DNA secondary structure

R. Negri, F. Delia Seta, E. di Mauro, and G. Camilloni, Topological evidence for allosteric transitions in DNA secondary structure, Biophys. J., submitted. 

Anyhow, a combination of the Scatchard technique and Raman spectroscopy shows (i) that SOAz actually interacts with DNA at the level of ribose backbones and (ii) that this kind of interaction does not drastically modify the DNA secondary structure, ethidium bromide encountering no more difficulty to intercalate between DNA plates SOAz being grafted or not on the nucleic acid. Thus, the behaviour of MYKO 63 and of SOAz appears quite different with respect to their mode of interaction with DNA despite their close chemical and molecular structure. This surprising observation may be of interest for understanding why SOAz does not induce any cumulative toxicity in vivo in contrast with MYKO 63. 

Fig. 1. The three structural levels of DNA-based Immunomodulatory sequence (DIMS). G-rich motifs are shown in blacK, sequences containing unmethylated CpG motifs shown in grey (corresponding to the color of motif background in Table 1) thin grey/mes indicate hydrogen bonds formed by Watson-Crick nucleotide pairs (DNA secondary structure level) or by Floogsteen hydrogen bonding (DNA tertiary structure level).

Baase WA, Johnson WC Jr (1979) Circular dichroism and DNA secondary structure. Nucleic Acids Res 2 797-814... 

A study has been made of the DNA secondary structure induced by the various nucleohistone complexes 342). The interaction of calf thymus DNA with the anticancer drug Cisplatin in water and heavy water has been studied. The carbonyl bands at 1710 and 1686 cm-1 of the control DNA disappear and shift to lower frequencies in the spectra of the products of the reaction. The drug induces a reorganization of the water molecules and the DNA structure is modified 340). 

In terms of physiological conditions, DNA exists almost totally in the double-helical conformation. Certain oligonucleotides also exhibit the ability to form triple-helixes with the DNA double strands. The stability of DNA secondary structures strongly depends on the environmental conditions, such as ionic strength, pH, temperature and solvents. Temperature is the most widely used environmental variable for the quantitative characterization of the helix-coil transitions. A commonly accepted characteristic of the thermal stability of DNA secondary structures is melting temperature, Tm. The binding of cationic species, such as multivalent... 

The interaction of divalent cations with DNA is extensively studied, DNA complexation with trivalent cations is less understood. It was shown that the interaction of Al with DNA produces several types of Al-DNA complexes depending on pH and metal ion concentration. However, the exact cation binding site and the effect of Al interactions on the DNA secondary structure are not determined, particularly at low cation concentrations. Martin [8]... 

Venner, H., and C. Zimmer Studies on nucleic acids VIII. Changes in the stability of DNA secondary structure by interaction with divalent metal ions. Biopolymers 4, 321 (1966). 

Further information on the binding of tilorone with DNA was derived by studying the thermal melting of the complex27,28. In order to characterize the stability of DNA secondary structure in the presence of tilorone, temperature profiles were run at tilorone/DNA-P molar ratio of 1 5. Tilorone hydrochloride shows a large increase in the thermal transition temperature (rm) of native DNA the Tm of calf thymus DNA was raised from 71.6 to 85.2 °C under these conditions. 

These footprinting analyses, based on enzymic and chemical digestion, are now widely used to define DNA (and RNA) and their complexes with various ligands. Recently active radical probes have been used as footprinting agents in protection assays in a variety of systems (e.g., Tullius and Dombroski, 1986 Chalepakis and Beato, 1989 Hayes and Tullius, 1989 Schickor et al., 1990). Such probes rely on active radical intermediates, most likely hydroxyl radicals, released by Fe(II) in the presence of an electron donor, probably via a Fenton reaction. In addition, hydroxyl radicals also appear to react with DNA in a conformation-specific manner which may allow some prediction of DNA secondary structure (see Burkhoft and Tullius, 1987 Zorbas et al., 1989 Lu et al., 1990). 

Intercalating agent. A chemical, usually containing aromatic rings, that can sandwich in-between adjacent base pairs in a DNA duplex. The intercalation leads to an adjustment in the DNA secondary structure, as adjacent base pairs are usually close-packed. 

The chromosomes of eukaryotes are linear, and replication of the free ends of these linear DNA molecules presents particular problems. The sequencing of the ends of chromosomes revealed that they consist of telomeres, hundreds of tandem repeats of a hexanucleotide sequence, which in all vertebrates is d(TTAGGG). These G-rich telomeric sequences can fold into a G-quadruplex, a DNA secondary structure consisting of stacked G-tetrad planes, or G-quartets (Figure 9.18), connected by a network of Hoogsteen hydrogen bonds the cavity in the centre... 

A., Kolbanovskaya, M., Chen, D., Chang, M., Bolton, J.L, and Geacintov, N.E. (2005) Base selectivity and effects of sequence and DNA secondary structure on the formation of covalent adducts derived from the equine estrogen metabolite 4-hydroxyequilenin. Chem. 

The discovery of both DNA secondary-structure formation within the NHE nil region of the c-myc promoter and proteins that bind specifically to the cytosine-rich strand, guanine-rich strand, or the duplex of the same region has led to a model of how the NHE IIIi controls c-myc expression (Figure 6). The model suggests the presence of three different DNA structural populations within the NHE IIIi two that cause activation and one that results in repression of c-myc transcription. First, when the NHE IIIi assumes a normal... 

Figure 6 Model of the three different DNA struetural populations within the c-myc NHE nil. Two eause aetivation through the binding of transcription factors and one causes repression through the formation of DNA secondary structures (i.e., G-quadruplex and i-motiff ...

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