DNA/protein complexes

Nucleosome (Section 28.9) A DNA-protein complex by which DNA is stored in cells. 

Characterization of various types of damage to DNA by oxygen-derived species can be achieved by the technique of gas chromatography-mass spectrometry (GC-MS), which may be applied to DNA itself or to DNA-protein complexes such as chromatin (Dizdaroglu, 1991). For GC-MS, the DNA or chromatin is hydrolysed (usually by heating with formic acid) and the products are converted to volatile derivatives, which are separated by gas chromatography and conclusively identified by the structural evidence provided by a mass spectrometer. Stable isotope-labelled bases may be used as internal standards... 

Overall, it can be envisioned that the Py-G group 47 represents an important label for the time-resolved studies of DNA dynamics and stacking interaction [123] and could be applied especially for assays in which conformational changes or base-flipping processes are essential in observation, such as in the investigation of DNA-protein complexes with DNA repair proteins. 

The HMQC approach has also been employed in the measurements of 3/(H3 P) and 3/(C4 P) coupling constants using a 2D 31P spin-echo difference constant-time experiment [44] to increase sensitivity by a factor of 1.5-2.4 in a 17 kDa DNA-protein complex. 

The tissue or cell sample is firstly homogenized in a buffer containing a detergent such as Triton X-100 and sodium deodecyl sulphate (SDS), which disrupts the cell and dissociates DNA-protein complexes. Protein and RNA are then removed by sequential incubations with a proteolytic enzyme (usually proteinase K) and ribonuclease. Finally the DNA is extracted into ethanol. Ethanol only precipitates long chain nucleic acids and so leaves the single nucleotides from RNA digestion in the aqueous layer. 

The higher-order architectures of DNA/protein complexes are achieved on the balance of the physical properties of DNA and the interactive forces of DNA-binding proteins (Hizume et al., 2002 Yoshimura et al, 2000). The superhelical strain of the DNA has been suggested to play a critical role in a variety of genome events such as transcriptional regulation and DNA replication (Opel et al, 2001). 

Table 15.1 Crystallization conditions for DNA-protein complexes using polyethylene glycol (PEG) as a precipitant... 

The low molecular weight L-histidine nickel complex can cross biological membranes (Sarkar 1984). How nickel gets inside of cells may determine the effects of the nickel compounds. If nickel ions are taken into the cytosol and bind to protein, they are not delivered to the nucleus, which prevents the interaction of nickel ions with DNA. Crystalline nickel compounds are phagocytized and nickel ions are delivered to the nucleus where they interact with DNA or DNA protein complexes (Costa 1995). 

Okada,T.,W.J Ramsey, J Munir, O.Wildner, and R.M. Blaese, Efficient directional cloning of recombinant adenovirus vectors using DNA-protein complex. Nucleic Acids Res, 1998.26(8) 1947-50. 

Pervushin et al.199 have measured both 2hJ(N, N) and lhJ(N, H) couplings for a DNA-protein complex and compared such values with those measured in the... 

Fluorescence determinations are important to analyze cysteine, guanidine, proteins, (LSD), steroids, a number of enzymes and coenzymes, and some vitamins, as well as several hundred more substances. A fluorometer can be used to verify conformational changes in multipartite operator recognition by. -repressor as explained in a journal article by Deb et al. (2000). Upon titration with single operators site, the tryptophan fluorescence quenches to different degrees, suggesting different conformations of the DNA-protein complexes. 

This principle has been extended to DNA-protein complexes or genes which can be entrapped and delivered to target cells, the major advantage of the systems being that they tend to be able to penetrate the cell walls, thereby enabling external materials such as genes to penetrate to the cell nucleus. 

DNA contains the genetic information transmitted to each daughter cell when cells divide. The DNA usually exists in the form of nucleoprotein (DNA-protein) complexes called chromosomes. A prokaryotic cell contains a single chromosome. Prior to cell division this chromosome duplicates and segregates so that an identical complement of DNA goes to each of two newly formed daughter cells. 

DNA in eukaryotic chromosomes is complexed with histone proteins in complexes called nucleosomes. These DNA-protein complexes are disassembled directly in front of the replication fork. The nucleosome disassembly may be rate-limiting for the migration of the replication forks, as the rate of migration is slower in eukaryotes than prokaryotes. The length of Okazaki fragments is also similar to the size of the DNA between nucleosomes (about 200 bp). One model that would allow the synthesis of new eukaryotic DNA and nucleosome formation would be the disassembly of the histones in front of the replication fork and then the reassembly of the histones on the two duplex strands. Histone synthesis is closely coupled to DNA replication. 

The stacking of nucleobases has been found to be involved in several DNA self-assembly processes, promoting the formation of DNA-DNA and DNA-protein complexes in vivo [44, 45], driving end-to-end interactions of DNA double- and triple-helices in semi-dilute solutions [46], or determining the geometry of DNA... 

Begusova M, Gillard N, Sy D, Castaing B, Charlier M, Spotheim-Mauizot M (2005) Radiolysis of DNA-protein complexes. Radiat Phys Chem 72 265-270 Bellon S, Ravanat J-L, Gasparutto D, Cadet J (2002) Cross-linked thymine-purine base tandem lesions synthesis, characterization, and measurement in y-irradiated isolated DNA. Chem Res Toxicol 15 598-606... 

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