Titlebook: Bacterial Chromatin; Methods and Protocol Remus T. Dame Book 2018 Springer Science+Business Media, LLC, part of Springer Nature 2018 nucleo

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Imaging of Transcription and Replication in the Bacterial Chromosome with Multicolor Three-Dimensionrevealing “bacterial nucleolus-like structure or organization,” “nucleolus-like compartmentalization of the transcription factories,” and “spatial segregation of the transcription and replication machineries” have enhanced our understanding of the dynamic landscape of the bacterial chromatin. This c

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Atomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization a simple cell manipulation procedure that enables step-wise dissection of the nucleoid. The procedure includes (1) on-substrate-lysis of cells, and (2) enzyme treatment, followed by atomic force microscopy. This type of dissection analysis permits analysis of nucleoid structure ranging from the fun

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Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteinslices. Detecting DNA bridge formation generally involves the use of complex single-molecule techniques (atomic force microscopy, magnetic, or optical tweezers). Although DNA bridging can be qualitatively described, quantification of DNA bridging and bridging dynamics using these techniques is challe

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Approaches for Determining DNA Persistence Length Using Atomic Force Microscopynical properties of DNA polymers depend on electrostatics and the strength of DNA base stacking by studying double-stranded DNA molecules incorporating several different neutral and charged base modifications. Here, we describe ten complementary approaches for determining DNA persistence length by A

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Quantitation of DNA-Binding Affinity Using Tethered Particle Motiony of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered Particle Motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to reliably measure binding constants of proteins binding to DNA, provided that they distort DNA.

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Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-Stretching with Single- chapter, we describe how the interaction between nucleoid-associated proteins and flow-stretched DNAs can be visualized on the single-molecule level. We describe three different experimental schemes that allow one to directly observe how these proteins that make up bacterial chromatin, associate wi

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