Acridine orange base pair

Similarly to quantitative determination of high surfactant concentrations, many alternative methods have been proposed for the quantitative determination of low surfactant concentrations. Tsuji et al. [270] developed a potentio-metric method for the microdetermination of anionic surfactants that was applied to the analysis of 5-100 ppm of sodium dodecyl sulfate and 1-10 ppm of sodium dodecyl ether (2.9 EO) sulfate. This method is based on the inhibitory effect of anionic surfactants on the enzyme system cholinesterase-butyryl-thiocholine iodide. A constant current is applied across two platinum plate electrodes immersed in a solution containing butyrylthiocholine and surfactant. Since cholinesterase produces enzymatic hydrolysis of the substrate, the decrease in the initial velocity of the hydrolysis caused by the surfactant corresponds to its concentration. Amounts up to 60 pg of alcohol sulfate can be spectrometrically determined with acridine orange by extraction of the ion pair with a mixture 3 1 (v/v) of benzene/methyl isobutyl ketone [271]. 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

When the stretched DNA-lipid film was soaked in an aqueous solution of ethidium bromide (itmax = 480 nm) for a day at room temperature, the transparent film turned red (itmax = 520 nm) and the aqueous solution became clear (Fig. 9a). Thus, the ethidium intercalated completely between base pairs of the DNA film. When the film was moved into the new aqueous buffer solution, the intercalated dye molecules were hardly removed from the film at least for a day. Similar intercalation behavior into the film was observed for other dyes such as proflavine, acridine orange, and safranine T [14-17]. 

Fig. 15 Photo-induced current of aligned-DNA films (20 x 10 mm, thickness 30 5 irm) in which one acridine orange intercalates per ca. 10 base-pairs, a At 0.01 V, b 0.05 V, and c 0.1 V of applied voltage to the comb electrodes, in which the DNA strands are aligned perpendicular to the two electrodes, d DNA strands in the film placed parallel to the two electrodes at 0.1 V applied voltage. The pulse light above 380 nm was irradiated from a 150 W xenon lamp at 25 °C...

Alternatively to the DNA modifications in the previous two sections where the chromophore was attached to one of the four DNA bases, chromophores can be incorporated as artificial DNA bases substituting a natural base or even a whole base-pair. There is a large number of recently reported syntheses of chromophores as DNA base surrogates, e.g. flavine derivatives [26] and thiazole orange derivatives [42]. Additionally, a variety of phosphoramidites as DNA building blocks for the introduction of fluorophores into DNA are commercially available, e.g. acridine derivatives. Clearly, the synthetic protocols for this kind of DNA modification do not follow a principle strategy which can be applied in a versatile fashion, as is the case for the DNA base modifications mentioned in the previous sections. It is important to point out that in many cases it turned out to be useful to replace the 2 -deoxyribose moiety with acyclic linker systems. This was also the case during our attempts to synthesize ethidium-modified DNA, which will be described here briefly. 

It has been shown that methylene blue binds to DNA in a manner similar to that of acridine orange, with the intercalated solute being coplanar with the base pairs at low dye/polymer ratios and low ionic strengths [89]. The induced CD data indicated the existence of two origins for the observed chirality. At low ratios of dye/polymer, the CD is... 

Fig. 2 Schematic of base pair in dsDNA (A) and acridine orange (AO) (B). The AO intercalates between sequential base pairs, extending the phosphate backbone.

DNA has also been applied for synkineses of molecular wires. One example applies aligned DNA fibers in which one acridine orange molecule intercalates per 10 base pairs. It shows photocurrents if a voltage is applied to the material placed between comb-form electrodes (Okahata et al., 1998). The dye-DNA complexes are probably not useful as parts of a charge separation system, but they clearly demonstrate extensive electronic communication between bound drug molecules—an influence that serves to raise the efficiency of transition dipole coupling at long distances. 

Energy tr msfer in one dimension was also studied using the FD method. In this case the donor was Acridine Orange (AO) and the acceptor was a weakly fluorescent dye, Nile Blue (NB). Binding of NB to AO-DNA at a low dye/base-pair ratio resulted in significant quenching of the... 

Figure IS.12. Emission spectra of Acridine Orange (AO) bound to DNA mth different concentrations of Nile Blue (NB) acceptor per DNA base pair. Fnm Ref. 18, Maltwal, B. P., Ku a. J.. and Lakowica. . R.. Fluorescence energy transfer in one dimension mequency domain fluorescence study of DNA-41uOT [ ie coriq>lexes, Biopotymtn 35 245-2SS. Copyri t C 1994.R cintcd withpemussionfeomJohn Wley and Sons, Inc.

There are numerous probes available that spontaneously bind to DNA, displaying enhanced emission. Ethidium bromide weakly fluoresces in water, but this intensity is greatly increased upon binding to DNA (Fig. 5). The mode of binding is due to the intercalation of the planar aromatic ring between base pairs of doublehelical DNA. Acridine orange also binds to... 

Acridine dyes (acridine orange, proflavine) (Fig. 7.2) will produce so-called frame-shift mutants. In this case, the intercalated dye mimics an additional base pair and, during replication, the daughter strands will contain an extra base at this point. By using carefully chosen point mutants, Crick et al. (13) proved the three-letter genetic code. 

The results were explained assuming that the acridine orange molecules are bound both as single molecules and as dye dimers. Mason [36] suggested a modified intercalation model in which the acridine orange molecules are located between the base pairs of the double helix (see Figure 8). 

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