Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators.

ABSTRACT: Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure-function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart str

SUBMITTER: Takahashi MK 

PROVIDER: S-EPMC4878617 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature