DNA stretching

FIG. 3 Three-dimensional (3D) DNA networks as crystallization matrices for the selective binding of DNA-recognition proteins [8]. The latter, represented by shaded spheres, bind specifically to recognition sites of the six-connected, cubic DNA lattice. For srmphfication, linear double-helical DNA stretches are represented by lines. 

In conclusion, the pBR nucleosome differs from the 5S nucleosome in two main respects its 1-bp untwisting at each of SHL 5 and —5, and its easy access to the positive conformation, which may result from a slight reorientation of entry/exit DNAs (see above). Importantly, these two features are necessarily related, at least statistically, because, as previously mentioned, each nucleosome represents an average of individual nucleosomes which differ from one another in a number of criteria, in addition to their twist (see below). Our model [29] proposed that reorientation is mediated by these local untwistings, which act at a distance to modify the interactions of H3 N-terminal tails with entry/exit DNAs at SHL 7 (Fig. 1(b)) and, perhaps, also further along them, through the rotation they inflict to the distal DNA stretches between SHL 5 to 7 and —5 to —7. 

Fig. 18 AFM image showing bacteriophage-2, DNA stretched between patterned polystyrene lines. White arrows point to the DNA. The distance between polystyrene lines is 17.5 mm and the height of the hnes is 300 nm [125]. Reprinted with permission...

The tob-Gene Cluster of S. sp. DSM 40477. For the sequence analysis of the tobramycin (tob) gene cluster of S. sp. DSM 40477, a persistent DNA stretch of 43,220 bp was analyzed, encoding 37 ORFs from which 20 genes are potentially attributed to the tofc-cluster. Eleven genes are dedicated properly to encode... 

Restriction enzymes are endonucleases which cleave specific sequences within double-stranded DNA stretches. The recognition and cleavage sequences of a routinely used group of endonucleases (called type 11 enzymes) may be four, five, six, or eight bases long and are symmetric across the two strands of DNA. Fig. 2.12 illustrates the cleavage specificity of a widely used sixbase-motif-specific endonuclease, EcoR 1. 

A. Lebrun, Z. Shakked and R. Lavery. Local DNA stretching mimics the distortion caused by the TATA box- binding protein. Proc. Natl. Acad. Sci. USA 94 (1997) 2993. 

Guo, L.J. Cheng, X. Chou, C.F. Fabrication of size-controllable nanofluidic channels by nanoimprinting and its application for DNA stretching. Nano Lett. 2004, 4 (1), 69-73. 

Short DNA stretches containing unmethylated CpG motifs (CpG-ODN) like bacterial DNA are known to be potent inducers of type 1-like immune responses, as indicated by the predominant production of IL-12 and IFN-y, but also IL-6 and TNF-a. Although CpG-ODN has been described as a very powerful inducer of the immune response, side effects caused by the strong induction of systemic IL-6 and TNF-a have been reported in rodents [36, 37]. 

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