Proton exchange and base pair opening in a DNA triple helix

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• DNA can form complex structures beyond the canonical double helix, including triplexes.
• Understanding base pair stability is crucial for DNA structure-function relationships.

Purpose of the Study:

• To characterize the opening dynamics and stability of individual base pairs in DNA triplex and hairpin double helix structures.
• To compare the stability of Hoogsteen versus Watson-Crick base pairs in these DNA architectures.

Main Methods:

• Nuclear magnetic resonance (NMR) spectroscopy was employed to study two DNA structures: a YRY triplex and its corresponding hairpin double helix.
• Imino proton exchange rates with solvent were measured using magnetization transfer and real-time exchange techniques.
• Experiments were conducted at 10°C in 100 mM NaCl and 5 mM MgCl2 at pH 5.5, with exchange catalysts.

Main Results:

• Imino proton exchange in protonated cytosines suggests Hoogsteen C+G base pair opening limits the process.
• Estimated Hoogsteen base pair opening parameters in the triplex are comparable to Watson-Crick base pairs in double helices.
• Watson-Crick base pair imino proton exchange rates in the triplex were up to 5000-fold lower than in the double helix.

Conclusions:

• DNA triplex formation significantly enhances the stability of Watson-Crick base pairs, potentially by up to 5 kcal/mol.
• This stabilization effect is dependent on the specific location of the base pair within the triplex structure.
• Hoogsteen base pair stability in triplexes is similar to Watson-Crick base pair stability in duplexes.