Binding of cationic dyes to DNA: distinguishing intercalation and groove binding mechanisms using simple experimental and numerical models

Castillo, Pilar; Horobin, RW; Blázquez‐Castro, Alfonso; Jc, Stockert

doi:10.3109/10520290903149620

Cited by 23 publications

(10 citation statements)

References 38 publications

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“…Localises in nuclear chromatin owing to dsDNA minor groove binding [40,41,70] log P > 8 A I > 8 or if 5 > AI > 3.5 and HGS > 400 (or HGH < À4) or if CBN > 40 and log P > À10…”

Section: Acknowledgementsmentioning

confidence: 99%

“…A cut‐off between intercalation and groove binding is seen at L values corresponding to the length of a base pair. Thus, in the absence of bulky substituents, the boundary between these two mechanisms is 10 simplistic bond number units . Chromatin accumulation also occurs with membrane permeant anionic dyes whose conjugated systems exceed a minimum size, owing to histone binding (8 > log P > 0, Z < 0, CBN > 16).…”

Section: Where Do Dyes Go Inside Live Cells? Predicting Localisationmentioning

confidence: 99%

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Where do dyes go inside living cells? Predicting uptake, intracellular localisation, and accumulation using QSAR models

Horobin

2014

Coloration Technology

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Uptake of dyes into living cells and organisms is of concern to several diverse groups of people. These include those not wishing dyes to enter cells (e.g. manufacturers and users of textile dyes, or laboratory workers using dyes as analytical reagents) and those requiring dye entry (e.g. biologists imaging cell contents, or clinicians using photoactive dyes as antitumour drugs). This diversity results in the need to consider an extremely wide range of dyes -and indeed of cells and organisms. An overview of methods for predicting uptake and intracellular localisation is provided, followed by a more detailed account of the concepts and procedures involved in decision-rule quantitative structure-activity relationship (QSAR) models. Some of these models permit the prediction of which dyes are likely to enter cells, and which dyes will be excluded. Other models predict where internalised dyes will localise within the live cells. Use of QSAR models to understand intracellular accumulation, redistribution, loss from the cell, and metabolic modification of dyes is also considered. In particular, the relationship of such predictions to toxicity is discussed. An extended case example is provided, describing the modelling of dye binding to nucleic acids in single-cell systems. A further case example then illustrates dye localisation in multicellular organisms. Finally, conclusions, critiques, and probable future directions concerning the QSAR modelling approach to dye uptake and localisation are given. A summary of key QSAR decision rules in the form of decision logic tabulations is provided.

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“…Localises in nuclear chromatin owing to dsDNA minor groove binding [40,41,70] log P > 8 A I > 8 or if 5 > AI > 3.5 and HGS > 400 (or HGH < À4) or if CBN > 40 and log P > À10…”

Section: Acknowledgementsmentioning

confidence: 99%

Section: Where Do Dyes Go Inside Live Cells? Predicting Localisationmentioning

confidence: 99%

Where do dyes go inside living cells? Predicting uptake, intracellular localisation, and accumulation using QSAR models

Horobin

2014

Coloration Technology

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“…In terms of binding mode, some of the previous reports revealed that AuO binds strongly to the minor groove formed by the AT region of the DNA . On the other hand, few reports have observed that AuO can bind exclusively by the intercalation binding mode or by a mixture of intercalation and groove binding modes. , Generally, the surface of minor grooves with AT-rich sequences has the highest negative electrostatic potentials . Naturally, the cationic AuO prefers to bind to the AT-rich minor grooves of DNA than the minor groove formed by the GC-bps.…”

Section: Resultsmentioning

confidence: 99%

DNA-Templated Modulation in the Photophysical Properties of a Fluorescent Molecular Rotor Auramine O by Varying the DNA Composition

et al. 2022

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This work delineates an integrative approach combining spectroscopic and computational studies to decipher the association-induced fluorescence properties of a fluorescent molecular rotor, viz., auramine O (AuO), after interacting with 20-mer duplex DNA having diverse well-matched base pairs. While exploring the scarcely explored sequence-dependent interaction mechanism of AuO and DNA, we observed that DNA could act as a conducive scaffold to the formation of AuO dimer through noncovalent interactions at lower molecular density. The photophysical properties of AuO depend on the nucleotide compositions as described from sequence-dependent shifting in the emission and absorption maxima. Furthermore, we explored such DNA base pair-dependent fluorescence spectral characteristics of AuO toward discriminating the thermodynamically most stable single nucleotide mismatch in a 20-mer sequence. Our results are interesting and could be useful in developing analogues with further enhanced emission properties toward mismatched DNA sequences.

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“…The titration data from Figure 3c show that there is no change in shape or peak position for the negative and positive CD bands of MGC with increased dye loading, suggesting that this dye does not change its binding mode from low to high site occupancy. 41 While MGC was suggested to bind both as an intercalator and as a groove binder, 42 the CD data from Figure 3c suggests that intercalation is more likely the binding mechanism. For polyAT the bisignate chiral signal at 600−700 nm is much stronger (Figure S2, SI), that is, the excitonic coupling between intercalated MGC dyes is much stronger compared to dyes intercalated with rdsDNA.…”

Section: ■ Intercalated Dna/mgc Complexmentioning

confidence: 97%

Energy Transfer from a Cationic Conjugated Polyelectrolyte to a DNA Photonic Wire: Toward Label-Free, Sequence-Specific DNA Sensing

2014

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We demonstrate a label-free, sequence specific DNA sensor based on fluorescence resonant energy transfer (FRET) occurring between a cationic conjugated polyelectrolyte and a small intercalating dye, malachite green chloride. The sensor combines (1) conjugated polymer chain conformation changes induced by the binding with DNA, with the conjugated polymer wrapping/twisting around the DNA helical duplex and experiencing a 3-fold increase in its photoluminescence quantum yield and (2) FRET from the conjugated polymer to the intercalated DNA. Owing to its small size, the dye intercalates at maximal, one-to-one dye-to-base pair load, making the intercalated DNA a molecular photonic wire with dyes excitonically coupled and chiroptically active. Any sequence mismatch between probe and target DNA degrades the intercalated DNA photonic wire by decreasing its brightness, excitonic coupling, and chiroptical properties, and this provides a signal transduction method for the DNA sensor. Coupling of intercalated DNA with the conjugated polymer via FRET provides target signal amplification and increased sensitivity toward sequence mismatch, with the FRET efficiency decreasing with added DNA sequence mismatch.

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Binding of cationic dyes to DNA: distinguishing intercalation and groove binding mechanisms using simple experimental and numerical models

Cited by 23 publications

References 38 publications

Where do dyes go inside living cells? Predicting uptake, intracellular localisation, and accumulation using QSAR models

Where do dyes go inside living cells? Predicting uptake, intracellular localisation, and accumulation using QSAR models

DNA-Templated Modulation in the Photophysical Properties of a Fluorescent Molecular Rotor Auramine O by Varying the DNA Composition

Energy Transfer from a Cationic Conjugated Polyelectrolyte to a DNA Photonic Wire: Toward Label-Free, Sequence-Specific DNA Sensing

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