Sequence dependence of transient Hoogsteen base pairing in DNA

Area of Science:

• Structural Biology
• Computational Chemistry
• Molecular Biophysics

Background:

• Hoogsteen (HG) base pairing represents a significant alternative to Watson-Crick-Franklin (WCF) base pairing, involving a 180° rotation of the purine base.
• Both WCF and HG conformations exist in a dynamic equilibrium within DNA, with HG pairs playing roles in various biological functions.
• Previous studies have explored HG base pairing, but systematic investigations across different DNA sequences were limited.

Purpose of the Study:

• To investigate the free-energy landscape of the WCF to HG base-pairing transition using advanced simulation methods.
• To systematically analyze the influence of sequence variations on the mechanisms and energetics of purine rotation.
• To identify key factors modulating the dynamic equilibrium between WCF and HG base pairs in DNA.

Main Methods:

• Employed advanced path-based computational methods to calculate free-energy profiles for base-pairing transitions.
• Simulated seven distinct DNA sequences, focusing on variations around a canonical A·T base pair in an A6-DNA context.
• Analyzed purine rotation mechanisms, distinguishing between transitions occurring within the double helix versus those involving external flipping.

Main Results:

• Confirmed that A·T steps favor HG base-pair stability, consistent with prior observations.
• Identified that triple-hydrogen-bonded neighboring base pairs can impede the transition to the HG conformation from within the helix.
• Discovered that the direction of purine (adenine) rotation is a dominant factor, with specific orientations correlating to lower or higher energy barriers for the WCF/HG transition.

Conclusions:

• DNA's intrinsic flexibility, particularly the directionality of purine rotation, acts as a critical modulator of the WCF/HG dynamic equilibrium.
• The study provides a robust computational methodology for future investigations into the proclivity of DNA sequences to form HG base pairs.
• Understanding these transitions is essential for comprehending DNA function and potential therapeutic targeting.