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- W4220921877 abstract "Abstract There is increasing interest in the roles of covalently modified nucleotides in RNA. There has been, however, an inability to account for modifications in secondary structure prediction because of a lack of software and thermodynamic parameters. We report the solution for these issues for N 6 -methyladenosine (m 6 A), allowing secondary structure prediction for an alphabet of A, C, G, U, and m 6 A. The RNAstructure software now works with user-defined nucleotide alphabets of any size. We also report a set of nearest neighbor parameters for helices and loops containing m 6 A, using experiments. Interestingly, N 6 -methylation decreases folding stability for adenosines in the middle of a helix, has little effect on folding stability for adenosines at the ends of helices, and increases folding stability for unpaired adenosines stacked on a helix. We demonstrate predictions for an N 6 -methylation-activated protein recognition site from MALAT1 and human transcriptome-wide effects of N 6 -methylation on the probability of adenosine being buried in a helix." @default.
- W4220921877 created "2022-04-03" @default.
- W4220921877 creator A5002272329 @default.
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- W4220921877 creator A5043782644 @default.
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- W4220921877 creator A5080705201 @default.
- W4220921877 date "2022-03-11" @default.
- W4220921877 modified "2023-10-14" @default.
- W4220921877 title "Secondary structure prediction for RNA sequences including N6-methyladenosine" @default.
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