Cotranscriptional kinetic folding of RNA secondary structures Including pseudoknots

Hong Thanh Vo*, Dani Korpela, Pekka Orponen

*Tämän työn vastaava kirjoittaja

Tutkimustuotos: LehtiartikkeliArticleScientificvertaisarvioitu

Abstrakti

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.

AlkuperäiskieliEnglanti
Sivut892-908
Sivumäärä17
JulkaisuJOURNAL OF COMPUTATIONAL BIOLOGY
Vuosikerta28
Numero9
Varhainen verkossa julkaisun päivämäärä26 huhtikuuta 2021
DOI - pysyväislinkit
TilaJulkaistu - syyskuuta 2021
OKM-julkaisutyyppiA1 Julkaistu artikkeli, soviteltu

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