The mechanical properties of transcription have recently been shown to play a central role in gene expression. However, a full physical characterization of this central biological process is lacking. In this Letter, we introduce a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase rotation, and DNA supercoiling are coupled. The resulting fram...

Studies of DNA minicircle structures show a strong dependence the shape on linking number. With increasing supercoiling, minicircles can buckle and writhe to relieve torsional stress, which results in complex that deviate greatly from existing models. Using linear elasticity theory, we successfully predict spectrum shapes given length defined We formulate analytical predictions for regime bound...

DNA supercoiling and topoisomerases have long been known to affect transcription initiation. In many studies, topA mutants were used to perturb chromosomal supercoiling. Although such studies clearly revealed that supercoiling could significantly affect gene expression, they did not tell much about the essential function(s) of DNA topoisomerase I, encoded by topA. Indeed, the topA mutants used ...

The combination of DNA force spectroscopy and polarization microscopy fluorescent intercalator dyes can provide valuable insights into the structure under tension. These techniques have previously been used to characterize S-DNA—an elongated conformation that forms when overstretches at forces ? 65 pN. In this way, it was deduced base pairs S-DNA are highly inclined, relative those in relaxed (...

BACKGROUND Transcription in Escherichia coli generates positive supercoiling in the DNA, which is relieved by the enzymatic activity of gyrase. Recently published experimental evidence suggests that transcription initiation and elongation are inhibited by the buildup of positive supercoiling. It has therefore been proposed that intermittent binding of gyrase plays a role in transcriptional burs...

DNA topology has fundamental control over the ability of transcription factors to access their target DNA sites at gene promoters. However, the influence of DNA topology on protein-DNA and protein-protein interactions is poorly understood. For example, relaxation of DNA supercoiling strongly induces the well-studied pathogenicity gene ssrA (also called spiR) in Salmonella enterica, but neither ...

We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an estimation of the effective supercoiling radius and of the twist rigidity of B-DNA. We find that unlike the bending rigidity, the twist rigidity of DNA seems ...

The DNA topoisomerases are a group of fascinating enzymes that play an essential but dangerous game with DNA. They break and rejoin either one or both strands of the double helix to solve the problems of tangling and linking that occur as a result of DNA manipulations (replication, transcription and recombination) in all cells. This basic problem with the DNA structure was recognized by Watson ...