Studies on the ability of minor groove binders to induce supercoiling in DNA

Störl, K.; Burckhardt, G.; Lown, J. William; Zimmer, Ch.

doi:10.1016/0014-5793(93)81678-s

Cited by 35 publications

(20 citation statements)

References 25 publications

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“…1, inset) at the concentrations used. In addition, the agreement between values for DNA in intact cells and values for solubilized DNA from these cells suggests that minimal error was attributable to changes in medium chemistry, packing effects, or binding hindrance by supercoiling (61). Thus, under restricted staining time, concentration, and temperature conditions used, DAPI appears to be a specific stain for the DNA of small nonpigmented bacterium-like organisms when it is used with a size parameter such as forward light scatter.…”

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confidence: 90%

“…Stains such as PicoGreen (62), Hoechst 33258, SYBR Green (4,38), SYTOX Green (66), Syto 13 (18), YOYO, YO-PRO (39), and TOTO (24) have also been used, but the specificity and species dependence of these stains have not been evaluated. Among these stains the in vitro binding of DAPI by DNA is best understood (61). DAPI is bright and stable enough and is minimally affected by DNA conformation (1).…”

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Determination of DNA Content of Aquatic Bacteria by Flow Cytometry

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Robertson

2001

Appl Environ Microbiol

108

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The distribution of DNA among bacterioplankton and bacterial isolates was determined by flow cytometry of DAPI (4,6-diamidino-2-phenylindole)-stained organisms. Conditions were optimized to minimize error from nonspecific staining, AT bias, DNA packing, changes in ionic strength, and differences in cell permeability. The sensitivity was sufficient to characterize the small 1-to 2-Mb-genome organisms in freshwater and seawater, as well as low-DNA cells ("dims"). The dims could be formed from laboratory cultivars; their apparent DNA content was 0.1 Mb and similar to that of many particles in seawater. Preservation with formaldehyde stabilized samples until analysis. Further permeabilization with Triton X-100 facilitated the penetration of stain into stain-resistant lithotrophs. The amount of DNA per cell determined by flow cytometry agreed with mean values obtained from spectrophotometric analyses of cultures. Correction for the DNA AT bias of the stain was made for bacterial isolates with known G؉C contents. The number of chromosome copies per cell was determined with pure cultures, which allowed growth rate analyses based on cell cycle theory. The chromosome ratio was empirically related to the rate of growth, and the rate of growth was related to nutrient concentration through specific affinity theory to obtain a probe for nutrient kinetics. The chromosome size of a Marinobacter arcticus isolate was determined to be 3.0 Mb by this method. In a typical seawater sample the distribution of bacterial DNA revealed two major populations based on DNA content that were not necessarily similar to populations determined by using other stains or protocols. A mean value of 2.5 fg of DNA cell ؊1 was obtained for a typical seawater sample, and 90% of the population contained more than 1.1 fg of DNA cellAquatic heterotrophic bacterioplankton, which are too small for observation by light microscopy, are commonly visualized with fluorescent DNA stains (14). The intensity of stain fluorescence as determined by flow cytometry, together with light scatter data, can help characterize natural populations (10,11,43,70), determine rates of growth (16), locate DNA-deficient organisms (49), provide a cell mass basis for comparative and absolute descriptions of organism affinity for nutrients (5), and identify low-mass particles (49) as bacteria in order to quantify a major component of aquatic living carbon (9).The mean DNA content of bacterioplankton has been estimated from analysis of filter-retained material and an organism count together with the number of organisms observed (17) and from analysis of images of individual cells (36), but mean values (17, 44) vary more than expected. In early studies, flow cytometry was used to observe differences among cells in monocultures of commonly grown large-cell species (60). Fluorescence from DAPI (4Ј,6-diamidino-2-phenylindole)-bound DNA was responsible for locating predominant very small oligobacteria (28). DAPI has been used to estimate the genome sizes of Synechococcus (3) and oligobacter...

