Structure-specific recognition proteins

Chemical and Genetic Probes—Nanotube-tipped atomic force microscopes can trace a strand of DNA and identify chemical markers that reveal DNA fine structure. A miniaturized sensor has been constructed based on coupling the electronic properties of nanotubes with the specific recognition properties of immobilized biomolecules by attaching organic molecules handles to these tubular nanostructures. In one study, the pi-electron network on the CNT is used to anchor a molecule that irreversibly adsorbs to the surface of the SWNT. The anchored molecules have a tail to which proteins, or a variety of other... 

Ma JB, Yuan YR, Meister G et al (2005) Structural basis for 5 -end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434 666-670... 

The leucine zipper itself does not participate in the recognition it is only utilized for dimerization of the proteins. The N-terminal end of the basic leucine zipper motif is relatively unstructured in the absence of DNA. A helical structure is induced upon binding to DNA allowing specific contacts to the recognition sequence. Dimer formation is a prerequisite for the exact positioning of the N-terminal basic end in the major groove of the DNA. Analogous to the dimeric structure of the protein, the DNA sequence displays 2-fold synunetry (see 1.2.4). 

There are always numerous H-bond contacts formed between the recognition sequence and the binding protein. The pattern of H-bond donors and H-bond acceptors is determined by the sequence and conformation of the DNA as well as by the specific structure of the protein. Both together lay the foundation for a specific recognition of the DNA by the protein. 

The detailed analysis of DNA structure in the region of contact with the binding protein often displays distinct divergence from the parameters of classical B-DNA structure. The specific sequence-determined conformation of the DNA is often a prerequisite for a specific recognition. This recognition mechanism is, for example, realized with the Trp-repressor, where the sequence determines a certain spatial arrangement of the... 

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