Sequence-Specific Fluorescence Detection of DNA by Polyamide−Thiazole Orange Conjugates

Fechter, Eric J.; Olenyuk, Bogdan; Dervan, Peter B.

doi:10.1021/ja054650k

Cited by 85 publications

(60 citation statements)

References 35 publications

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“…We chose also cyanine dyes, known to change their fluorescence properties (quantum yield and emission wavelength) upon the interaction with DNA. [35][36][37]62,63 Two commercially available cyanine fluorophores Cy3 and Cy5 were used. 64 They display the desirable properties and can be eventually used for FRET experiments.…”

Section: Properties Of Fluorophores and Polyamide Labelingmentioning

confidence: 99%

Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA

Nozeret

Yarmoluk

Новопашина

et al. 2015

Bioorganic & Medicinal Chemistry

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Section: Properties Of Fluorophores and Polyamide Labelingmentioning

confidence: 99%

Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA

Nozeret

Yarmoluk

Новопашина

et al. 2015

Bioorganic & Medicinal Chemistry

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“…[21][22][23][24][25][26][27][28][29][30][31][32][33] Usually, cyanine dyes or other DNA stains [34,35] have been linked to nucleic acids by means of a flexible tether. Previous work by ourselves and others has shown that the tether plays an important role as far as the responsiveness of fluorescence and the stability of probe-target duplexes are concerned.…”

Section: Introductionmentioning

confidence: 99%

Exploring Base‐Pair‐Specific Optical Properties of the DNA Stain Thiazole Orange

Jarikote

Krebs

Tannert

et al. 2006

Chemistry A European J

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Double‐stranded DNA offers multiple binding sites to DNA stains. Measurements of noncovalently bound dye–nucleic acid complexes are, necessarily, measurements of an ensemble of chromophores. Thus, it is difficult to assign fluorescence properties to base‐pair‐specific binding modes of cyanine dyes or, vice versa, to obtain information about the local environment of cyanines in nucleic acids by using optical spectroscopy. The feasibility to stain DNA and simultaneously probe local perturbations by optical spectroscopy would be a valuable asset to nucleic acid research. So‐called FIT probes (forced intercalation probes) were used to pinpoint the location of the DNA stain thiazole orange (TO) in PNA⋅DNA duplexes. A detailed analysis of the base‐pair dependence of optical properties is provided and enforced binding of TO is compared with “classical” binding of free TO‐PRO1. UV‐visible absorbance, circular dichroism (CD) and fluorescence spectroscopy, and melting‐curve analyses confirmed site‐specific TO intercalation. Thiazole orange exhibited base‐specific responses that are not observed in noncovalent dye–nucleic acid complexes, such as an extraordinary dependence of the TO extinction coefficient (±60 % variation of the averaged εmax of 57 000 M−1 cm−1) on nearest‐neighbor base pairs. TO signals hybridization, as shown by increases in the steady‐state fluorescence emission. Studies of TO fluorescence lifetimes in FIT–PNA and in DNA⋅DNA and PNA⋅DNA complexes highlighted four different fluorescence‐decay processes that may be closed or opened in response to matched or single‐mismatched hybridization. A very fast decay process (0.04–0.07 ns) and a slow decay process (2.33–3.95 ns) provide reliable monitors of hybridization, and the opening of a fast decay channel (0.22–0.48 ns) that resulted in an attenuation of the fluorescence emission is observed upon the formation of mismatched base pairs.

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“…[7–8] PAs 2 and 3 were then prepared through a combination of standard solid phase synthesis protocols and a new triphosgene-activation approach (Figure S1). [9] The tether length utilized in the design of PA 2 separated the YO intercalator and the PA by two base pairs relative to the β-alanine tail terminus,[8b, 10] equating to an overall 9 base pair binding profile for PA 2 . We initially investigated the capacity of PA 2 to selectively bind to the sequence 5′-ATGGACA-3′ using isothermal binding and fluorescence enhancement measurements.…”

mentioning

confidence: 99%

Site‐Specific Assembly of DNA‐Based Photonic Wires by Using Programmable Polyamides

Schuster

Bagshaw

et al. 2011

Angew Chem Int Ed

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Relay race: The first example of a programmable DNA photonic wire is reported utilizing fluorophore‐tethered pyrrole‐imidazole polyamides for site‐directed fluorophore assembly along a pre‐formed DNA duplex (see scheme; PB=Pacific Blue, Cy3=Cyanine 3; orange rectangles=fluorophore). The importance of such control is revealed by efficient energy transport over distances in excess of 27 nm.

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Sequence-Specific Fluorescence Detection of DNA by Polyamide−Thiazole Orange Conjugates

Cited by 85 publications

References 35 publications

Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA

Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA

Exploring Base‐Pair‐Specific Optical Properties of the DNA Stain Thiazole Orange

Site‐Specific Assembly of DNA‐Based Photonic Wires by Using Programmable Polyamides

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