Binding ratio

Reynolds, J.A., Tanford, C. (1970). Binding of dodecyl sulfate to proteins at high binding ratios. Possible implications for the state of proteins in biological membranes. Proc. Natl. Acad. Sci. USA 66, 1002-1007. 

One would still like to examine the effect of ethidium on the torsional rigidity and dynamics at high binding ratios. One would also like to test the Forster theory for excitation transfer between bound ethidium molecules, since it has been questioned/65- This is possible in principle by deconvoluting the effects of depolarization by excitation transfer on the FPA, as will be shown subsequently. DLS also provides crucial information on this same question. 

At binding ratios r > 0.27, both linear and supercoiled DNAs show evidence of a marked structural change. A component with intermediate lifetime (t 5 ns) appears in the ethidium fluorescence decay, which may represent a partially intercalated species. The apparent torsion constants become highly nonuniform and exhibit considerably altered values. The long-range torsion constant increases appreciably for the linear DNA, but decreases for the supercoiled DNAs, which are substantially positively supercoiled at that point.(53)... 

The DNA might actually stiffen, as found also for chloroquine at somewhat higher binding ratio (r 0.30). 

A related observation is that fully relaxed supercoiled DNA/dye complexes are somehow different from nicked circular DNA/dye complexes in the presence of the same concentration of free dye, where the binding ratios should be the same. This is readily seen in gel electrophoresis in the presence of sufficient dye concentration so that at least one, but not all, of the topoisomers is positively supercoiled. The slowest moving, presumably fully relaxed, topoisomer migrates significantly faster than the nicked circle, and this difference increases with the amount of dye present. This is not observed with chloroquine, perhaps because the effect is too small. However, it is readily apparent in the original gels of Keller0 61) in which ethidium was used to unwind the topoisomers. We have confirmed this effect for ethidium and have observed similar behavior for proflavine, 9-aminoacridine, and quinacrine. 

FPA studies at extremely low binding ratios (1/400-1/700 bp) to assess the DNA motion were carried out on ethidium intercalated in calf thymus121 60) and chicken ied-cell(61) chromatin. Under the conditions of these experiments, ethidium is believed to be intercalated only in the linker DNA, and excitation transfer is believed to be negligible. The amplitude of angular motion, or depolarization, at any given time is much lower than in... 

The contents are mixed thoroughly, and are allowed to come to equilibrium (1 hour at 4°C). During this incubation period, the appropriate number of filters are soaked in ice-cold buffer. We routinely use Whatman GF/C filters since we have found that these yield the best specific/nonspecific binding ratio in our experiments. For other applications, the suitability of other types of filters may have to be experimentally determined. 

S,R)-p F]Fluoro-CGP 12388 4 was prepared as the less hydrophilic counterpart of the promising non-subtype-selective jS-AR radioligand (S)-[ C]CGP 12388 [97]. PET studies of both, the F- and C-derivative, in male Wistar rats resulted in pulmonary total-to-nonspecific binding ratios of 2.0 for... 

Table 7.2 Values of Binding Ratio and Computed Descriptors for Muscarinic Agonists...

The weakest parts of this study are that unknown base sequences intervene between D/A pairs at any given separation distance and an indirect argument must be made to establish the D/A distances. Dye binding studies show that at saturation EB+ and AOH+ have binding ratios of 0.5 dye/base pair, while DAP2+ has a... 

Kurz H, Trunk H, Weitz B (1977) Evaluation of Methods to Determine Protein-binding of Drugs. Arzneimittelforschung (Drug Research) 27(7) 1373-1380 Nakai D, Kumamoto K, Sakikawa C et al. (2003) Evaluation of the Protein Binding Ratio of Drugs by A Micro-Scale Ultracentrifugation Method. Journal of Pharmaceutical Sciences 93 847... 

Numerous cannabinoids, anandamides and heterocyclics have been compared for CBj and CB2 binding [87], Most compounds did not differ significantly in their binding values for the two receptors except the specific CBj antagonist SR141716A (see below) which binds weakly to CB2 and the indole compound JWH-015 (20) which showed a CBj/CB2 binding ratio of 27.75. Busch-Petersen etal. synthesized a series of cannabinoids in which rotation around the Cj -C2 bond was blocked [102]. The compound with the cis-heptene side-chain (21) had the highest affinity for CBj (0.89 [iM) with the widest separation between CBj and CB2 affinities. Pertwee et al. showed... 

The detectable amount of adsorbed species can be extremely low. A retention time shift of Atr=0.310 at a modest G (103 g) with w=250 pm results in only -10 17gof adsorbed mass (density 1.4 g/cm3). This mass corresponds to a very small layer, only 0.6 A thick on a 0.2 pm sphere [186]. The above approach has been used to measure protein adsorbed on latex surfaces [186-188], which is relevant to immunodiagnostic assays and biomedical implants. Complete adsorption isotherms can be measured [186] and antigen-antibody binding ratios determined [187]. 

A 38-year-old man with schizophrenia secretively smoked marijuana during a neuroimaging study. A comparison of two sets of images, before and after marijuana inhalation, showed a 20% reduction in the striatal dopamine D2 receptor binding ratio, suggestive of increased synaptic dopaminergic activity. 

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