Protein/DNA contacts

Nielsen PE, Jeppesen C, Buchardt 0 (1988) Uranyl salts as photochemical agents for cleavage of DNA and probing of protein-DNA contacts. FEBS Lett 235 122-124... 

Another direct comparison between the photophores, although not in an activity-based setting, was reported by Tate and coworkers [87]. They synthesized dUTP analogs containing four different photoreactive moieties 84a-d (Fig. 9a) and incorporated them enzymatically into DNA constructs. With these, the DNA PAL of yeast RNA polymerase III transcription complexes was studied. It was shown that photolabeling with the diazirine construct (84d) rendered many protein-DNA contacts, whereas labeling with the other three photoreactive moieties (84a-c) proved only marginal. 

Fig. 20.16. Stereo view of the phosphate backbone of the 20 base-pairs long operator DNA fragment in complex with the a-carbon backbone of the dimeric 434 repressor fragment. The dashed lines connect phosphates in the minor groove, which is compressed in the center. HI to HS denote helices 1 to 5, arrows point at close protein-DNA contacts (from [711])...

Meier-Andrejszki L, Bjehc S, Naud JF, Lavigne P, Jelesarov I. Thermodynamics of b-HLH-LZ protein binding to DNA the energetic importance of protein-DNA contacts in site-specific E-box recognition by the complete gene product of the Max p21 transcription factor. Biochemistry. 2007 46 12427-12440. 

Uranyl(III) salts such as U02(0Ac)2 or U02(N03)2 have been used as photochemical agents for DNA cleavage and for probing of protein-DNA contacts (198-199). Single-strand DNA breaks are induced by uranyl acetate or uranyl nitrate under irradiation in the 420-nm region. The binding constant of the UO2 dication is estimated to be of... 

Geyer, H., Geyer, R., and Pingoud, V. (2004) A novel strategy for the identification of protein-DNA contacts by photocrosslinking and mass spectrometry. Nucleic Acids Res., 32 (16), el32. 

Inherent technical limitations of cytological and biochemical methods described could not illuminate the molecular structure of protein-DNA contacts within chro-... 

For a successful analysis the response value at the equilibrium Req for each protein concentration must be known. This requires long protein-DNA contact times, which can be achieved by injecting protein solutions at a slow flow rate (mass transfer does not influence the Req value). The second important parameter for analysis is the response value at protein saturation Rmax- K can be difficult to reach, especially for negatively cooperative interaction. In this case the theoretical maximum binding value can be used ... 

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