Sequence specificity complex

Cheng, X.H., Morin, P.E., Harms, A.C. et al. (1996) Mass spectrometric characterization of sequence-specific complexes of DNA and transcription factor PU.l DNA binding domain. Anal. Biochem., 239 (1), 35 40. 

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

The promoter proximal elements are usually 100 to 200 base pairs long and relatively close to the site of initiation of transcription. Within each of these elements there are DNA sequences specifically recognized by several different transcription factors which either interact directly with the preinitiation complex or indirectly through other proteins. 

TFIIB is arranged in two domains, both of which have the cyclin fold described in Chapter 6. Both domains bind to the TBP-TATA box complex at the C-terminal stirrup and helix of TBP. The phosphate and sugar moities of DNA form extensive non-sequence-specific contacts with TFIIB both upstream and downstream of the middle of the TATA box. 

Figure 9.10 Schematic diagrams illustrating the complex between DNA (orange) and one monomer of the homeodomain. The recognition helix (red) binds in the major groove of DNA and provides the sequence-specific interactions with bases in the DNA. The N-terminus (green) binds in the minor groove on the opposite side of the DNA molecule and arginine side chains make nonspecific interactions with the phosphate groups of the DNA. (Adapted from C.R. Kissinger et al Cell 63 579-590, 1990.)...

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). 

Figure 10.6 One sequence-specific interaction occurs more frequently than others in protein-DNA complexes two hydrogen bonds form between an arginine side chain of the protein and a guanine base of the DNA, as shown in this diagram.

Figure 16.20 The structure of the complex between a dimer of the coat protein of bacteriophage MS2 and the RNA fragment shown in Figure 16.19. One subunit of the coat protein dimer is green, the other is violet and the RNA fragment is orange. Bases that form sequence specific interactions with the protein are red. (Adapted from a diagram provided by L. Liijas.)...

Valegard, K., et al. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific pro-tein-RNA interactions. /. Mol. Biol. 270 724-738,... 

The proteins impose precise distortions on the B-DNA in the complexes Sequence-specific protein-DNA interactions recognize operator regions... 

Muliprotein complexes that do not directly bind DNA, but are recruited by sequence-specific transcription factors and mediate their capacity to activate genes (coactivators) and to repress genes (corepressors). 

All earlier studies [155-158] reported the complexation of berberine with calf thymus DNA and suggested by a mechanism of intercalation. Maiti and coworkers [159-162] demonstrated first the base- and sequence-specificity of berberine from studies with several naturally occurring DNAs (Clostridium perfringenes, cholera bacteriophage 02, calf thymus, Escherichia coli, Micrococcus lysodeikticus) and synthetic DNAs ((poly(dG-dC) poly(dG-dC), poly(dG)-poly(dC), poly(dA-dT) poly(dA-dT), poly(dA)-poly(dT)) using various physicochemical techniques. Several aspects of the interaction were reported ... 

As discussed above, alternative recombinant DNA techniques are necessary to efficiently generate genome-scale clone sets. One alternative exploits the ability of the Vaccinia virus DNA topoisomerase I to both cleave and rejoin DNA strands with high sequence specificity (Shuman, 1992a Shuman, 1992b). In the reaction, the enzyme recognizes the sequence 5 -CCCTT and cleaves at the final T whereby a covalent adduct is formed between the 3 phosphate of the cleaved strand and a tyrosine residue in the enzyme (Fig. 4.1). The covalent complex can combine with a heterologous acceptor DNA that has a 5 hydroxyl tail complementary to the sequence on the covalent adduct to create a recombinant molecule (Shuman, 1994). 

Physical binding studies (8,9,27) suggest that physical complex formation with DNA by intercalation appears to be sequence-specific. Thus, BaPT and pyrene intercalate much more strongly in poly(dA-... 

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