On the Electronic Structure of Ethidium

Luedtke, Nathan W.; Liu, Qi; Tor, Yitzhak

doi:10.1002/chem.200400559

Cited by 61 publications

(39 citation statements)

References 46 publications

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“…This binding would occur through the interaction of partial positive charges caused by localized deficits in p-orbital electrons associated with three of the four nitrogen atoms of PI (Luedtke et al, 2005) coordinating with negatively charged carboxyl and hydroxyl groups on homogalacturonans (HGs), as has been suggested in Oedogonium bharuchae (Estevez et al, 2008).Our findings indicate that both hypotheses are satisfied. Notably, oscillatory changes in apical PI fluorescence occur and are observed to anticipate oscillations in growth rate in Arabidopsis (Arabidopsis thaliana) root hairs and Arabidopsis pollen tubes.…”

supporting

confidence: 59%

“…While there are no published studies on the electronic structure of PI, we can look to investigations of ethidium bromide, which contains an identical phenanthridine core. X-ray crystallography, UV/ visible and IR absorption, fluorescence emission, and NMR spectroscopy studies (Luedtke et al, 2005) show that the carbon and hydrogen atoms of the phenanthridium structure have relatively high electron densities, while nitrogen atoms are electron deficient, resulting in three positively charged regions in the molecule spaced 6 to 7 Å apart. We reasoned that if PI were interacting with the negative carboxyl groups in HGs, as our pollen tube and root hair data suggested (McKenna et al, 2009) .…”

Section: Pi Fluorescence Oscillations Precede Growth Rate Oscillationmentioning

confidence: 99%

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Propidium Iodide Competes with Ca2+ to Label Pectin in Pollen Tubes and Arabidopsis Root Hairs

et al. 2011

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We have used propidium iodide (PI) to investigate the dynamic properties of the primary cell wall at the apex of Arabidopsis (Arabidopsis thaliana) root hairs and pollen tubes and in lily (Lilium formosanum) pollen tubes. Our results show that in root hairs, as in pollen tubes, oscillatory peaks in PI fluorescence precede growth rate oscillations. Pectin forms the primary component of the cell wall at the tip of both root hairs and pollen tubes. Given the electronic structure of PI, we investigated whether PI binds to pectins in a manner analogous to Ca 2+ binding. We first show that Ca 2+ is able to abrogate PI growth inhibition in a dose-dependent manner. PI fluorescence itself also relies directly on the amount of Ca 2+ in the growth solution. Exogenous pectin methyl esterase treatment of pollen tubes, which demethoxylates pectins, freeing more Ca 2+ -binding sites, leads to a dramatic increase in PI fluorescence. Treatment with pectinase leads to a corresponding decrease in fluorescence. These results are consistent with the hypothesis that PI binds to demethoxylated pectins. Unlike other pectin stains, PI at low yet useful concentration is vital and specifically does not alter the tip-focused Ca 2+ gradient or growth oscillations. These data suggest that pectin secretion at the apex of tip-growing plant cells plays a critical role in regulating growth, and PI represents an excellent tool for examining the role of pectin and of Ca 2+ in tip growth.

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supporting

confidence: 59%

Section: Pi Fluorescence Oscillations Precede Growth Rate Oscillationmentioning

confidence: 99%

Propidium Iodide Competes with Ca2+ to Label Pectin in Pollen Tubes and Arabidopsis Root Hairs

et al. 2011

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“…[21] NMR spectroscopy studies by Leupin et al using 3-and 8-deaminoethidium revealed that the removal of the 8-amino group had little effect on the binding to DNA, whereas the removal of the 3-amino group greatly affected the intercalation. [25] The most recent study by Tor and co-workers showed the influence of such modifications on the electronic structure of E. [26] This study included 5-ethyl-6-phenylphenanthridinium (3,8-dideaminoethidium, 1) that was also previously described by others. [24,[27][28][29] On the other hand, several theoretical chemical calculations have shown that the quaternization at position 5 adds significantly to the intercalation properties of phenanthridines.…”

Section: Introductionmentioning

confidence: 99%

Optical, Redox, and DNA‐Binding Properties of Phenanthridinium Chromophores: Elucidating the Role of the Phenyl Substituent for Fluorescence Enhancement of Ethidium in the Presence of DNA

