DNA gyrase is a target of quinolone antibacterial agents, but the molecular details of the quinolone-gyrase interaction are not clear. Quinolone resistance mutations frequently occur at residues Ser(83) and Asp(87) of the gyrase A subunit, suggesting that these residues are involved in drug binding. Single and double alanine substitutions were created at these positions (Ala(83), Ala(87), and A...

MOTIVATION Completely sequenced genomes allow for detection and analysis of the relatively weak periodicities of 10-11 basepairs (bp). Two sources contribute to such signals: correlations in the corresponding protein sequences due to the amphipatic character of alpha-helices and the folding of DNA (nucleosomal patterns, DNA supercoiling). Since the topological state of genomic DNA is of importa...

DNA gyrase is an essential type II topoisomerase found in bacteria. We have previously characterized DNA gyrase from Mycobacterium tuberculosis and Mycobacterium smegmatis. In this study, several monoclonal antibodies were generated against the gyrase A subunit (GyrA) of M. smegmatis. Three, MsGyrA:C3, MsGyrA:H11 and MsGyrA:E9, were further analyzed for their interaction with the enzyme. The mo...

Transcription of highly expressed genes has been shown to occur in stochastic bursts. But the origin of such ubiquitous phenomenon has not been understood. Here, we present the mechanism in bacteria. We developed a high-throughput, in vitro, single-molecule assay to follow transcription on individual DNA templates in real time. We showed that positive supercoiling buildup on a DNA segment by tr...

The short supercoiled circular DNA molecules are shown to be glassy systems and canonical Metropolis Monte Carlo simulations of the systems tend to get stuck in local metastable energy basins. A Monte Carlo algorithm is developed to alleviate the problem of "ergodicity breaking" of the glassy systems, in which the Markov process is driven by an explicitly analytic weight factor with enhanced pr...

The application of forces and torques on the single molecule level has transformed our understanding dynamic properties biomolecules, but rare intermediates have remained difficult to characterize due limited throughput. Here, we describe a method that provides 100-fold improvement in throughput force spectroscopy measurements with topological control, which enables routine imaging 50,000 molec...

The paper by Sawitzke and Austin (1) ties together all three conclusions. Their work concerns the Muk (from the Japanese mukaku, meaning anucleate) protein complex of Escherichia coli, which was discovered and characterized by Hiraga and coworkers (2). Mutations in any of the three muk genes, mukB, mukE, and mukF, disrupt chromosome segregation such that many progeny have missing or incomplete ...

Objective: In this paper, we have introduced topoisomerase inhibitors, mechanism of action and types of them. DNA topoisomerases are ubiquitous enzymes that catalyze essential enzymes to solve the topological problems accompanying key nuclear processes such as DNA replication, transcription, repair and chromatin assembly by introducing temporary single or double strand breaks in the DNA. Result...