DNA, interaction

Teratogenic effects have been noted with 2- and 4-aminophenol in the hamster, but 3-aminophenol was without effect in the hamster and rat (129,130). 4-Aminophenol is known to inhibit DNA synthesis and alter DNA stmcture in human lymphoblasts (131,132) and is mutagenic in mouse micronuclei tests (133). The aminophenols have been shown to be genotoxic, as evidenced by the induction of sister chromatid exchanges (134,135), but they also exert a protective effect against DNA interaction with other noxious chemicals (136). After assessment of available data a recent report stated that the aminophenols were safe as cosmetic ingredients in their present uses and concentrations (137). 

Fig. 4. Structures of DNA interactive agents are given in Table 3. In structure (38) L-MeVal is 1-/V-metby1 valine.

The specific protein-DNA interactions described in this book are all with DNA in its regular B-form, or, in some cases with distorted B-DNA. In biological systems DNA appears not to adopt the A conformation, although double-stranded RNA does preferentially adopt this conformation in vivo. Whether or not Z-DNA occurs in nature is a matter of controversy. However, the formation of A-DNA and Z-DNA in vitro does illustrate the large structural changes that DNA can be forced to undergo. 

Only a rather limited number of base pairs is needed to provide unique and discriminatory recognition sites in the major groove. This is illustrated in Figure 7.8, which gives the color codes for the hexanucleotide recognition sites of three different restriction enzymes—Eco Rl, Bal 1, and Sma 1. It is clear that these patterns are quite different, and each can be uniquely recognized by specific protein-DNA interactions. 

The x-ray structure of DNA complexes with 434 Cro and repressor revealed novel features of protein-DNA interactions... 

Sequence-specific protein-DNA interactions recognize operator regions... 

The protein-DNA interactions have been analyzed in detail at high resolution in the complex between the 434 repressor fragment and the ORl containing 20mer DNA. A pseudo-twofold symmetry axis relates the halves of this complex. The symmetry is not exact since the nucleotide sequence of the DNA is slightly different in each half (see Table 8.2). However, the interactions between one protein subunit and one half of the DNA are very similar to those between the second subunit and the other half of the DNA since most of the bases that interact with the protein are identical in both halves. Details of the interaction are very similar to those in the complex with the palindromic synthetic 14mer of DNA shown in Figures 8.14 and 8.15. The base pairs at one end of the DNA, 1-14, 2-13, etc. are called base pairs 1, 2, etc. 

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.

Figure 8.16 Nonspecific protein-DNA interactions are frequently formed by hydrogen bonds (red) between backbone phosphate oxygen atoms of DNA and main-chain NH groups of the protein.

Wharton, R.P., Brown, E.L., Ptashne, M. Substituting an a helix switches the sequence-specific DNA interactions of a repressor. Cell 38 361-369, 1984. 

The sharp bend of DNA at the TATA box induced by TBP binding is favorable for the formation of the complete DNA control module in particular, for the interaction of specific transcription factors with TFIID. Since these factors may bind to DNA several hundred base pairs away from the TATA box, and at the same time may interact with TBP through one or several TAFs, there must be several protein-DNA interactions within this module that distort the regular B-DNA structure (see Figure 9.2). The DNA bend caused by the binding of TBP to the TATA box is one important step to bring activators near to the site of action of RNA polymerase. 

TFIIA and TFIIB are two basal transcription factors that are involved in the nucleation stages of the preinitiation complex by binding to the TBP-TATA box complex. Crystal structures of the ternary complex TFIIA-TBP-TATA box have been determined by the groups of Paul Sigler, Yale University, and Timothy Richmond, ETH, Zurich, and that of the TFIIB-TBP-TATA box by Stephen Burley and collaborators. The TBP-DNA interactions and the distortions of the DNA structure are essentially the same in these ternary complexes as in the binary TBP-TATA complex. 

The NMR study by Wiithrich and coworkers has shown that there is a cavity between the protein and the DNA in the major groove of the Antennapedia complex. There are several water molecules in this cavity with a residence time with respect to exchange with bulk water in the millisecond to nanosecond range. These observations indicate that at least some of the specific protein-DNA interactions are short-lived and mediated by water molecules. In particular, the interactions between DNA and the highly conserved Gin 50 and the invariant Asn 51 are best rationalized as a fluctuating network of weak-bonding interactions involving interfacial hydration water molecules. 

Figure 9.22 Most tumorigenic mutations of pS3 are found in the regions of the polypeptide chain that are involved in protein-DNA interactions. These regions are loops L2 (green) and L3 (red) and a region called LSH (blue) which comprises part of p strand 9 as well as the C-terminal a helix.

Kissinger, C.R., et al. Crystal structure of an engrailed homeodomain DNA complex at 2.8 A resolution a framework for understanding homeodomain-DNA interactions. Cell 63 579-590, 1990. 

The GAL4 recognition module therefore contains only one protein side chain, Lys 18, that provides specific interactions with the DNA. The remaining specific interactions with DNA are from main-chain atoms and depend critically on the correct conformation of the protein. The correct positioning of the C-terminus of the a helix is particularly important for recognition. This is to date the only example of a protein-DNA interaction in which... 

Max and MyoD recognize the DNA HLH consensus sequence by different specific protein-DNA interactions... 

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

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