Interaction with DNA

Assays have shown that hydraziae can interact with DNA to eflcit mutagenic effects. The mutagenicity of hydraziae has been reviewed (171). 

Another class of DNA-binding proteins are the polymerases. These have a nonspecific interaction with DNA because the same protein acts on all DNA sequences. DNA polymerase performs the dual function of DNA repHcation, in which nucleotides are added to a growing strand of DNA, and acts as a nuclease to remove mismatched nucleotides. The domain that performs the nuclease activity has an a/P-stmcture, a deep cleft that can accommodate double-stranded DNA, and a positively charged surface complementary to the phosphate groups of DNA. The smaller domain contains the exonuclease active site at a smaller cleft on the surface which can accommodate a single nucleotide. 

Dibenzo[a,g]quinolizinium salts in cancer chemotherapy, 2, 571 hydroxylation, 2, 532 interaction with DNA, 2, 527 reactions... 

The mechanism of interaction with DNA is suggested. Ethidium bromide (EB) displacement assay was performed. We determine the binding constant of Tb-E to DNA to be in the order of Ig K = 6.47 0.4. The bathochromic and hypsochromic effects in the absorption spectra of investigated complex were observed and the interaction is assumed to be mainly of the mono-intercalating type. 

Anderson, W.F., et al. Structure of the Cro repressor from bacteriophage X and its interaction with DNA. 

Residues 3, 5, 6, and 8 in the N-terminal arm lie in the minor groove and form contacts with either the edge of the bases or with the DNA backbone. Almost all homeodomains contain four conserved residues, Asn 51, Arg 53, Trp 48 and Phe 49, in the middle of the long recognition helix. The first two conserved polar residues interact with DNA. The second two are part of the hydrophobic core of the homeodomain, and are important for the accurate positioning of the recognition helix and the N-terminal arm with respect to... 

The finger region of the classic zinc finger motif interacts with DNA... 

Figure 10.4 Detailed view of the binding of the second zinc finger of Zif 268 to DNA. Two side chains, Arg 46 and His 49, form sequence-specific interactions with DNA. There are also three nonspecific interactions between phosphate groups of the DNA and the side chains of Arg 42, Ser 45, and His 53.

Three residues in the recognition helix provide the sequence-specific interactions with DNA... 

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... 

Although great progress has been made in study of the mode of action of the azinomycins, a full understanding of their interaction with DNA will require future structural characterization of azinomycin-DNA crosslinks by NMR or X-ray crystallography. 

Many complexes and coordination compounds exist as isomers, compounds that contain the same numbers of the same atoms but in different arrangements. For example, the ions shown in (13a) and (13b) differ only in the positions of the Cl ligands, but they are distinct species, because they have different physical and chemical properties. Isomerism is of more than academic interest for example, anticancer drugs based on complexes of platinum are active only if they are the correct isomer. The complex needs to have a particular shape to interact with DNA molecules. 

Although, as stated above, we wiU mostly focus on hydrolytic systems it is worth discussing oxidation catalysts briefly [8]. Probably the best known of these systems is exemphfied by the antitumor antibiotics belonging to the family of bleomycins (Fig. 6.1) [9]. These molecules may be included in the hst of peptide-based catalysts because of the presence of a small peptide which is involved both in the coordination to the metal ion (essential co-factor for the catalyst) and as a tether for a bisthiazole moiety that ensures interaction with DNA. It has recently been reported that bleomycins will also cleave RNA [10]. With these antibiotics DNA cleavage is known to be selective, preferentially occurring at 5 -GpC-3 and 5 -GpT-3 sequences, and results from metal-dependent oxidation [11]. Thus it is not a cleavage that occurs at the level of a P-O bond as expected for a non-hydrolytic mechanism. 

Activated PAMAM dendrimers interact with DNA to form a DNA-dendrimer complex with a toroid-like structure (Fig. 2). Such DNA-dendrimer complexes have diameters of 50-100 nm [10],which means that the DNA molecules are highly condensed in these complexes. A 6-kb plasmid alone, for example, has an extended structure several hundred nanometers in diameter. In transfection experiments, typically an 8- to 12-fold excess of positive amino groups over negatively... 

TTx represents the hydrophobicity of the substituents at position 10. Its positive coefficient (+0.75) suggests that the presence of highly hydrophobic substituents at position 10 increases the activity. The outlier (X = OH) is much more active than expected by 11 times the standard deviation. This may be due to the formation of a phenoxyl radical that interacts with DNA [48]. The other derivative (X = NH2) is also considered as an outher due to being much more active than expected by 14 times the standard deviation. This anomalous behavior may be attributed to its nature as an aniline. This could result in hydrogen abstraction, or involve microsomal N-oxidation [48,49]. 

The negative ClogP term shows that highly hydrophilic molecules for this data set would present better inhibitory activities against topo I. Two compounds (Ri = R3 = R4 = R5 = H, R2 = NO2 and Ri = R3 = R4 = R5 = H, R2 = F) in Table 4 for the development of QSAR Eq. 6 were deemed to be outliers on the basis of their deviation (>2s). The outlier (Ri = R3 = R4 = R5 = H, R2 = NO2) is much more active than expected, by three times the standard deviation. This may be due to the formation of nitro anion radicals that interact with DNA [48]. The other derivative (Ri = R3 = R4 = R5 = H, R2 = F) is... 

It is now almost 50 years since the structure of DNA was elucidated by Watson and Crick (1) (Fig. 1). Since then the double helix has become an icon for modern scientific achievement. With the rapid growth of molecular biology and the consequent success of the human genome project (2) we are now firmly in a post-genomic era. However, in spite of, or perhaps because of this, efforts to understand fundamental aspects of metal-ion interactions with DNA continue to be vigorously pursued. 

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