Computer programs for nucleic acids studies. Atomic coordinates of helices and their graphic display.

Area of Science:

• Computational Chemistry
• Structural Biology
• Biophysics

Background:

• Accurate calculation of physicochemical properties for nucleic acids is crucial for understanding their function.
• Existing methods for structural analysis and property prediction have limitations.

Purpose of the Study:

• To develop a computational tool for calculating NMR and other physicochemical properties of nucleic acids.
• To provide detailed atomic coordinates and facilitate structural analysis of double-stranded nucleic acid helices.

Main Methods:

• A FORTRAN-based computer program was developed to compute atomic coordinates (Cartesian and cylindrical) for nucleic acid helices.
• The program supports A, A', and B conformations with user-defined base sequences.
• Calculations include interatomic distances and distances from base ring centers to helix atoms.

Main Results:

• The program successfully generated atomic coordinates for double-stranded nucleic acid helices.
• Calculated ring current effects for 1H chemical shifts showed satisfactory agreement with experimental and model data.
• Structural visualization and manipulation were achieved on a CRT terminal.

Conclusions:

• The developed program is a valuable tool for calculating physicochemical properties of nucleic acids.
• It enables detailed structural analysis and aids in predicting NMR properties.
• The computational approach complements traditional methods like model construction.