Acridine orange intercalator

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...

N-Acetylalanyl N -methylamide, 2ll3f Aclacinomycin A, 8i1,87f Acridine orange intercalator, 125f Adrenocorticotropic hormone (ACTH) D-amino acids and activity, 155-58 biological and physicochemical properties, 158-62 chain length and... 

FIGURE 12.16 The structures of ethidiutn bromide, acridine orange, and actinomycin D, three intercalating agents, and their effects on DNA structure. 

Figure 9 summarizes the electrode responses toward a variety of DNA-binding substrates [14c]. For intercalators (quinacrine, acridine orange, and safranin) and groove binders (spermine and spermidine), a steep rise followed by a saturation of the concentration response curve is commonly observed. If one compares the specific concentration which gives a 50% response in the increment of the cathodic peak current (A/p ) for each substrate, a selectivity order of quinacrine acridine orange > spermine > spermidine > safranin can be estimated. The binding constants measured in aqueous media for the affinity reaction with ds DNA are as follows quinacrine, 1.5 x 10 (38 mM NaCl)... 

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... 

Using specific fluorescent transport substrates, inhibitors and kinetic analysis Using fluorescent xenobiotics or fluorescent analogue of xenobiotics Using special fluorescent xenobiotics or fluorescent analogues of xenobiotics Vital tests with acridine orange or neutral red Metachromatic fluorescence of intercalated or bound acridine orange, 590/530 nm microfluorometry... 

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]. 

Cp6 together with the Intercalator acridine orange solved at atoaiic resolution (36). It can be seen tha the 3 end of the double helical RNA fragment has adopted the C2 endo conformation while the S end maintains the normal C3 endo conformation. A large number of intercalator structures of this type have been solved and they have been summaried elsewhere. Sobell and his colleages pointed out that the Intercalation is associated with a modification of the pucker of the ribonucleotide chain on the 3 end of the intercalator (37-38). Although intercalation is generally associated with the conformations similar to those seen in Fig. 10. a number of alternative conformations have been found with more complex Intercalators. 

In the thermodynamic study of duplex formation, a variety of complementary pairs of relatively simple, well-defined oligonucleotides are employed, " while the intercalation thermodynamics was examined with more complex or natural DNA duplexes. " Typical intercalating agents examined are acridine orange, acriflabine, actinomycin, daunomycin, ethidium bro-... 

Acridine orange is able to penetrate cells independently of the integrity of the cell membrane. It intercalates the bases in double strands of DNA and emits green fluorescent light. It can also form complexes with RNA and single-stranded DNA, but in this case it does not intercalate the bases and emits red fluorescent light. Thus, a viable cell can be visualized with a green nucleus and, possibly, reddish spots in the cytoplasm. 

Linear response polarizability theory of spectral bandshapes was applied to the numerical analysis of the chiroptical spectra obtained for DNA-acridine orange complexes [85]. After analysis of various models of conformation, it was concluded that a dimer-pairs repeating sequence model was best able to account for the observed spectral trends. In another work, the CD induced in the same band system was studied at several ionic strengths [86]. The spectra were able to be interpreted in terms of the long-axis-polarized electronic transitions of the dyes, with the induced CD being attributed to intercalated and non-intercalated dye species superimposed by degenerate vibronic exciton interactions between these. 

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.

The static and dynamic properties of DNA have been studied by the temperature-dependent Stokes shift of the intercalated dye acridine orange [192] and by molecular dynamic simulation [193]. A large part of the Stokes shift of the intercalated dye in DNA is found to be frozen out at low temperature, as in the solution. Thus, the interior of DNA is found to have the diffusive and viscous dynamic characteristics of a fluid rather than the purely vibrational characteristics of a crystal. The results suggest that the probe dye molecule senses the movement of DNA and at high viscosity the rate of DNA motion is limited by the rate of solvent motion. 

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. 

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