Homogeneous DNA-detection Based on the Non-enzymatic Reactions Promoted by Target DNA

Ihara, Toshihiro; Mukae, Motoko

doi:10.2116/analsci.23.625

Cited by 15 publications

(11 citation statements)

References 70 publications

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“…[2] This sensing method relies on two functionalized oligonucleotide probes, which hybridize to a common target strand; the proximity of the probes accelerates a reaction between the attached functionalities, resulting in a fluorescence signal. Templated fluorescence activation can be selective to single mismatch polymorphisms [3] and imposes minimal requirements for equipment and personnel.…”

Section: Introductionmentioning

confidence: 99%

7‐Azidomethoxy‐Coumarins as Profluorophores for Templated Nucleic Acid Detection

Franzini

Kool

2008

ChemBioChem

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Templated nucleic acid detection is an emerging bioanalytical method that makes use of the target DNA or RNA strand to initiate a fluorogenic reaction. The Staudinger reduction holds particular promise for templated sensing of nucleic acids because the involved functional groups are highly chemoselective. Here, the azidomethoxy group, which can be removed under Staudinger conditions, is used to cage 7-hydroxycoumarin fluorophores. The reduction by phosphines and the subsequent loss of the azidomethoxy substituent induce a significant bathochromic shift of the major absorbance band in the near UV region. When excited at the appropriate wavelength, this change in the absorbance spectrum translates into a substantial fluorescence turn-on signal. The described profluorophores are readily conjugated to amino-modified DNAs and are rapidly uncaged by a triphenylphosphine-DNA probe under the control of a DNA template. In addition, turnover of the probes on the target strand is demonstrated, yielding substantial signal amplification.

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Section: Introductionmentioning

confidence: 99%

7‐Azidomethoxy‐Coumarins as Profluorophores for Templated Nucleic Acid Detection

Franzini

Kool

2008

ChemBioChem

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“…Hence, diagnostic molecules that could directly detect specific double-stranded DNA (dsDNA) sequences obviating the need for denaturation, hybridization, washing, or labeling of the DNA samples have been gaining immense interest owing to their potential clinical applications. [1][2][3][4] Accordingly, molecular beacons and DNAbinding molecules have been demonstrated as powerful tools to probe for the specific DNA sequences.…”

Section: Introductionmentioning

confidence: 99%

Design of a new fluorescent probe: Pyrrole/imidazole hairpin polyamides with pyrene conjugation at their γ-turn

Vaijayanthi

Bando

Hashiya

et al. 2013

Bioorganic & Medicinal Chemistry

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Fluorophores that are conjugated with N-methylpyrrole-N-methylimidazole (Py-Im) polyamides postulates versatile applications in biological and physicochemical studies. Here, we show the design and synthesis of new types of pyrene-conjugated hairpin Py-Im polyamides (1-5). We evaluated the steady state fluorescence of the synthesized conjugates (1-5) in the presence and absence of oligodeoxynucleotides 5'-CGTATGGACTCGG-3' (ODN 1) and 5'-CCGAGTCCATACG-3' (ODN 2) and observed a distinct increase in emission at 386nm with conjugates 4 and 5. Notably, conjugate 5 that contains a β-alanine linker had a stronger binding affinity (K(D)=1.73×10(-8)M) than that of conjugate 4 (K(D)=1.74×10(-6)M). Our data suggests that Py-Im polyamides containing pyrene fluorophore with a β-alanine linker at the γ-turn NH(2) position can be developed as the competent fluorescent DNA-binding probes.

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“…Probes for use in solution are expected to emit a signal only when they bind to their targets. [6][7][8][9][10][11][12] This is an essential requirement for bioprobes providing a spatiotemporal response.…”

Section: Introductionmentioning

confidence: 99%

Rational Design for Cooperative Recognition of Specific Nucleobases Using β‐Cyclodextrin‐Modified DNAs and Fluorescent Ligands on DNA and RNA Scaffolds

Futamura

Uemura

Imoto

et al. 2013

Chemistry A European J

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We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.

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Homogeneous DNA-detection Based on the Non-enzymatic Reactions Promoted by Target DNA

Cited by 15 publications

References 70 publications

7‐Azidomethoxy‐Coumarins as Profluorophores for Templated Nucleic Acid Detection

7‐Azidomethoxy‐Coumarins as Profluorophores for Templated Nucleic Acid Detection

Design of a new fluorescent probe: Pyrrole/imidazole hairpin polyamides with pyrene conjugation at their γ-turn

Rational Design for Cooperative Recognition of Specific Nucleobases Using β‐Cyclodextrin‐Modified DNAs and Fluorescent Ligands on DNA and RNA Scaffolds

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