Strands grooves

Most sequence-specific regulatory proteins bind to their DNA targets by presenting an a helix or a pair of antiparallel p strands to the major groove of DNA. Recognition of the TATA box by TBP is therefore exceptional it utilizes a concave pleated sheet protein surface that interacts with the minor groove of DNA. Since the minor groove has very few sequence-specific... 

The only sequence-specific hydrogen bonds between TBP side chains and the bases in the minor groove occur at the very center of the TATA box (Figure 9.7). The amide groups of two asparagine side chains donate four hydrogen bonds, two each to adjacent bases on the same DNA strand (Asn 69... 

Figure 9.19 shows the sequence of the DNA that was used for the structure determination of the p53-DNA complex the bases involved in sequence-specific binding to the protein are shaded. One molecule of the DNA-bind-ing domain of p53 binds to the minor and the major grooves of the DNA making sequence-specific interactions with both strands (Figure 9.20). 

Tropomyosin is thought to lie in the groove formed between the associated actin strands. The sites at which the myosin crossbridges attach are affected by the relationship between tropomyosin and the actin strands. The role of tropomyosin in smooth muscle is completely undefined while in striated muscle it is clearly involved in the activation of contraction. The difference is made clear by the absence from smooth muscle of the protein, troponin, which in striated muscle provides the binding site for the triggering calcium. 

An analysis of the hydration structure of water molecules in the major and minor grooves in B-DNA has shown that there is a filament of water molecules connecting both the inter and the intra phosphate groups of the two strands of B-DNA. However, such a connectivity is absent in the case of Z-DNA confirming earlier MC simulation results. The probability density distributions of the counterions around DNA shows deep penetration of the counterions in Z-DNA compared to B-DNA. Further, these distributions suggest very limited mobility for the counterions and show well defined counter-ion pattern as originally suggested in the MC study. 

After hybridization and washing, the samples were stained with DAPI (4, 6-di-amidino-2-phenylindole), which apparently associates in the minor groove of double-stranded DNA (Kapuscinski 1990). DAPI from Sigma was used. Binding of DAPI to double-stranded DNA occurs with about a 20-fold fluorescence enhancement, which usually does not occur with single-stranded DNA (Haugland 1992). 

Figure 35-2. A diagrammatic representation of the Watson and Crick modei of the doubie-heiicai structure of the B form of DNA.The horizontai arrow indicates the width of the doubie heiix (20 A), and the verticai arrow indicates the distance spanned by one compiete turn of the doubie heiix (34 A). One turn of B-DNA in-ciudes ten base pairs (bp), so the rise is 3.4 A per bp. The centrai axis of the doubie heiix is indicated by the verticai rod. The short arrows designate the poiarity of the antiparaiiei strands. The major and minor grooves are depicted. (A,adenine C, cytosine G, guanine ...

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