NUPARM-Plus

NUPARM-Plus analyzes and generates sequence-dependent structural variations in nucleic acids by computing local inter-basepair and intra-basepair geometric parameters for DNA and RNA.

Key Features:

• Local Inter-Basepair Parameters: Computes tilt, roll, twist, shift, slide, and rise for successive base pairs and parameterizes polymeric geometry across all 16 possible dinucleotide steps.
• Intra-Basepair Parameters: Represents propeller twist, buckle angle, opening angle, and C6...C8 distance to model variations within individual base pairs while maintaining a fixed sugar-phosphate backbone conformation per nucleotide.
• Versatility Across Nucleic Acid Types: Supports analysis of single-stranded and double-stranded helices for both DNA and RNA.
• Model Generation Capabilities: Generates double-helical models with the sugar-phosphate backbone fixed in B-form DNA by default and can produce A-form DNA and RNA duplex structures via modified input parameters.

Scientific Applications:

• Structural Biology: Enables modeling and analysis of DNA and RNA conformational geometry and sequence-directed structural variation.
• Genomics and Molecular Biology: Facilitates studies of sequence-specific structural effects relevant to genetic regulation and molecular interactions.
• Drug Design and Development: Supports modeling of nucleic acid conformations to inform design of molecules targeting specific DNA or RNA sequences.

Methodology:

Computes geometric and coordinate-based parameters defining local inter-basepair (tilt, roll, twist, shift, slide, rise) and intra-basepair (propeller twist, buckle, opening, C6...C8 distance) values derived from empirical data; parameterizes all 16 dinucleotide steps; fixes the sugar-phosphate backbone in standard conformations while allowing variations in other structural elements; accepts modified input parameters to generate B-form (default) or A-form DNA and RNA duplex models.