biostudies-literatureKierzek EU.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of HealthFundacja na rzecz Nauki PolskiejNIGMS NIH HHS1271https://www.ebi.ac.uk/biostudies/studies/S-EPMC8917230biostudies-literatureUnknown13(1)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 N⁶-methyladenosine (m⁶A), allowing secondary structure prediction for an alphabet of A, C, G, U, and m⁶A. 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 m⁶A, using experiments. Interestingly, N⁶-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 N⁶-methylation-activated protein recognition site from MALAT1 and human transcriptome-wide effects of N⁶-methylation on the probability of adenosine being buried in a helix.Nature communicationsSecondary structure prediction for RNA sequences including N⁶-methyladenosine.PMC8917230R01GM076485UMO-2019/33/B/ST4/01422R01 GM076485UMO-2020/01/0/NZ6/00137Watson RMKennedy SDKierzek EZhang XSzabat MKierzek RMathews DHfalseSecondary structure prediction for RNA sequences including N⁶-methyladenosine.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 N⁶-methyladenosine (m⁶A), allowing secondary structure prediction for an alphabet of A, C, G, U, and m⁶A. 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 m⁶A, using experiments. Interestingly, N⁶-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 N⁶-methylation-activated protein recognition site from MALAT1 and human transcriptome-wide effects of N⁶-methylation on the probability of adenosine being buried in a helix.2022-01-01T00:00:00Z2022 Mar2026-05-09T14:25:06.165Z2025-04-06T19:37:01.398ZS-EPMC89172303527747610.1038/s41467-022-28817-4