Cotranscriptional kinetic folding of RNA secondary structures Including pseudoknots

Hong Thanh Vo*, Dani Korpela, Pekka Orponen

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review


Computational prediction of ribonucleic acid (RNA) structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation. We investigate RNA secondary structure formation, including pseudoknots, that takes into account the cotranscriptional effects. We propose a single-nucleotide resolution kinetic model of the folding process of RNA molecules, where the polymerase-driven elongation of an RNA strand by a new nucleotide is included as a primitive operation, together with a stochastic simulation method that implements this folding concurrently with the transcriptional synthesis. Numerical case studies show that our cotranscriptional RNA folding model can predict the formation of conformations that are favored in actual biological systems. Our new computational tool can thus provide quantitative predictions and offer useful insights into the kinetics of RNA folding.

Original languageEnglish
Pages (from-to)892-908
Number of pages17
Issue number9
Early online date26 Apr 2021
Publication statusPublished - Sep 2021
MoE publication typeA1 Journal article-refereed


  • cotranscriptional folding
  • kinetic simulation
  • RNA secondary structure


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