Nucleic acid stains

Friedlander synthesis, 2, 445 Acridine-1,8-diones, hexahydro-synthesis, 2, 482 Acridine Orange colour and constitution, 1, 346 nucleic acid stain, 1, 179... 

Another way in which Pt could bind to DNA is through the formation of intercalation compounds. The parallel here is with the hydrocarbon carcinogens and the nucleic acid stains, the acridines. It has been shown that metal chelates will form this same type of jt-complex. For example, palladium oxinate will form exactly the same type of -complexes as anthracene (88). 

Some fluorescent DNA stains can also be used for chromosome counterstaining, for detection of hybridized metaphase or interphase chromosomes in fluorescence in situ hybridization assays or for identifying apoptotic cells in cell populations (http //probes.invitrogen.com/handbook/sections/0806.html). For instance, Vybrant Apoptosis Assay Kit 4 (Molecular Probes) detects apoptosis on the basis of changes that occur in the permeability of cell membranes. This kit contains ready-to-use solutions of both YO-PRO-1 and propidium iodide nucleic acid stains. YO-PRO-1 stain selectively passes through the plasma membranes of apoptotic cells and labels them with moderate green fluorescence. Necrotic cells are stained red-fluorescent with propidium iodide. 

The fluorescence spectra of the monomeric cyanine nucleic acid stains family (PO-PRO-1, BO-PRO-1 and YO-PRO-1) introduced by Molecular Probes (http // probes.invitrogen.com) cover the entire visible wavelength range. These dyes may also be used with ultraviolet trans- or epi-illuminator excitation sources. The monomeric cyanine nucleic acid stains exhibit large degrees of fluorescence enhancement upon binding to DNA (or RNA) up to 1,800-fold. Consequently,... 

TABLE 8.1. Characteristics of Some Nucleic Acid Stains... 

Figurel9.1 Confocal imagesofhuman hepatocyteson PEEK-WC-PU membranes byactin staining with FITC-phalloidin (green) and by nucleic acid staining with DAPI (blue). Scale bar 10pm.

Haugland RP (1992) Nucleic acid stains. In Moleuclar Probes Handbook of Fluorescent Probes and Research Chemicals, KD Laniston, Ed., pp. 221 -228. Molecular Probes, Eugene, OR. 

Figure 21 Comparison of vertical distribution of biomarker and microbial abundances in oceanic water columns, (a) Contour plots of concentration (ngL ) of hexadecanoic acid, (b) Crenarcheol at various depths in the water column and distances from shore on a northwest-to-southeast transect off Oman in the Arabian Sea (after Sinninghe Damste et al, 2002). Hexadecanoic acid serves as a biomarker proxy for eukaryotic and bacterial biomass and clearly shows the expected surface maximum, with concentrations dropping off steeply with increasing water depth. In contrast, crenarcheol, a molecular biomarker for planktonic crenarcheota, shows two maxima with one near 50 m and the other —500 m. (c) Vertical distributions of microbial concentrations in the North Pacific subtropical gyre bacteria (solid squares) and planktonic crenarcheota (open squares). Effectively, there are two microbial domains which were determined using a DAPI nucleic acid stain (after Karner et al., 2001). These data show the increasing proportion of planktonic archea in deep waters, with the result that at depths greater than 2,000 m, the crenarcheota are as abundant...

This same procedure can also be used in microscopy or FACS analysis coupled with a nuclear dye such as ethidium homodimer-1, a red fluorescent nucleic acid stain (ex/em 495/ 635 nm) that is only able to pass through the compromised membranes of dead cells, and indicates the proportion of live vs. dead cells. (The viability assay kit including calcein-AM and ethidium homodimer-1 is sold by Molecular Probes, Cat. L-3224.)... 

Fig. 10 Stability of RNAi compounds in serum. Standard siRNA duplex (A) and the corresponding chemically modified sequence (B) at 0, 4, 8, 24, 48, and 72 hr following incubation in 10% calf, mouse, or human serum. Samples were incubated in serum and separated by gel electrophoresis. The remaining products were visualized by nucleic acid staining. (Courtesy of Invitrogen Corporation.)...

Broxterman, H. J., Schuurhuis, G. J., Lankelma, J., Oberink, J. W., Eekman, C. A., Claessen, A. M. E., Hoekman, K., Poot, M., and Pinedo, H. M. (1997) Highly sensitive and specific detection of P-glycoprotein function for hematological and solid tumor cells using a novel nucleic acid stain. Br. J. Cancer 76, 1029-1034. 

To evaluate nucleic acid transfection complex association with cells, prepare transfection complexes as described in Subheading 3.6 steps 1-3. Then, add 1 pi of the 1 mM solution in DMSO of the cell-impermeable intercalating nucleic acid stain YOYO-1 iodide per 360 pi complex (corresponds to one dye molecule per 5.5 bp), incubate for 15 min in the dark, and perform dilutions as described in Subheading 3.6 step 5. Perform transfections according to steps of Subheading 3.7. To visualize the association/localization of YOYO-1-labeled transfection complexes with cells, after incubation at 37°C in a 5% CO atmosphere, use a fluorescence microscope and observe with 490/509 nm green fluorescence. Sample results are shown in Fig. 4a. 

SYBR dyes for sensitive detection in gels and blots, Chemically reactive SYBR dyes for bioconjugates. The three classes of classic nucleic acid stains are Intercalating dyes (ethidium bromide and propidium iodide), Minor-groove binders, (DAPI and the Hoechst dyes ). Miscellaneous nucleic acid stains with special properties (acridine orange, 7-AAD and hydroxystilbamidine). 39... 

BlueView Nucleic Acid Stain (Sigma-Aldrich) (see Note 5). 

SYTOX blue nucleic acid cell stain S11348 Molecular probes Xex 470 nm 480 nm SYTOX blue nucleic acid stain is an excellent blue-fluorescent nuclear and chromosome counterstain that is impameant to live cells, making it a useful indicator of dead cells within a population. 

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