CHIMERA_NA: A Customizable\nMutagenesis Tool for Structural\nManipulations in Nucleic Acids and Their Complexes

Studying the structure and dynamics of nucleic acids\nand their\ncomplexes is crucial for understanding fundamental biological processes\nand developing therapeutic interventions. However, the limited availability\nof experimentally characterized nucleic acid structures poses a challenge\nfor exploring their properties comprehensively. To address this, we\ndeveloped a customizable mutagenesis tool, CHIMERA_NA, to manipulate\nnucleic acid structures and their complexes. Utilizing the user-friendly\nCHIMERA_NA, researchers can perform mutations in nucleic acid structures,\nenabling the exploration of diverse structural configurations and\ndynamic behaviors. The tool offers the flexibility to generate all\npossible combinations of mutations or specific user-defined mutations\nbased on research requirements. CHIMERA_NA leverages the capabilities\nof UCSF Chimera software, a widely used platform for molecular structure\nanalysis, to facilitate the generation of mutations in nucleic acids.\nOur tool modifies the reference structure of nucleic acids or their\ncomplexes to generate initial coordinates of mutated structures/complexes\nwithin seconds for further computational exploration. This capability\nallows users to extend their investigations beyond structural repositories,\nenabling the study of DNA/RNA drug recognition, nucleic acid–protein\ninteractions, and the intrinsic structural and dynamic properties\nof nucleic acids. By providing a user-friendly and customizable approach\nto nucleic acid mutagenesis, CHIMERA_NA contributes to advancing our\nunderstanding of nucleic acid biology and facilitating drug discovery\nefforts targeting nucleic acid-based mechanisms. CHIMERA_NA is freely\navailable in the Supporting Information of this article.