Nicked proteins

Current analytical methods have difficulty detecting picogram levels of nucleic acids, particularly when high levels of other biopolymers (e.g., proteins) are present. The most widely used assay method employed by the pharmaceutical industry involves a nick translation DNA hybridization method (1). This assay offers high sensitivity and selectivity but has a number of drawbacks. 

DNase 1 j Under appropriate conditions, produces j single-stranded nicks in DNA. Nick translation mapping of hypersensitive sites mapping protein-DNA interactions. 

Horiuchi, M., Nicke, A., Gomeza, J., Aschrafi, A., Schmalzing, G. and Betz, H. (2001) Surface-localized glycine transporters 1 and 2 function as monomeric proteins in Xenopus oocytes. Proc. Natl. Acad. Sci. USA 98,1448-1453. 

Excision Reactions. UvrD protein and DNA polymerase 1 excise the damaged bases and then resynthesize the strand, using the sister strand as a template. The Uvr complex then breaks down, leaving a restored, but nicked, strand. 

N. S. Berrow, The Protein Production Facility, Henry Wellcome Building of Genome Medicine, University of Oxford, UK. nick strubi.ox.ac.uk... 

Knall, C. Young, S. Nick, J.A. Buhl, A.M. Worthen, G.S. Johnson, G.L. Interleukin-8 regulation of the Ras/Raf/mitogen-activated protein kinase pathway in human neutrophils. J. Biol. Chem., 271, 2832-2838 (1996)... 

Figure 5-17 Electron micrograph of a six-noded knot made by the Tn3 resolvase which is involved in movement of the Tn3 transposon (Chapter 27) from one location to another within the genome. Putative six-noded knot DNA was isolated by electroelution from an agarose gel. The knots, which are nicked in one strand, were denatured to allow the nicked strand to slide away and leave a ssDNA knot. This was coated with E. coli rec A protein (Fig. 27-24) to greatly thicken the strand and to permit the sign of each node (designated in the tracing) to be seen. From Wasserman et a/.184...

Isolated "naked" bacterial DNA, from which proteins have been removed, is supercoiled. DNA in the bacterial chromosome is also supercoiled. When naked DNA is nicked, its supercoiling is abolished. In contrast nicking the chromosomal DNA does not abolish its supercoiling. Explain. 

Transketolase 733,736 Translation of genetic information, 5. See also Protein synthesis definition of 5 nick 257 regulation of 536 Translocation... 

If bacterial cells are lysed under certain conditions, e.g., in 1 M NaCl or in the presence of a "physiological" 5 mM spermidine, the entire bacterial chromosome can be isolated.10 The DNA in these isolated chromosomes retains some torsional tension that, however, can be relaxed by nicking with nucleases or by y-irradiation. However, a single nick relaxes the DNA very little. The explanation appears to be that the DNA is held by proteins of the nucleoid matrix in a series of loops (Fig. 27-2). A single nick relaxes just... 

In the second and third stages of replication ( )X174 RF molecules are themselves replicated and are then used for synthesis of new viral (+) strands. At both stages a virally encoded gene A protein, which has endonuclease activity, nicks the duplex. Cutting the (+) strand it leaves a free 3-OH on DNA residue 4305, while the 5 -phospho group of residue 4306 becomes... 

Poly (ADP-ribose). A eukaryotic peculiarity, which is not well understood, is the synthesis of poly(ADP-ribose) chains attached to many sites in nuclear proteins (see also Eq. 15-16). Increased synthesis is observed following damage to DNA.761 763a The poly (ADP-ribose) polymerase binds to DNA near strand breaks or nicks and, using NAD+ as a substrate, synthesizes the highly branched polymer attached to a small number of nuclear target proteins. 

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