2025/01/11 by Tomasz Wirecki, Grzegorz Łach, Nagendar Goud Badepally +6 · 2 voices
Biochemistry, Genetics and Molecular Biology · #RNA Research and Splicing #RNA and protein synthesis mechanisms #RNA modifications and cancer
paper · pdf · doi:10.1093/nar/gkae1306
openalex publication_date 2025/01/11 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
Designing RNA sequences that form a specific structure remains a challenge. Current computational methods often struggle with the complexity of RNA structures, especially when considering pseudoknots or restrictions related to RNA function. We developed DesiRNA, a computational tool for the design of RNA sequences based on the Replica Exchange Monte Carlo approach. It finds sequences that minimize a multiobjective scoring function, fulfill user-defined constraints and minimize the violation of restraints. DesiRNA handles pseudoknots, designs RNA-RNA complexes and sequences with alternative structures, prevents oligomerization of monomers, prevents folding into undesired structures and allows users to specify nucleotide composition preferences. In benchmarking tests, DesiRNA with a default simple scoring function solved all 100 puzzles in the Eterna100 benchmark within 24 h, outperforming all existing RNA design programs. With its ability to address complex RNA design challenges, DesiRNA holds promise for a range of applications in RNA research and therapeutic development.