Electrostatic potential modulations on polynucleotides as a function of ionic content: potentiometric determinations

Area of Science:

• Biochemistry
• Molecular Biology
• Physical Chemistry

Background:

• Polynucleotides like poly C and poly I possess ionizable residues, specifically cytidine.
• The ionization state of these residues is crucial for polynucleotide structure and function.
• Understanding the local environment around polynucleotides is key to interpreting their behavior.

Purpose of the Study:

• To determine the pK values of cytidine ionization in poly C and poly I.
• To investigate the influence of ionic strength (Na+) and magnesium ion (Mg2+) concentration on these pK values.
• To explore the concept of a local pH environment near polynucleotides and its implications.

Main Methods:

• Potentiometric titration was employed to measure pK values.
• Experiments were conducted as a function of varying ionic strength (Na+) and Mg2+ concentration.
• The pH-stat method was considered for detecting proton release.

Main Results:

• The pK values of cytidine ionization were found to be dependent on ionic strength and Mg2+ concentration.
• Results suggest the existence of a local pH near the polynucleotides, which is lower than the bulk solution pH.
• This local pH is directly related to the electrostatic potential (ψ) of the polynucleotide's phosphate groups.

Conclusions:

• The electrostatic potential of polynucleotides significantly influences the local pH and ionization behavior of residues.
• Modulation of ionic strength and Mg2+ concentration alters the electrostatic potential and, consequently, the local pH.
• These findings have potential implications for understanding the functional mechanisms within genetic translation systems.