.
• To synthesize and analyze oligonucleotide families forming intramolecular triple helices.

Main Methods:

• Synthesis of two oligonucleotide families forming hairpin intermediates and intramolecular triple helices.
• Confirmation of structures using P1 nuclease probing, Circular Dichroism (CD) spectroscopy, and UV spectroscopy.
• Thermal stability analysis under varying pH and ionic strength conditions.

Main Results:

• Third strand binding energy is dependent on protonated cytosine content and pH.
• Below pH 7.1, binding affinity increases with cytosine content (global effect).
• Above pH 7.1, binding affinity decreases with cytosine content; local effects (crowding) can override global composition effects.

Conclusions:

• The local arrangement of protonated cytosines significantly impacts DNA binding affinity, sometimes reversing the trend predicted by global composition.
• Oligonucleotide thermal stability is sensitive to pH and ionic strength, highlighting the complex interplay of electrostatic factors.
• Understanding these sequence-dependent electrostatic effects is key for nucleic acid structure and function studies.