CHIMERA_NA: A Customizable Mutagenesis Tool for Structural Manipulations in Nucleic Acids and Their Complexes

Abstract

Studying the structure and dynamics of nucleic acids and their complexes is crucial for understanding fundamental biological processes and developing therapeutic interventions. However, the limited availability of experimentally characterized nucleic acid structures poses a challenge for exploring their properties comprehensively. To address this, we developed a customizable mutagenesis tool, CHIMERA_NA, to manipulate nucleic acid structures and their complexes. Utilizing the user-friendly CHIMERA_NA, researchers can perform mutations in nucleic acid structures, enabling the exploration of diverse structural configurations and dynamic behaviors. The tool offers the flexibility to generate all possible combinations of mutations or specific user-defined mutations based on research requirements. CHIMERA_NA leverages the capabilities of UCSF Chimera software, a widely used platform for molecular structure analysis, to facilitate the generation of mutations in nucleic acids. Our tool modifies the reference structure of nucleic acids or their complexes to generate initial coordinates of mutated structures/complexes within seconds for further computational exploration. This capability allows users to extend their investigations beyond structural repositories, enabling the study of DNA/RNA drug recognition, nucleic acid–protein interactions, and the intrinsic structural and dynamic properties of nucleic acids. By providing a user-friendly and customizable approach to nucleic acid mutagenesis, CHIMERA_NA contributes to advancing our understanding of nucleic acid biology and facilitating drug discovery efforts targeting nucleic acid-based mechanisms. CHIMERA_NA is freely available in the Supporting Information of this article.