Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Describing the spatial orientation of DNA base pairs is crucial for understanding DNA structure and function.
• Traditional helical variables like twist, roll, and tilt can be complex to interpret and compute.
• Existing methods for analyzing base pair orientation may not fully capture the nuances of DNA flexibility.

Purpose of the Study:

• To propose a new, simplified method for calculating relative orientation variables for DNA base pair sequences.
• To provide a more direct physical comprehension of DNA conformations and the behavior of self-complementary sequences.
• To compare the proposed method with traditional rotation methods (Euler angles) for generating conformational variables.

Main Methods:

• A new method based on rotation about a space-fixed (local helix) axis is introduced.
• Orientation variables are determined by rotating base pairs around this axis.
• This method is compared to a conventional approach using three consecutive Euler angle rotations.

Main Results:

• The new method defines orientation variables that uniquely determine helical variables analogous to roll, tilt, and twist.
• The proposed identification of roll and tilt with direction cosines of the rotation axis aligns with customary definitions.
• Both methods generate structurally different but energetically equivalent spatial arrangements of base pairs, highlighting DNA flexibility.

Conclusions:

• The new orientation variables offer advantages over traditional twist, roll, and tilt angles for both static and average DNA forms.
• This method facilitates a more intuitive physical understanding of DNA conformations.
• The approach is applicable to interpreting crystal coordinates and statistical calculations of DNA ensembles.