Prunkl

Pichlmaier

Winter

et al. 2010

Chemistry A European J

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The phenanthridinium chromophores 5-ethyl-6-phenylphenanthridinium (1), 5-ethyl-6-methylphenanthridinium (2), 3,8-diamino-5-ethyl-6-methylphenanthridinium (3), and 3,8-diamino-5-ethyl-6-(4-N,N-diethylaminophenyl)phenanthridinium (4) were characterized by their optical and redox properties. All dyes were applied in titration experiments with a random-sequence 17mer DNA duplex and their binding affinities were determined. The results were compared to well-known ethidium bromide (E). In general, this set of data allows the influence of substituents in positions 3, 6, and 8 on the optical properties of E to be elucidated. Especially, compound 4 was used to compare the weak electron-donating character of the phenyl substituent at position 6 of E with the more electron-donating 4-N,N-diethylaminophenyl group. Analysis of all of the measurements revealed two pairs of chromophores. The first pair, consisting of 1 and 2, lacks the amino groups in positions 3 and 8, and, as a result, these dyes exhibit clearly altered optical and electrochemical properties compared with E. In the presence of DNA, a significant fluorescence quenching was observed. Their binding affinity to DNA is reduced by nearly one order of magnitude. The electronic effect of the phenyl group in position 6 on this type of dye is rather small. The properties of the second set, 3 and 4, are similar to E due to the presence of the two strongly electron-donating amino groups in positions 3 and 8. However, in contrast to 1 and 2, the electron-donating character of the substituent in position 6 of 3 and 4 is critical. The binding, as well as the fluorescence enhancement, is clearly related to the electron-donating effect of this substituent. Accordingly, compound 4 shows the strongest binding affinity and the strongest fluorescence enhancement. Quantum chemical calculations reveal a general mechanism related to the twisted intramolecular charge transfer (TICT) model. Accordingly, an increase of the twist angle between the phenyl ring in position 6 and the phenanthridinium core opens a nonradiative channel in the excited state that depends on the electron-donating character of the phenyl group. Access to this channel is hindered upon binding to DNA.

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“…4,9-diazapyrene) were often applied for an "aryl" component due to characteristic structural features like a permanent or pH induced positive charge, high polarizability, high electron affinity and highly polar amino groups. 4 In addition, it was shown that the chemical modulation of the phenanthridine exocyclic amines is a profitable option to tune the nucleic acid recognition properties of phenanthridinium dyes. 5 A lot of experimental data on ethidium derivatives have been collected over the last three decades 6 including a design of two-colour RNA intercalating probe for cell imaging applications 7 , photoaffinity labelling 8 and antibiotic as well as antitumor activity.…”

Section: Introductionmentioning

confidence: 99%

The phenanthridine biguanides efficiently differentiate between dGdC, dAdT and rArU sequences by two independent, sensitive spectroscopic methods

et al. 2011

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At submicromolar concentrations two novel phenanthridine biguanides exhibit distinctly different spectroscopic signals for dGdC and dAdT sequences, respectively, by opposite fluorimetric changes (quenching for dGdC and increase for dAdT) and especially bis -biguanide derivative gives opposite ICD response (negative ICD for dGC and strong positive for dAdT). This speci fic signalling was explained by ability of compounds to switch binding mode from intercalation into dGdC to minor groove binding into dAdT sequences. Both compounds bind to rArU by intercalation, yielding different fluorimetric and CD response in compariso n to any of aforementioned ds-DNA. Moreover, both compounds revealed significantly higher affinity toward ds-polynucleotides in comparison to previously studied alkylamine-and urea-analogues. Furthermore, DNA/RNA binding properties of novel compounds could be controlled by pH, due to the protonation of heterocyclic nitrogen. Low in vitro cytotoxicity of both compounds against human cell lines makes them interesting spectrophotometric probes.

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On the Electronic Structure of Ethidium

Cited by 61 publications

References 46 publications

Propidium Iodide Competes with Ca2+ to Label Pectin in Pollen Tubes and Arabidopsis Root Hairs

Propidium Iodide Competes with Ca2+ to Label Pectin in Pollen Tubes and Arabidopsis Root Hairs

Optical, Redox, and DNA‐Binding Properties of Phenanthridinium Chromophores: Elucidating the Role of the Phenyl Substituent for Fluorescence Enhancement of Ethidium in the Presence of DNA

The phenanthridine biguanides efficiently differentiate between dGdC, dAdT and rArU sequences by two independent, sensitive spectroscopic methods

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