NUCGEN

NUCGEN generates atomic models of nucleic acid structures from sequence-directed local inter- and intra-basepair parameters to model sequence-dependent structural variation.

Key Features:

• Local Inter-Basepair Parameters: Uses tilt, roll, twist, shift, slide, and rise defined for each of the 16 possible dinucleotide steps to set spatial relationships between successive base pairs.
• Intra-Basepair Variability: Allows modification of intra-basepair parameters including propeller twist, buckle angle, opening angle, and C6...C8 distance to capture intra-pair geometry.
• Fixed Backbone Conformation: Maintains a fixed sugar-phosphate backbone conformation across nucleotides while varying inter- and intra-basepair parameters.
• Versatile Structure Generation: Generates double-helical models with a B-form DNA backbone by default and can be adapted through input modifications to produce A-form DNA and RNA duplex structures.

Scientific Applications:

• DNA structural modeling: Produces sequence-dependent models of double-stranded and single-stranded DNA, including B-form and A-form variants.
• RNA duplex modeling: Generates A-form RNA duplex structures through parameter adaptation.
• Sequence-directed structural analysis: Enables analysis of how dinucleotide-dependent inter- and intra-basepair parameters drive local and global nucleic acid conformations.

Methodology:

Transforms local doublet parameters into helical parameters which are applied successively to base pairs, aligns the topmost base pair within the (x-y) plane, and adjusts inter- and intra-basepair parameters while maintaining a fixed sugar-phosphate backbone conformation.