Coherent interactions of dyes assembled on DNA

Asanuma, Hiroyuki; Fujii, Tomoyuki; Kato, Tomohiro; Kashida, Hiromu

doi:10.1016/j.jphotochemrev.2012.04.002

Cited by 79 publications

(106 citation statements)

References 59 publications

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“…UV-Vis absorption and steady-state fluorescence emission spectra of X / Y / Z -modified ONs in the presence or absence of complementary DNA/RNA targets were recorded next to further ascertain intercalative binding modes of the pyrene moieties, as intercalation is known to induce bathochromic shifts of pyrene absorption peaks 27 and nucleobase-mediated quenching of pyrene fluorescence. 27a,28 Indeed, X / Y / Z -modified ONs generally display hypochromic and bathochromic shifts in the pyrene absorption spectra upon hybridization with DNA and RNA targets (Δ λ max = 0–5 nm, Table 3; Figures S2–S4 in the ESI † ).…”

Section: Resultsmentioning

confidence: 99%

“…27a,28 Indeed, X / Y / Z -modified ONs generally display hypochromic and bathochromic shifts in the pyrene absorption spectra upon hybridization with DNA and RNA targets (Δ λ max = 0–5 nm, Table 3; Figures S2–S4 in the ESI † ). Slightly greater bathochromic shifts are generally observed upon hybridization with DNA than RNA targets, which again may reflect the preference of intercalators for the less compressed geometry of B -DNA.…”

Section: Resultsmentioning

confidence: 99%

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Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2′-alkylated RNA monomers

et al. 2014

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Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and - more recently - engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2′-alkylated uridine monomers X–Z by means of thermal denaturation experiments, optical spectroscopy, force-field simulations and recognition experiments using DNA hairpins as model targets. We demonstrate that Invaders with +1 interstrand zippers of X or Y monomers efficiently recognize mixed-sequence DNA hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔTm/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2′-alkylated RNA monomers

et al. 2014

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“…Hydrophobically interacting base pairs are not new and have also been studied in the case of other chromophores by other groups. 40,62,63 However, the fluorescence shift in the case of two paired dyes of type 21 is quite interesting. 63 Moreover, the dye pair of 21 (thiazole orange) and 23 (thiazole red) represent a promising pair for energy transfer ( Figure 5).…”

Section: Bodipy and Cyanine Dyesmentioning

confidence: 99%

“…40,62,63 However, the fluorescence shift in the case of two paired dyes of type 21 is quite interesting. 63 Moreover, the dye pair of 21 (thiazole orange) and 23 (thiazole red) represent a promising pair for energy transfer ( Figure 5). The emission is shifted from the thiazole orange typical value of 530 nm (green) to 670 nm (red).…”

Section: Bodipy and Cyanine Dyesmentioning

confidence: 99%

Organic Chemistry of DNA Functionalization; Chromophores as DNA Base Substitutes versus DNA Base/2′-Modifications

