Detection of genetic polymorphisms with high sensitivity by DNA–perylene conjugate

Kashida, Hiromu; Takatsu, Tomohiko; Asanuma, Hiroyuki

doi:10.1016/j.tetlet.2007.07.084

Cited by 18 publications

(21 citation statements)

References 28 publications

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“…The excitation wavelength of the PB dimer (505 nm) is in the range of typical bioanalytical fluorescence readers. Moreover, the high photostability of PB as the smallest representative of the rylene dyes [22] makes PB dimer-based DNA assays superior to the application of other organic chromophores including pyrene, perylene, and cyanine derivatives.…”

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confidence: 99%

Perylene Bisimide Dimers as Fluorescent “Glue” for DNA and for Base‐Mismatch Detection

2008

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Perylene-3,4:9,10-tetracarboxylic acid bisimide ("PB") and its derivatives are applied as fluorescent dyes in organic materials owing to their excellent photochemical stability as well as the high fluorescence quantum yields. [1,2] The strong hydrophobic stacking interactions between the PB chromophores make this dye an important building block for functional supramolecular architectures. [1,3] Based on these properties, PB in the dimeric form should be also of potential interest as a probe for fluorescent DNA/RNA analytics as well as for functionalized DNA-based architectures. Its noncovalent DNA-binding interactions have been studied with PB derivatives that had been modified with spermine [4] or other amines.[5] Moreover, an increasing number of publications about covalent modifications of oligonucleotides with PB have appeared over the last few years. [6][7][8][9][10][11][12] Recently, we presented a facile route for the synthetic incorporation of PB as an artificial DNA base in order to study the stacking interactions of this dye at specific sites in duplex DNA.[13]Herein, we present the evaluation of fluorescent PB dimers for the optical functionalization of DNA using three representative duplexes (DNA1, DNA3, and DNA4 a). For the synthetic modification of the corresponding oligonucleotides with the PB chromophore (Scheme 1), the 2-deoxyribofuranoside moiety was replaced by an acyclic linker system which is tethered to one of the imide nitrogens of the PB dye.[13] This linker allows the chromophore to intercalate in the base stack while providing high chemical stability during the automated phosphoramidite chemistry. [13,14] DNA1 bears one interstrand PB dimer inside the duplex, whereas DNA3 contains a PB monomer outside the duplex at each 5' end. Both duplexes contain palindromic sequences. When DNA1 and DNA3 are excited at 505 nm, the fluorescence spectra of both duplexes (Figure 1) are dominated by a broad band at % 660 nm without fine structure. This band corresponds to the excimer-type emission of the PB dimer that has been observed in nanoaggregates of perylene bisimides. [3,8,15] The UV/Vis spectra of DNA1 and DNA3 (Figure 2) at low temperatures show two major bands that are hyposochromically (506 nm) or bathochromically (545 nm) shifted in comparison to the 0!1 and 0!0 vibronic transitions of the PB monomer.[16] This result shows the strong p-p excitonic interactions of the two PB chromophores inside (DNA1) and outside (DNA3) of the duplex. [15] Both the excimer-type fluorescence band and the shifted absorption bands of DNA1 vanish at higher temperatures. It is remarkable that this occurs cooperatively at a temperature (75.9 8C) that corresponds to the cooperative thermal dehybridization of the whole DNA duplex, which is typically measured at 260 nm (T m = 78.6 8C). Apparently the intact helical duplex is required as a framework for the PB dimer formation. In comparison to the unmodified DNA2 (T m = 76.2 8C) the duplex DNA1 is stabilized by 2.4 8C through the Scheme 1. PB-modified duplexes DNA1-DNA3...

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confidence: 99%

Perylene Bisimide Dimers as Fluorescent “Glue” for DNA and for Base‐Mismatch Detection

2008

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“…By use of a FRET pair, the apparent Stokes shift of these new probes was much larger (115 nm) than that of the previous probe composed of only perylene (35 nm). [25] As shown in Table 3, the I 550 /I 461 ratios of ODN5/C2-ODN9/C2 did not show much change, which demonstrated that the polymorphism-discrimination ability did not decrease despite the fact that many donors were inserted. Even exciplex emission, which should be observed when a pyrene-perylene heterodimer is formed, [47,48] was not observed at all.…”

Section: Discussionmentioning

confidence: 86%

“…[23] We have developed ODN probes detecting base-deletion polymorphisms. [24,25] Here, we demonstrate that the Stokes shift of the fluorescent probe can be extended by locating donors in proximity to the acceptor. This strategy has a potential to be used for other fluorescent probes tethering intercalators.…”

