Sequence-specific recognition pattern

Because of the preceding properties, our profile procedure appears to produce highly sensitive and specific common pattern representations from limited numbers of defining sequences compared with other current methods (Figs. 5 and 7). This was shown by the construction of such profiles from more than 50 completely unrelated functional families. In more than 90% of the families, the sensitivity and specificity are more than 98%. This is also supported by the repeated sampling study of the complex bacterial transcription initiation factors. Finally, these methods allow for the localized recognition of entire domains within multidomain structures, as seen in Fig. 6. 

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. 

There is now a new version of PromoterScan available, PromoterScan 2.0. This new version is supposed to provide more information from inside the black box which a promoter used to be for version 1.0 and is also able to compare a predicted promoter to EPD promoter sequences on the basis of the pattern of TF sites. Although this moves promoter comparisons with PromoterScan 2.0 effectively closer to the specific recognition of individual elements this approach is not used for the initial promoter prediction. PromoterScan is available via WWW, which is a definitive advantage for occasional promoter testing. 

Figure 11.9. Tolerance to amino acid variations in the 11 sequence positions with respect to proliferation of the TCC 5G7. Data were calculated as described from the allele-specific DR2b- Activity Pattern and from the Recognition Pattern of TCC 5G7. Letters indicate amino acids from MBP (85-95).

We can also mention the use of bio-sourced building blocks based on cellulose or dextran. Kadla et al. described value-added materials from naturally abundant polymers for system that may serve as a platform for the design and development of biosensors [197]. A hierarchically strucmred honeycomb film from dextran-ft-PS amphiphilic linear diblock copolymers has also been described by Chen et al. leading to ordered porous bio-hybrid films. [198] Honeycomb patterned surfaces functionalized with biomolecules for specific recognition of proteins or bacteria have been also achieved either by self-assembly of amphiphilic copolymers based on galactose moieties [155] or by post-modification with peptide sequences [199]. 

Direct recognition The order of bases can determine the pattern of weak interaction and the specificity of the complex formation. In this case there is a direct recognition of the sequence by the protein. 

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