Gene machines

Abstract:

Despite extensive studies on transcription mechanisms, it is unknown how termination complexes are disassembled, especially in what order the essential components dissociate. Our single-molecule fluorescence study unveils that RNA transcript release precedes RNA polymerase (RNAP) dissociation from the DNA template much more often than their concurrent dissociations in intrinsic termination of bacterial transcription. As termination is defined by the release of product RNA from the transcription complex, the subsequent retention of RNAP on DNA constitutes a previously unidentified stage, termed here as recycling. During the recycling stage, post-terminational RNAPs one-dimensionally diffuse on DNA in downward and upward directions, and can initiate transcription again at the original and nearby promoters in the case of retaining a sigma factor. The efficiency of this event, termed here as reinitiation, increases with supplement of a sigma factor. In summary, after releasing RNA product at intrinsic termination, recycling RNAP diffuses on the DNA template for reinitiation most of the time.

Abstract:

In this work we present a mathematical approach to model the kinetic behavior of DNA enzymes (DNAzymes) in order to predict their activity, which will assist future sequence designs. The model has been designed based on multiple previous reports since no general reaction mechanism has been fully described for DNAzymes to date. To better understand this, we also present first of its kind study of the DNAzyme catalytic reaction at the single molecule (SM) level.