4MRNA: a new approach for nucleic acid molecular replacement using models with diverse parameter patterns

Abstract

Structural analysis of nucleic acids lags behind that of proteins, partly because most fundamental structural analysis techniques have been primarily developed for proteins. The molecular replacement (MR) method, commonly used for phase determination in protein crystallography, encounters unique challenges when applied to nucleic acids. Nucleic acids can have different three-dimensional structures even with the same sequence, which often renders database entries or predicted models unsuitable as search models for MR. To overcome the limitation, we developed a novel strategy termed 4MRNA, which stands for Massive Multi-type Model Molecular Replacement for Nucleic Acids. This method introduces a new principle for MR, which is the systematic creation of diverse search models through parameter adjustment. By identifying the parameters that critically influence MR and generating models based on their statistical analysis, 4MRNA can provide search models that closely approximate target structures and thereby improve the success rate of MR. Its effectiveness was validated across comprehensive test cases including canonical duplexes, duplexes with bulges and internal loops, the more complex structure of transfer RNA, and a previously unreported DNA structure. 4MRNA is anticipated to become an indispensable tool for nucleic acid structure determination, profoundly advancing fundamental research and extending its impact to wide-ranging applications including structure-based drug design and nucleic acid nanotechnology.