Biochemical probes

Antibiotic Mg complex induced alteration in the ultrastructural changes in the native and HI depleted chromatin were monitored by thermal melting analysis, polyacrylamide gel mobility assay, dynamic light scattering experiments and transmission electron microscopic studies. Micrococcal nuclease digestion is the biochemical probe to assess the accessibility of the antibiotic Mg + complexes to nucleosomal DNA. 

One experimental tool in this direction is provided by some enveloped animal viruses which mature at the cell surface of infected cells (K Sri inen and Renkonen, 1977 Lenard, 1978). Such viruses include influenza virus, Semliki Forest virus (SFV), Sindbis virus, and vesicular stomatitis virus (VSV). They are extremely simple in makeup and hence are very well characterized. They can be tagged with biochemical probes in many different ways. They infect many animal cells in culture, and after infection turn the cells into factories for the production of virus progeny. The protein-synthesizing machinery of the host cell is programmed by the viral RNA to make viral proteins exclusively and these include the viral surface glycoproteins. These are synthesized with signal peptides and inserted into the ER membrane (Katz et ai, 1977 Garoff et... 

The structural modification of natural products is useful in several ways. The known pharmacology of bisindole alkaloids is enriched by the diversity of chemical structures that are made available by structure modification and total synthesis. These molecules have served as biochemical probes in several areas of biology, especially in those of microtubule assembly and drug resistance. The most elusive prize, however, has remained the discovery of new compounds with clinical activity. In recent years several compounds have been evaluated in clinical trials, but vinblastine and vincristine remain the only bisindole alkaloids approved for the treatment of cancer in the United States. These compounds are joined by vindesine in Europe, and at least two new derivatives are the subject of ongoing clinical trials. Considering the breadth of chemical research in this area, the overall yield as measured by new compounds with clinical activity has been relatively low, but this observation is not unique in history of analog development in cancer research. Nevertheless, the search continues, and this chapter details the chemical endeavors to discover a new bisindole alkaloid with clinical activity. 

ClPCNB (Figure 2), was chosen as the primary biochemical probe to extend studies on GSH conjugate catabolism In higher plants for the following reasons ... 

The naturally occurring nucleoside/nucleotide antibiotics, which have been isolated from bacteria, fungi, blue-green algae, and marine sponges, have proven to be useful biochemical probes in eucaryotic, procaryotic, viral, fungal, and plant systems. Some excellent reviews on the nucleo-side/nncleotide antibiotics are available. 

Analogues of complex saccharides, in which one or other of the acetal oxygens is replaced by a methylene residue or other heteroatoms, have received attention as biochemical probes and as potential therapeutic agents. The use of l-thio-1,2-isopropylidene acetals (TIA s) as annulating synthons for highly hydroxylated systems is illustrated by the synthesis of (3-C-, p-aza-C- and P-carba- galacto disaccharides. 

Park, C.-H. and Givens, R.S. (1997) New photoactivated protecting groups. 6. p-Hydroxyphenacyl A phototrigger for chemical and biochemical probes. Journal of the American Chemical Society, 119, 2453-2463. 

Chau LK, Lin YF, Cheng SF et al (2006) Fiber-optic chemical and biochemical probes on localized surface plasmon resonance. Sensors Actuators B Chem 113 100-105... 

Natural product research is at its highest level now due to unmet needs, remarkable diversity of structures and activities, utility as biochemical probes, novel and sensitive assay methods, improvements in isolation, purification and characterization, and new production methods." Many new products have been made by genetic methods involving modification or exchange of genes between organisms to create hybrid molecules the technique is known as combinatorial biosynthesis. ... 

A number of biochemical probes containing diazirine moieties as arylcarbene precursors have been synthesized. These include a photolabile oligodeoxyribonu-cleotide, a photoactivatable antagonist for the binding site of the tachykinin NK2 receptor, and a biotinylated lactose derivative as a photoprobe for GM3 synthase. ... 

Avermectins and the related milbemycins may be a very useful biochemical probe for understanding the function and mechanism of nervous systems in invertebrates and vertebrates. 

Fig. 2. Biochemical probes for NM conversion in vitro. The N and M regions of Sup35 have distinct sensitivities to the proteases chymotrypsin (CHY) and endoproteinase Glu-C (V8) CHY sites are exclusively found in N, while V8 sites are limited to M. V8 Anti-Sup35 Western blot of NM alone (—) or following digestion with V8 (arrow). NM was removed from an assembly reaction over a time course, and each sample was then treated with protease for the same amount of time. CHY Anti-Sup35 Western blot of NM alone (—) or following digestion with CHY (arrow) as for V8. SDS Anti-Sup35 Western blot of NM following incubation in 2% SDS at either 100°C or 25°C for 10 min. Samples were taken over the same time course as for V8 and CHY.

Numerous studies have used natural product-hased biochemical probes to investigate the interaction between HIE-let protein and Hsp90. The molecular chaperone Hsp90 binds to the HIE-let PAS domains and stabilizes HIE -1 ct protein, and the HIE -1/3/ARNT subunit competes for the same binding sites with Hsp90 to stabilize HIE-lct protein. " GA (14) has been shown to inhibit the activation of HIE-1 by promoting pVHL-independent proteasomal degradation of HIE-let protein under both normoxic and hypoxic condi-... 

Detailed time course analysis of NM fiber formation provided insight into the mechanism of nucleation (Serio et al., 2000). Specifically, a series of biochemical probes and microscopy techniques were used in concert to determine if preformed NM fibers acted as nuclei for con-... 

Other novel biochemical probes prepared from the ornithine analogue (VIIL268) were the diazo compounds (VIII,313) and (VIIL314) [376], and the biotin derivative (VIIL315) [376]. Another interesting biotin derivative (VIIL228) vide supra) has been prepared from a- -butylMTX by condensation with biotin hydrazide followed by acidolysis [333]. 

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