We studied the interaction between the integration host factor (IHF), a major nucleoid-associated protein in bacteria, and single DNA molecules. Force-extension measurements of DNA and an analysis of the Brownian motion of small beads tethered to a surface by single short DNA molecules, in equilibrium with an IHF solution, indicate that: (i) the DNA-IHF complex retains a random, although more compact, coiled configuration for zero or small values of the tension, (ii) IHF induces DNA compaction by binding to multiple DNA sites with low specificity, and (iii) with increasing tension on the DNA, the elastic properties of bare DNA are recovered. This behavior is consistent with the predictions of a statistical mechanical model describing how proteins bending DNA are driven off by an applied tension on the DNA molecule. Estimates of the amount of bound IHF in DNA-IHF complexes obtained from the model agree very well with independent measurements of this quantity obtained from the analysis of DNA-IHF crosslinking. Our findings support the long-held view that IHF and other histone-like proteins play an important role in shaping the longscale structure of the bacterial nucleoid.T he genetic material in bacterial cells is organized in a structure called the nucleoid (1-3). In Escherichia coli, this nucleoprotein complex consists of a single circular DNA molecule 4.7 million bp long, RNA, and a large variety of bound proteins. Among these, about 10 so-called histone-like proteins, including HU, integration host factor (IHF), and H-NS (1-3), shape the short-scale structure of the nucleoid by bending DNA locally on binding. These proteins therefore play an important role in compacting the DNA molecule, in addition to other factors such as supercoiling (4), macromolecular crowding (5), and osmotic effects (6).The level of nucleoid-associated proteins changes as a function of bacterial growth. For example, the level of IHF was shown to increase on entry to the stationary phase of growth, becoming one of the major histone-like proteins in the cell (7-10). By binding to specific DNA sites, IHF participates in forming higher-order DNA structures required for replication, sitespecific recombination, phage packaging, and regulation of transcription initiation (8). IHF can also bind to DNA nonspecifically and can be substituted by HU. In fact, IHF and HU possess similar overall structures and share several regions of conserved homologies (11,12).Very little is known about the structural modifications on DNA induced by histone-like proteins in nucleoid formation. In particular, the degree of compaction induced by each of these proteins has not been quantified, and information about the large-scale structure of nucleoprotein complexes is scarce. This deficiency stems in part from the fact that classical techniques used in molecular biology are designed for studying relatively strong DNA-binding sites and cannot appropriately assess the contribution of nonspecific low-affinity interactions. Furthermore, analyses based on electron micr...

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Pattern formation in 3D random media has been a topic of interest in soft matter and biological systems. However, the onset of long-range microscopic ordering has not been explored in randomly moving self-propelled particles due to a lack of model systems as well as local probe techniques. In this article, we report on a novel experiment, using motile Escherichia coli bacteria as a model system, to study the onset of dynamic correlation and collective movement in three-dimension. We use fluctuation of an optically trapped micron-size bead as a detector of correlated bacterial motion, and further study this behavior by analyzing the motility of fluorescent bacteria in a confocal volume. We find evidence of dynamic correlation at very low volume fractions (0.01). We show that the magnitude of this correlation strongly depends on the interbacterial distances and their coupling modes. This opens up possibilities to probe long-range pattern formation in actively propelled cells or organisms coupled through hydrodynamics and/or chemical signaling.

We introduce a method for detecting and tracking small particles in a solution near a surface. The method is based on blocking the backreflected illumination beam in an objective-type total internal reflection microscope, leaving unhindered the light scattered by the particles and resulting in dark-field illumination. Using this method, we tracked the motion of 60-nm polystyrene beads with a signal-tonoise ratio of 6 and detected 20-nm gold particles with a signal-to-noise ratio of 5. We illustrate the method's use by following the Brownian motion of small beads attached by short DNA tethers to a substrate.