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Determination of DNA Content of Aquatic Bacteria by Flow Cytometry

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Robertson

2001

Appl Environ Microbiol

108

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“…So, the compounds probably accumulate on DNA without binding it. Störl et al reported that 6 well-known DNA minor groove-binding agents could change the Lk number like the intercalators did, but in a different way (Störl et al, 1993). The ability of BM3 and BM4 to change the Lk number depends on how many of them bind per 1 base pair of DNA.…”

Section: Human Topoisomerase Iia Inhibition Mechanisms Of Bm3mentioning

confidence: 99%

“…This situation could be explained as these compounds could accumulate on DNA minor grooves and they could give different results depending on their concentrations. It was reported that the agents without intercalation properties could still bind on DNA minor grooves to inhibit enzymes that manipulate DNA (Störl et al, 1993;Reddy et al, 1999;Racane et al, 2010). For example, it was shown that the agents that induce structural changes on DNA were active on topo I and II catalysis and DNAprotein interactions in vitro (Bailly et al, 1999).…”

Section: Human Topoisomerase Iia Inhibition Mechanisms Of Bm3mentioning

confidence: 99%

Benzothiazole derivatives as human DNA topoisomerase IIα inhibitors

et al. 2013

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Benzothiazole derivatives resembling the structure of DNA purine bases were tested to determine their topoisomerase inhibition activities. Based on DNA topoisomerase I and II relaxation assay results, all 12 derivatives acted as human topoisomerase IIa inhibitors, whereas only two compounds inhibited Calf thymus topoisomerase I. 3-amino-2-(2-bromobenzyl)-1,3-benzothiazol-3-ium 4-methylbenzensulfonate (BM3) was observed to be the most effective human topoisomerase IIa inhibitor with the lowest IC 50 value of 39 nM. The mechanistic studies suggested that BM3 was neither a DNA intercalator nor a topoisomerase poison, it was only a DNA minor groovebinding agent. BM3 initially bound to the DNA topoisomerase IIa enzyme, then to DNA. As a result, the tested benzothiazole derivatives were obtained as strong topoisomerase IIa inhibitors. The benzothiazole tosylated salt form BM3 was found as the most effective topoisomerase IIa inhibitor. BM3's mechanisms of action might be its direct interaction with the enzyme. BM3's minor groove-binding property might also contribute to this action. Hence, BM3 could be a good candidate as a new anticancer agent.

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“…The catalytic reaction requires a high-energy cofactor and occurs by ATP hydrolysis. Members of these, clinically relevant, drugs are defined by their ability to interrupt the breaking/reunion reaction of DNA topoisomerase I by trapping reversible topoisomerase I cleavable complexes (Storl et al, 1993;Megan et al, 1993;Chen et al, 1993). The possibility of monitoring variations in DNA supercoiling, mediated by small organic molecules, is of considerable interest for obtaining information about the determinants of topological changes involved in DNA structural transitions, affecting transcriptional regulatory activity.…”

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Torsional Dynamics and Orientation of DNA−DAPI Complexes

Barcellona

Gratton

1996

Biochemistry

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The flexibility of calf thymus DNA and several polynucleotides was measured using the anisotropy decay of DAPI bound to DNA, a minor groove probe. DNA torsional dynamics were analyzed using the Schurr model [Allison, S. A., & Schurr, J. M. (1979) Chem. Phys. 41, 35-44] in the infinite polymer length approximation. Time-resolved fluorescence depolarization was measured using a frequencydoubled mode-locked dye laser and frequency-domain acquisition methods. At very high P/D ratios, the anisotropy decay is dominated by DNA torsional dynamics. The recovered values of the torsional elastic constant were in good agreement with literature values obtained using other DNA probes. The exact knowledge of the angle between the probe emission dipole transition moment and the helix axis is critical for the determination of the polymer elastic constant. At low P/D ratios, energy transfer between dye molecules strongly contributes to the anisotropy decay. We have developed a statistical model that describes the anisotropy decay, when the correct geometrical factors are included. At low P/D ratios the anisotropy decay is dominated by fluorescence homotransfer. In this regime, it is possible to determine the orientation of the dye molecule with respect to the polymer with accuracy. The values obtained for the distance and orientation of the DAPI molecules in solution using the fluorescence measurements are in excellent agreement with those from the crystal structure of the oligonucleotides-DAPI complex by Dickerson's group [Larsen T.

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Studies on the ability of minor groove binders to induce supercoiling in DNA

Cited by 35 publications

References 25 publications

Determination of DNA Content of Aquatic Bacteria by Flow Cytometry

Determination of DNA Content of Aquatic Bacteria by Flow Cytometry

Benzothiazole derivatives as human DNA topoisomerase IIα inhibitors

Torsional Dynamics and Orientation of DNA−DAPI Complexes

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