proto-Nucleic Acid Builder

proto-Nucleic Acid Builder models three-dimensional structures of DNA, RNA, and diverse nucleic acid analogs, enabling construction of alternative backbones and nucleobases to explore xeno nucleic acids (XNAs) and related prebiotic polymers.

Key Features:

• Versatile modeling capabilities: Accepts 3D structures of isolated backbones or nucleobases to construct a wide range of nucleic acid analogs.
• Helical and backbone conformation searches: Performs helical parameter searches and backbone conformation searches guided by geometric and energetic criteria to identify plausible structures.
• Torsion-driven conformation search: Uses a torsion-driven procedure that systematically adjusts torsional angles to predict conformations that align with experimental data and relate helical structure to backbone conformation.

Scientific Applications:

• XNA polymer design and exploration: Enables rational design and computational exploration of novel xeno nucleic acids (XNAs) and alternative nucleic acid chemistries.
• Origin-of-life and prebiotic chemistry: Identifies plausible nucleic acid analogs and prebiotic polymers that could inform hypotheses about early genetic systems.
• Synthetic biology and biotechnology: Supports modeling of alternative backbones and nucleobases for development of novel nucleic acid structures with potential therapeutic or industrial properties.

Methodology:

pNAB employs torsion-driven conformation searches that systematically adjust torsional angles, supplemented by helical parameter and backbone conformation searches, and applies geometric and energetic evaluation criteria to select structures consistent with experimental data.