Intercalating dye

Wang S, Gaylord BS, Bazan GC (2004) Fluorescein provides a resonance gate for FRET from conjugated polymers to DNA intercalated dyes. J Am Chem Soc 126 5446-51... 

Scheme 5 Schematic illustration of the working mechanism of CCP/intercalating dye/DNA sensor...

To overcome the nonspecific interactions between ssDNA-C and CCP, Fan et al. introduced a magnetic microparticle assisted assay [54], which allows DNA detection in human serum with 0.1 nM sensitivity. In addition, DNA intercalating dyes were introduced for DNA detection as shown in Scheme 5. These special dyes have much higher fluorescence quantum yields upon intercalation with dsDNA relative to those in the presence of ssDNA or in their free states. As a result, when complementary ssDNA strands (target and probe) are present, the intercalating dye... 

Pu KY, Liu B (2008) Intercalating dye harnessed cationic conjugated polymer for real-time naked-eye recognition of double-stranded DNA in serum. Adv Funct Mater 19 1371-1378... 

Lee K, Maisel K, Rouillard JM, Gulari E, Kim J (2008) Sensitive and selective label-free DNA detection by conjugated polymer-based microarrays and intercalating dye. Chem Mater 20 2848-2850... 

A.R. Bahrami, M.J. Dickman, M.M. Matin, J.R. Ashby, P.E. Brown, M.J. Conroy, G.J.S. Fowler, J.P. Rose, Q.I. Sheikh, A.T. Yeung and D.P. Hornby, Use of fluorescent DNA-intercalating dyes in the analysis of DNA via ion-pair reversed-phase denaturing high-performance liquid chromatography. Anal. Biochem., 309 (2002) 248-252. 

It is conceivable that diffusion of kinks, or overdamped solitons, along the DNA could act to relax the FPA with a time dependence similar to that predicted for torsional deformation/31 32) High levels of intercalated dyes would be expected to alter both the equilibrium population of kinks and their mobility along the DNA. Hence, this question is addressed by examining the effect of intercalating dyes on the torsional dynamics. 

For ethidium/DNA complexes, we usually represent S(t) by two exponentials, StU) and S2(t), plus a delta function to account for a small amount of Raman shifted light from the solvent. S,(<) represents intercalated dye... 

It is conceivable that the equilibrium orientation of the intercalated dye in its Sj excited state differs from that in its S0 ground state and that this is what is responsible for the rapid initial relaxation. If so, the rms amplitudes of internal Brownian motion estimated above would be upper limits to the actual values. 

These observations, together with those on supercoiled DNAs relaxed by intercalating dyes and by topoisomerase I, indicate that complete conversion from the prevalent secondary structures in supercoiled DNAs to the normal B-helix must be severely hindered kinetically. It is also clear that the free energies per base pair of the secondary structure states a and b must be nearly identical in order for these states to be interconverted by such a small environmental perturbation. 

No measure of the relative amounts of intercalated and free dye, or the existence of partially intercalated dye, is available from the fluorescence decay. 

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]. 

When a polarized spectrum of the film was taken in the dry state, a small dichroic ratio was observed (A L/A// = 1.3, see Fig. 9c). This is due to the slant structures of base pairs and intercalated dyes to the axis of the strands, since the DNA strands were confirmed to be aligned along the stretching direction even in the dry film (see Fig. 7c). These changes of polarized absorption spectra dependent on water moisture were reversible at least 10 times. 

Cationic amphiphiles 2Ci8-glu-N spread on pure water, in the solution of 10 xM DNA containing 10 xM intercalating dyes (proflavine). The dye-intercalated DNA anions were expected to adsorb to the cationic lipid mono-layer due to electrostatic interactions and was transferred to a hydrophobized glass plate at a surface pressure of 35 mN m at 20 °C. From a moving area of a barrier, two layers of the monolayer were confirmed to be transferred in each one cycle (Y-type deposition). When the QCM plate was employed as a transfer plate, the transferred mass could be calculated from frequency decreases (mass increase on the QCM) [29-31]. It was confirmed that 203 10 ng of two lipid monolayers and 74 5 ng of DNA strands were transferred on to the substrate per dipping cycle, which means ca. 95% of the monolayer area was covered by DNA molecules. 

The fluorescence of the composite showed a somewhat different profile from that of the dye solution. The intensity of fluorescence, especially, was considerably reduced, and the value of also shifted towards higher wavelengths by increasing the quantity of intercalated dye. Representative data of fluorescence excited at 387 nm for the PY-SA composite and at 354 nm for the R590-SA composite are shown in the figures. It was noted that the changes of d-spacing, relative intensity and involved almost the same tendencies as a... 

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