A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N⁶-Methyladenosine.

ABSTRACT: RNA folding free energy change parameters are widely used to predict RNA secondary structure and to design RNA sequences. These parameters include terms for the folding free energies of helices and loops. Although the full set of parameters has only been traditionally available for the four common bases and backbone, it is well known that covalent modifications of nucleotides are widespread in natural RNAs. Covalent modifications are also widely used in engineered sequences. We recently derived a full set of nearest neighbor terms for RNA that includes N⁶-methyladenosine (m⁶A). In this work, we test the model using 98 optical melting experiments, matching duplexes with or without N⁶-methylation of A. Most experiments place RRACH, the consensus site of N

SUBMITTER: Szabat M 

PROVIDER: S-EPMC11235186 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature