Helligkeit durch lokale Rigidifizierung – LNA‐verstärkte FIT‐Sonden zur bildgebenden Darstellung von Ribonukleotidpartikeln in vivo

Hövelmann, Felix; Gáspár, Imre; Loibl, Simon; Ermilov, Eugeny; Röder, Beate; Wengel, Jesper; Ephrussi, Anne; Seitz, Oliver

doi:10.1002/ange.201406022

Cited by 9 publications

(8 citation statements)

References 52 publications

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“…These valuesw erec lose to or higher than the reported values for TO boundt od sDNA, [40,41] and those of FIT-DNA, FIT-RNA duplexes. [14,42] P2, P4,a nd P5,o nt he other hand, had smaller F values( < 0.1 in most cases). Althoughs ignificant UV/Viss pectral changes in the TO absorption were observed for P4 and P5,t he fluorescence response was weak due to the small F values.…”

Section: Fluorescence Responseoft He Probesmentioning

confidence: 88%

Optimization of the Alkyl Linker of TO Base Surrogate in Triplex‐Forming PNA for Enhanced Binding to Double‐Stranded RNA

Sato

Nishizawa

2017

Chemistry A European J

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A series of triplex-forming peptide nucleic acid (TFP) probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found that the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base. Isothermal titration calorimetry experiments revealed that the increased binding affinity resulted from the gain in the binding enthalpy, which could be explained by the enhanced π-stacking interaction between the TO base surrogate and the dsRNA part of the triplex. We expect that these results will provide a molecular basis for designing strong binding tFIT probes for fluorescence sensing of various kinds of purine-rich dsRNAs sequences including those carrying a pyrimidine-purine inversion. The obtained data also offers a new insight into further development of the universal bases incorporated in TFP.

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Section: Fluorescence Responseoft He Probesmentioning

confidence: 88%

Optimization of the Alkyl Linker of TO Base Surrogate in Triplex‐Forming PNA for Enhanced Binding to Double‐Stranded RNA

Sato

Nishizawa

2017

Chemistry A European J

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“…Of note, the sensing of local flexibility renders FIT probes dark when TO is positioned in the vicinity of a single base mismatched base pair. 19 , 22–24 We, and others, used FIT probes for live-cell RNA imaging 25 26 27 28 and real-time PCR 20 23 if desired with single nucleotide specificity. 23 24 28 The FIT concept was also applied in double-stranded RNA detection 29 and in signaling aptamers.…”

Section: Introductionmentioning

confidence: 99%

New Thiazole Orange Derivatives for Improved Fluorescence Signaling of DNA FIT Probes

Homer

Seitz

2023

Synthesis

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Forced intercalation probes (FIT-probes) probes are nucleic acid probes in which an intercalator dye of the thiazole orange (TO) family serves as a surrogate nucleobase. Hybridization of FIT probes is accompanied by enhancements of fluorescence. Looking for ways to increase turn-on and brightness of fluorescence, we herein report the synthesis of new fluorogenic base surrogates. In total, 9 different TO derivatives were introduced into FIT probes. Fluorescence measurements in 6 different sequence revealed that substitution at both the quinoline and the benzothiazole part affects fluorescence turn on upon hybridization and brightness of probe-target duplexes. A TO derivative containing a tricyclic benzothiazole provided FIT probes signaling hybridization by up to 19-fold enhancement of fluorescence. Improved fluorescence quantum yields (Φds up to 0.53) and a high extinction coefficients (ε518 up to 91.000∙M−1∙cm−1) make this dye an interesting, and in some sequences superior alternative to the canonical thiazole orange used previously in FIT probes.

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“…[1,2] Functional nucleic acids with the ability to generate an emission based on ab inding event in the presence of target molecules have been designed and characterized. [3][4][5][6][7][8][9][10] Molecular beacons (MBs) are DNA hairpin structures with a pair of fluorophore and quencher molecules, which are designed to convertr ecognition events into af luorescences ignal through conformational changesi nt he DNA hairpin from the closed to open form, and are utilized in DNA/RNA targeting applications, intracellularm RNA imaging, real-time PCR, and fluorescenceb iosensors. [11][12][13][14][15][16][17][18] To improve thes ensitivitya nd specificity of the MBs to target molecules, many approaches have been applied.…”

Section: Introductionmentioning

confidence: 99%

Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex

Takada

Ishino

Takata

et al. 2018

Chemistry A European J

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The preparation of homo- and heterocomplexes composed of the parent perylene diimide (PH) and pyrrolidine-substituted perylene diimide (PN) in DNA and rapid electron transfer in these complexes, which has been analyzed by steady-state fluorescence and femtosecond transient absorption measurements, have been demonstrated. The DNA molecules possessing PH and PN were prepared through a recently developed method that involved the reaction of enzymatically generated abasic sites with the amino groups of the perylene diimide molecules, through which these molecules can be incorporated as base surrogates within the DNA base stack. Melting temperature analysis showed that the PH and PN monomers, and their homo- and heterodimers, contribute to the stabilization of the DNA duplex, and is comparable to that of natural base pairs. Fluorescence measurements showed that PH in a single-stranded oligopyrimidine showed a strong fluorescence, whereas the fluorescence of PH was completely quenched upon pairing with PN (PH/PN) through duplex formation. The transient absorption measurements showed that a rapid electron-transfer reaction in the stacked PH/PN heterodimer occurred on a sub-picosecond timescale, which allowed highly efficient fluorescence quenching. The PH/PN pair, which served as a fluorophore and quencher, were utilized to design molecular beacon probes with a high signal/noise ratio. The PH/PN pair was also capable of forming a stable, stacked dimer structure and induced rapid electron transfer that could serve as a good signal reporter for fluorescent nucleic acid detection.

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Helligkeit durch lokale Rigidifizierung – LNA‐verstärkte FIT‐Sonden zur bildgebenden Darstellung von Ribonukleotidpartikeln in vivo

Cited by 9 publications

References 52 publications

Optimization of the Alkyl Linker of TO Base Surrogate in Triplex‐Forming PNA for Enhanced Binding to Double‐Stranded RNA

Optimization of the Alkyl Linker of TO Base Surrogate in Triplex‐Forming PNA for Enhanced Binding to Double‐Stranded RNA

New Thiazole Orange Derivatives for Improved Fluorescence Signaling of DNA FIT Probes

Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex

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