NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

Area of Science:

• Structural biology
• Computational chemistry
• Bioinformatics

Background:

• Understanding nucleic acid structure is crucial for molecular biology.
• Sequence-directed structural variations present challenges for modeling.
• Existing tools may not fully capture the nuances of non-uniform nucleic acid structures.

Purpose of the Study:

• To introduce NUPARM and NUCGEN software packages.
• To provide tools for analyzing and generating non-uniform nucleic acid structures.
• To facilitate the study of sequence-directed structural variations.

Main Methods:

• Definition of local inter basepair parameters (tilt, roll, twist, shift, slide, rise) using two successive basepairs.
• Inclusion of intra basepair parameters (propeller, buckle, opening, C6...C8 distance).
• Generation of polymeric structures with varying geometries for all 16 dinucleotide steps.

Main Results:

• NUPARM enables analysis of both DNA and RNA, including single and double-stranded helices.
• NUCGEN generates double helical models, with default B-form DNA backbone.
• NUCGEN can be adapted to generate A-form DNA and RNA duplex structures.

Conclusions:

• NUPARM and NUCGEN offer a robust framework for modeling sequence-directed structural variations.
• The software facilitates the creation of diverse nucleic acid geometries.
• These tools are valuable for research in nucleic acid structure and function.