Specificity indirect readout

DNA. By far, the most common secondary structure for DNA is the double helix. Sequence-specific recognition of double-helical DNA relies on several factors. First, the array of fimctional groups exposed in the major and minor grooves can be read by DNA-binding ligands. This is referred to as direct readout. However, more subtle factors may also be involved, such as sequence-dependent variation in the shape, flexibility, and hydration of the DNA. Ligands which discriminate among sequences based on these parameters utilize indirect readout of the sequence information. 

The split-ubiquitin system enables signal amplification from a transcription factor-mediated reporter readout (36,37). In one application, the interaction of two membrane proteins forces reconstitution of two halves of ubiquitin, leading to a cleavage event mediated by ubiquitin-specific proteases that release an artificial transcription factor to activate a reporter gene. As discussed, indirect readout of the reporter limits kinetic analysis, and the released transcription factor must translocate to the nucleus. 

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