Stringency relation

The concentration of a specific nucleic acid sequence in a sample can be measured by hybridization with a suitable labeled DNA probe. After hybridization, nuclease is used to destroy unhybridized probe and the probe remaining is a measure of the concentration of the target sequence. The hybridization conditions can be altered to ensure that only identical sequences (high stringency conditions) or identical plus related sequences (low stringency conditions) will hybridize with the probe and hence be detected. 

Paramount to the success of this approach is that efficient and reliable methods and multi-step sequences for the total synthesis of natural products and analogues thereof on polymeric supports are available. The corresponding transformations must proceed with a degree of selectivity and robustness typical of related classical solution phase transformations, irrespective of the stringencies and differing demands imposed by the anchoring to the polymeric support. 

Hybridization can be used to classify the DNAs of various organisms. For example, human DNA is 98 percent identical to that of chimpanzees, and these two DNAs form a duplex under stringent conditions. Related sequences of humans and birds can also form hybrids, but only at a much lower stringency. 

Set the threshold for PWMs identity. TFBS that are predicted using PWMs are assigned scores during the identification process. This threshold sets a minimum relative score of a TFBS hit to be considered in the analysis, in percentages. The lower PWM threshold, the more sites will be predicted but also more false-positives are found. The default value is set to 80%. Decrease the stringency for analysis of diverged sequences (e.g., from human and fish) and increase when closely related species are analyzed. 

The above discrepancies seem to be due mainly to the stringencies of the end-points in each test. However, one can also doubt the applicability of these tests for cannabinoids. These tests were developed for opiates and may not necessarily parallel and be fully relevant to THC activity in man. Indeed, recent work on electrodes implanted into several distinct brain areas of the rat led to the conclusion that the apparent analgesia produced by the cannabinoids is more related to their disruption of discharge in response to some synthetic impact rather than to a depression of pain pathways [130]. The question whether cannabinoids cause analgesia by interference with pain reception or with pain perception is still unresolved. 

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