Streptavidin biotin binding site

Nitration of the tyrosine rings in the four binding pockets of avidin or streptavidin can be done to increase the steric hinderance within the biotin binding sites (Morag et al., 1996). This process yields chromogenic proteins that have reduced binding affinity for biotin, thus allowing elution of biotinylated molecules under mild conditions. 

Strepavidin A 60 kD extracellular protein of Streptomyces avidinii with four high-affinity biotin binding sites. Unlike avidin, streptavidin has a near neutral isoelectric point and is free of carbohydrate side chains. 

Streptavidin is another biotin binding protein isolated from Streptomyces avidinii that can overcome some of the nonspecificities of avidin (Chaiet and Wolf, 1964). Similar to avidin, streptavidin contains four subunits, each with a single biotin binding site. After some postsecretory modifications, the intact tetrameric protein has a molecular mass of about 60,000 D, slightly less than that of avidin (Bayer et al., 1986, 1989). 

Secondary, nonradioactive labels are usually bulky nucleotide analogues which are less good substrates for most polymerases. For instance, BIO-4-dUTP (biotin attached with a 4-atom spacer arm to C-5 of dUTP Fig. 7.10) is a much better substrate than BIO-16-dUTP. On the other hand, the biotin binding sites are deeply buried in two pairs in the tetrameric avidin molecule. This explains why BIO-4-dUMP residues in DNA, in contrast to those with longer spacer arms, bind poorly to avidin or streptavidin (Leary et al., 1983) whereas antibodies to biotin bind to all BlO-nucleotide analogues equally well. Optimum binding is achieved when about 30 base analogues are introduced per kilobase, otherwise either decreased specific activity or decreased duplex stability is observed. 

Figure 2.8 Models of the QD-b-PE conjugate structure/conformation. (A) b-PE is parallel to the QD surface, and (B) b-PE is fully extended away from the QD. The central QD with a radius of 29 A shown in blue is surrounded by a crimson shell of 25 A thickness representing the DHLA-PEG-biotin. The intermediary streptavidin (SA) protein is shown in yellow with biotin binding sites highlighted in purple. The b-PE ring structure is shown in white, with the multiple chromophores highlighted in red. The inner concentric white circle corresponds to the predicted 53 A Fdrster distance (i ) for the 540 nm QD-b-PE assembly. The second outer white circle is a visual distance marker set at 95 A from the QD center and represents the closest approach of the b-PE to the QD. (Reproduced with permission from I. L. Medintz, T. Pons, K. Susumu, K. Boeneman, A. M. Dennis, D. Farrell, J. R. Deschamps, J. S. Melinger, G. Bao and H. Mattoussi,/. Phys. Chem. C, 2009,113,18552. Copyright (2009) American Chemical Society.) ...

We have also observed that using the streptavidin-biotin interaction as the basis for array fabrication confers an additional major advantage the very high affinity of the streptavidin-biotin interaction means that we quickly start to saturate the available biotin-binding sites on the surface this means that a crude normalisation of protein loading can be achieved without pre-adjusting the concentrations of the crude lysates to... 

Figure 5. Schematic depictions of possible streptavidin configurations on the polymer-coated surfaces (a) binding of more than two PEG—biotin groups to a single (tilted) streptavidin molecule and (b) blocking of biotin-binding sites on streptavidin by a neighboring streptavidin molecule.

For the helically wrapped CNT, two biotin-binding sites face the aqueous solution. As a result, streptavidin-coated CNTs could be coated with biotinylated compounds such as proteins or DNA fragments. Consequently, the streptavidin-bound CNTs could be used as bioreactive docking matrices for applications like drug delivery, gene therapy, and imaging applications. 

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