Section: Introductionmentioning

confidence: 76%

“…This value was eight-times larger than that of ODN7/ C2 (0.07) corresponding to full match. [35,36] ODN5, a probe without pyrene as an antenna, [25] showed similar results: I 550 / I 461 was 0.84 for the deletion mutant C1, whereas it was 0.05 for full-match C2 when excited at 425 nm at which perylene has its absorption maximum (see Table 3 and Figure S6 in the Supporting Information for the actual fluorescence spectra of ODN5/C1 and ODN5/C2). Note that the Stokes shift of ODN5 was as small as 35 nm, whereas that of ODN7, which has pyrenes as an antenna was as large as 115 nm.…”

Section: C2mentioning

confidence: 83%

“…On the other hand, in a one-base-deletion mutant, two perylenes should come close to each other by forming a bulge-like structure so that an excimer of two perylenes should be formed. [25] The fluorescence emission spectra of ODN7/C1 and ODN7/C2, excited at 345 nm, are shown in Figure 4. When ODN7 was hybridized with full-matched target (C2), strong monomer emission of perylene was observed.…”

Section: C2mentioning

confidence: 99%

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An Efficient Fluorescence Resonance Energy Transfer (FRET) between Pyrene and Perylene Assembled in a DNA Duplex and Its Potential for Discriminating Single‐Base Changes

Kashida

Takatsu

Sekiguchi

et al. 2010

Chemistry A European J

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To increase the apparent Stokes' shift of perylene, pyrene (donor) and perylene (acceptor) were assembled in a DNA duplex to achieve the efficient fluorescence resonance energy transfer (FRET) from pyrene to perylene. Multiple donors were introduced in the vicinity of acceptors through D-threoninol and natural base pairs were inserted between the dyes. Accordingly, donors and acceptors could be accumulated inside the DNA without forming an undesired excimer/exciplex. When two pyrene moieties were located in proximity to one perylene with one base pair inserted between them, efficient FRET occurred within the duplex. Thus, strong emission at 460 nm was observed from perylene when excited at 345 nm at which pyrene has its absorption. The apparent Stokes' shift became as large as 115 nm with a high apparent FRET efficiency (Phi>1). However, the introduction of more than two pyrenes did not enhance the fluorescence intensity of perylene, due to the short Förster radius (R(0)) of the donor pyrene. Next, this FRET system was used to enlarge the Stokes' shift of the DNA probe, which can discriminate a one-base deletion mutant from wild type with a model system by incorporation of multiple donors into DNA. Two perylene moieties were tethered to the DNA on both sides of the intervening base, and two pyrenes were further inserted in the vicinity of the perylenes as an antenna. Hybridization of this FRET probe with a fully matched DNA allowed monomer emission of perylene when the pyrenes were excited. In contrast, excimer emission was generated by hybridization with a one-base deletion mutant. Thus, the apparent Stokes' shift was enhanced without loss of efficiency in the detection of the deletion mutant.

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DNA‐Conjugated Organic Chromophores inDNAStacking Interactions

Filichev

Pedersen

2008

Wiley Encyclopedia of Chemical Biology

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Since the discovery of the intercalation of acridine derivatives into DNA (1961), chemists have synthesized many intercalators tethered to DNA. Advances in the chemical synthesis of modified nucleosides along with progress in oligonucleotide synthesis have made it possible to introduce organic chromophores in any desired position of the sequence. As an outcome of such fascinating research, we gained a deeper knowledge and understanding of nucleic acid structures, which is pivotal for future progress within nucleic acid technology and for development of novel approaches in drug design. The current review presents those efforts in the design of intercalators/organic chromophores as oligonucleotide conjugates that form a foundation for the generation of novel nucleic acid architectures.

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Detection of genetic polymorphisms with high sensitivity by DNA–perylene conjugate

Cited by 18 publications

References 28 publications

Perylene Bisimide Dimers as Fluorescent “Glue” for DNA and for Base‐Mismatch Detection

Perylene Bisimide Dimers as Fluorescent “Glue” for DNA and for Base‐Mismatch Detection

An Efficient Fluorescence Resonance Energy Transfer (FRET) between Pyrene and Perylene Assembled in a DNA Duplex and Its Potential for Discriminating Single‐Base Changes

DNA‐Conjugated Organic Chromophores inDNAStacking Interactions

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