Schmucker¹,

Wagenknecht²

2012

Synlett

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Nucleic acids are suitable scaffolds for the precise arrangement of different kinds of artificial functionalities inside or along the double helix. In this account, we summarize our synthetic efforts over the last ten years to modify DNA chemically with organic chromophores, fluorescent probes, and metal-ion ligands. We used three different approaches: (i) replacement of DNA bases (substitutes/surrogates), (ii) modifications of DNA bases (mainly 2′-deoxyuridine), and (iii) sugar modifications at the 2′-position. The first two types of modifications were achieved mainly by the DNA building block approach, whereas the latter type is based on postsynthetic methodologies. The different synthetic concepts are described and the influence of representative modifications on the melting temperature is compared. IntroductionDNA plays the central biological role since it encodes the genetic information of all living organisms. Beside its biological functionality, DNA represents an increasingly important structural scaffold for the development of architectures and materials in nanosciences. Nucleic acids are suitable scaffolds for the precise arrangement of different kinds of artificial functionalities inside or along the double helix, such as chromophores, metal-ligand complexes, spin labels, and others. 1-6 The following key features make nucleic acids so attractive in this context: 7 (i) Selfassembly: Encoded by the canonical base pairing, two oligonucleotides assemble spontaneously into double helical or more complex tertiary structures. (ii) Geometry: Due to the base-to-base distance, double helical structures of the A-and B-type provide the ideal basis for photophysical interactions of functionalities inside or along the helix.(iii) Synthesis: Automated oligonucleotide chemistry makes DNA available in any desired base sequence and also in sufficient quantities. (iv) Structural and conformational modulations: Artificial backbones, such as peptide nucleic acids (PNA), 8 typically used in the antisense technology, represent tools to alter the double helical geometries. Moreover, conformation of the oligonucleotides can be modulated by, for example, locked nucleic acids (LNA 9 ) or pyrrolidinyl PNA. 10 (v) Hierarchically structured complexity: Highly complex tertiary and other folded structures can be realized purely based on DNA, such as 2D networks, 11 3D objects, 12 and DNA origami. 13The great advantage of nucleic acids from a synthetic organic chemistry point of view is that they are synthesized by building blocks. In this bottom-up approach, artificial functionalities can be introduced synthetically into nanoarchitectures by providing the corresponding artificial DNA building blocks. 14 Moreover, if building blocks are not synthetically obtainable, postsynthetic methodologies allow the modification of oligonucleotides. This is especially important for functionalities that are not compatible with the broadly applied phosphoramidite chemistry. 15,16 In the last few years, polymerase-assisted biochemical synthesis of ...

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“…UV-vis absorption and steady-state fluorescence emission spectra of S -modified ONs, in the presence or absence of cDNA/cRNA targets, were recorded to further ascertain the binding mode of the pyrene moiety, as intercalation is known to induce bathochromic shifts of pyrene absorption bands due to ground-state electronic interactions with nucleobases, 27 and nucleobase-mediated quenching of pyrene fluorescence. 28 Indeed, hybridization of S -modified ONs with cDNA and cRNA results in bathochromic shifts of the pyrene absorption maxima (Table 3 and Figure S2), although the shifts are smaller than with O - or N -modified ONs, suggesting weaker interactions with nucleobases and less pronounced intercalation.…”

mentioning

confidence: 99%

Synthesis and characterization of oligodeoxyribonucleotides modified with 2′-thio-2′-deoxy-2′-S-(pyren-1-yl)methyluridine

Anderson

Hrdlicka

2015

Bioorganic & Medicinal Chemistry Letters

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Pyrene-functionalized oligonucleotides are intensively explored for applications in materials science and diagnostics. Here, we describe a short synthetic route to 2′-S-(pyren-1-yl)methyl-2′-thiouridine monomer S, its incorporation into oligodeoxyribonucleotides (ONs), and biophysical characterization thereof. Pseudorotational analysis reveals that the furanose ring of this monomer has a slight preference for South-type conformations. ONs modified with monomer S display high cDNA affinity but decreased binding specificity. Hybridization is associated with bathochromic shifts of pyrene absorption bands and quenching of pyrene fluorescence consistent with an intercalative binding mode of the pyrene moiety. Monomer S was also evaluated as a building block for mixed-sequence recognition of double-stranded DNA via the Invader strategy. However, probes with +1 interstrand arrangements of monomer S were found to be less efficient than Invader probes based on 2′-O-(pyren-1-yl)methyluridine or 2′-N-(pyren-1-yl)methyl-2′-N-methyl-2′-aminouridine.

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Coherent interactions of dyes assembled on DNA

Cited by 79 publications

References 59 publications

Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2′-alkylated RNA monomers

Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2′-alkylated RNA monomers

Organic Chemistry of DNA Functionalization; Chromophores as DNA Base Substitutes versus DNA Base/2′-Modifications

Synthesis and characterization of oligodeoxyribonucleotides modified with 2′-thio-2′-deoxy-2′-S-(pyren-1-yl)methyluridine

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