Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

ABSTRACT: Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic meas

SUBMITTER: Phan A 

PROVIDER: S-EPMC5393185 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature