DNA-Templated Assembly of Helical Cyanine Dye Aggregates:  A Supramolecular Chain Polymerization

Hannah, Kristen C; Armitage, Bruce A.

doi:10.1021/ar030257c

Cited by 319 publications

(223 citation statements)

References 44 publications

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“…The results thus suggest that the metal complex cations upon binding to the oligonucleotides would self-assemble into a helical supramolecular assembly of different handedness. The magnitude of the induced CD intensity is also in the same range as other related helical systems (26,27).…”

Section: Resultssupporting

confidence: 65%

Single-stranded nucleic acid-induced helical self-assembly of alkynylplatinum(II) terpyridyl complexes

Chan

Wong

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

172

124

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Single-stranded nucleic acids, which carry multiple negative charges in an aqueous medium at near neutral pH, are found to induce the aggregation and self-assembly of the positively charged alkynylplatinum(II) terpyridyl complexes via electrostatic binding of the platinum complexes to the single-stranded nucleic acids, as revealed by the appearance of new UV-vis absorption and emission bands upon addition of single-stranded nucleic acids to a buffer solution of the complex. Changes in the intensity and pattern of circular dichroism (CD) spectroscopy are also observed, many of which are consistent with the assembly of the platinum complexes into helical structures, via metal⅐⅐⅐metal and ⅐⅐⅐ stacking interactions. The induced spectroscopic property changes are found to depend on the structural properties of the nucleic acids.helicity ͉ noncovalent interactions ͉ platinum complex N ucleic acids are, in a sense, the most fundamental and important class of biomolecules in a living cell. Detection of nucleic acids, analysis of their sequence, structure, and the corresponding properties, as well as their self-replication, interactions with regulation factors, and the details of transcription and translation are among the major foci of numerous biochemical and biophysical research works (1, 2). Single-stranded nucleic acid sensing and characterization are therefore of great importance, which not only can help us to understand how the cell functions and to assist biological research, but also facilitate the development of new tools for disease diagnosis and treatment and new drug developments.It has been known for many years that many of the square planar metal complexes arrange themselves into highly ordered extended linear chain or oligomeric structures in the solid state. Depending on the extent of the metal⅐⅐⅐metal and the ligand ⅐⅐⅐ stacking interactions, different colors could be observed (3, 4). Square planar platinum(II) complexes belong to a particularly interesting class of this type of complexes, as a result of their rich spectroscopic and luminescence properties revealed during the past few decades (3-16).Recently, we have synthesized a number of platinum(II) polypyridyl alkynyl complexes that show interesting spectroscopic and luminescence properties (17-21). One particularly interesting observation is that solvents of different polarity and also polyacrylate could induce the aggregation of the positively charged platinum complexes in organic solvent mixtures (19, 21). As a result, remarkable spectroscopic property changes were observed. Because single-stranded nucleic acids carry multiple negatively charged phosphate functional groups, they are polyanions. It is therefore reasonable to envisage that single-stranded nucleic acids may have the possibility to induce the self-assembly of the square planar platinum(II) complexes in an aqueous environment. Here, we describe the synthesis and characterization of a water-soluble platinum(II) terpyridyl alkynyl complex, [Pt(tpy)C'CC'CCH 2 OH]OTf (1) (Fig. 1), and it...

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Section: Resultssupporting

confidence: 65%

Single-stranded nucleic acid-induced helical self-assembly of alkynylplatinum(II) terpyridyl complexes

Chan

Wong

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

172

124

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“…The occurrence of two sets of signals for the dye both in absence and in the presence of Succ-β-CyD suggests that different types of aggregates are present. This is consistent with what was proposed by Armitage and coworkers [10] of a stepwise formation of facial (H-type) aggregates of Disc 2 (5) and then end-end interaction of these dimers to give rise to tetramers, hexamers and higher aggregates, a process which can make use of the PNA-DNA duplexes as templates. Therefore, the presence of the cyclodextrin could prevent the end-end interactions, only allowing for a monomer-dimer equilibrium and thus hampering the formation of higher aggregates on the PNA-DNA duplexes.…”

Section: Binding Affinity Of the Cyanine Dye Disc 2 (5) To Pna-dna Dusupporting

confidence: 92%

Fast and easy colorimetric tests for single mismatch recognition by PNA–DNA duplexes with the diethylthiadicarbocyanine dye and succinyl-β-cyclodextrin

Tedeschi¹,

Sforza²,

Ye³

et al. 2007

Journal of Biochemical and Biophysical Methods

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The 3,3′-diethylthiacarbocyanine (DiSC 2 (5)) dye is able to aggregate on full matched PNA-DNA duplexes by changing its absorption properties, which are manifested by an instantaneous colour shift from blue to purple. However the spontaneous aggregation of the dye also on mismatched duplexes and even on free PNA strands makes the test quite aspecific. Here it is demonstrated that the addition of succinyl-β-cyclodextrin (Succ-β-CyD) to the solutions containing PNA-DNA duplexes and the dye strongly enhances the specificity of the colour shift, allowing for a fast, very specific and extremely sensitive visual recognition of mismatches in DNA strands by using PNA probes in combination with the DiSC 2 (5) dye. The phenomenon has been studied by CD and NMR spectroscopies. The method has been optimized and preliminarily applied for the recognition of an apoE gene mutation in human DNA samples.

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“…It is known that cyanine dyes undergo aggregation, [44][45][46][47] a phenomenon that is mainly due to a strong hydrophobic effect. Aggregation dramatically changes the photophysical properties of the dyes in solution compared to the monomeric species, in particular the absorption and fluorescence band shape and position ( Figure 2).…”

Section: Resultsmentioning

confidence: 99%

Structure–Fluorescence Contrast Relationship in Cyanine DNA Intercalators: Toward Rational Dye Design

Fürstenberg

Deligeorgiev

Gadjev

et al. 2007

Chemistry A European J

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The fluorescence enhancement mechanisms of a series of DNA stains of the oxazole yellow (YO) family have been investigated in detail using steady‐state and ultrafast time‐resolved fluorescence spectroscopy. The strong increase in the fluorescence quantum yield of these dyes upon DNA binding is shown to originate from the inhibition of two distinct processes: 1) isomerisation through large‐amplitude motion that non‐radiatively deactivates the excited state within a few picoseconds and 2) formation of weakly emitting H‐dimers. As the H‐dimers are not totally non‐fluorescent, their formation is less efficient than isomerisation as a fluorescent contrast mechanism. The propensity of the dyes to form H‐dimers and thus to reduce their fluorescence contrast upon DNA binding is shown to depend on several of their structural parameters, such as their monomeric (YO) or homodimeric (YOYO) nature, their substitution and their electric charge. Moreover, these parameters also have a substantial influence on the affinity of the dyes for DNA and on the ensuing sensitivity for DNA detection. The results give new insight into the development and optimisation of fluorescent DNA probes with the highest contrast.

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DNA-Templated Assembly of Helical Cyanine Dye Aggregates: A Supramolecular Chain Polymerization

Cited by 319 publications

References 44 publications

Single-stranded nucleic acid-induced helical self-assembly of alkynylplatinum(II) terpyridyl complexes

Single-stranded nucleic acid-induced helical self-assembly of alkynylplatinum(II) terpyridyl complexes

Fast and easy colorimetric tests for single mismatch recognition by PNA–DNA duplexes with the diethylthiadicarbocyanine dye and succinyl-β-cyclodextrin

Structure–Fluorescence Contrast Relationship in Cyanine DNA Intercalators: Toward Rational Dye Design

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