A Pyrene‐Labeled G‐Quadruplex Oligonucleotide as a Fluorescent Probe for Potassium Ion Detection in Biological Applications

Nagatoishi, Satoru; Nojima, Takahiko; Juskowiak, Bernard; Takenaka, Shigeori

doi:10.1002/anie.200501506

Cited by 177 publications

(128 citation statements)

References 25 publications

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“…Just after the submission of this work, a pyrene excimer probe for potassium ion was reported (33), which further proves the wide applicability the excimer signaling approach. Such an inorganic ion probe, with the time-resolved fluorescence measurement method described here, should find useful applications for monitoring potassium ion in complex biological environments.…”

Section: Discussionsupporting

confidence: 55%

Light-switching excimer probes for rapid protein monitoring in complex biological fluids

Yang

Jockusch²,

Vicens³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

336

265

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Quantitative protein bioanalysis in complex biological fluids presents considerable challenges in biological studies and disease diagnosis. The major obstacles are the background signals from both the probe and the biological fluids where the proteins reside. We have molecularly engineered light-switching excimer aptamer probes for rapid and sensitive detection of a biomarker protein, platelet-derived growth factor (PDGF). Labeled with one pyrene at each end, the aptamer switches its fluorescence emission from Ϸ400 nm (pyrene monomer) to 485 nm (pyrene excimer) upon PDGF binding. This fluorescence wavelength change from monomer to excimer emission is a result of aptamer conformation rearrangement induced by target binding. The excimer probe is able to effectively detect picomolar PDGF in homogeneous solutions. Because the excimer has a much longer fluorescence lifetime (Ϸ40 ns) than that of the background (Ϸ5 ns), time-resolved measurements were used to eliminate the biological background. We thus were able to detect PDGF in a cell sample quantitatively without any sample pretreatment. This molecular engineering strategy can be used to develop other aptamer probes for protein monitoring. Combined with lifetime-based measurements and molecular engineering, light-switching excimer aptamer probes hold great potential in protein analysis for biomedical studies.aptamer ͉ biomarker ͉ platelet-derived growth factor ͉ pyrene ͉ time-resolved fluorescence

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Section: Discussionsupporting

confidence: 55%

Light-switching excimer probes for rapid protein monitoring in complex biological fluids

Yang

Jockusch²,

Vicens³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

336

265

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“…[5] The adaptive binding property has been used to design fluorescence resonance energy transfer (FRET)-based sensors with end-labeled fluorophores since FRET is known to be sensitive to such distance changes. Many molecules include adenosine/ATP, [6] cocaine, [7] arginiamide, [8] K I , [9][10][11][12] Mg II /Ca II , [13] Ag I , [14] Hg II , [15,16] thrombin, [17] and (platelet-derived growth factor) PDGF [18,19] have been detected using this method. One particularly interesting example is the Hg II binding DNA shown in Figure 1A.…”

Section: Introductionmentioning

confidence: 99%

Metal‐Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications

Kiy

Jacobi

Liu

2011

Chemistry A European J

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Abstract.Metal induced nucleic acid folding has been extensively studied with ribozymes, DNAzymes, tRNA and riboswitches. These RNA/DNA molecules usually have a high content of double-stranded regions to support a rigid scaffold. On the other hand, such rigid structural features are not available for many in vitro selected or rationally designed DNA aptamers; they adopt flexible random coil structures in the absence of target molecules. Upon target binding, these aptamers adaptively fold into a compact structure with a reduced end-to-end distance, making fluorescence resonance energy transfer (FRET) a popular signaling mechanism. However, non-specific folding induced by mono-or divalent metal ions can also reduce the end-to-end distance and thus lead to false positive results. In this study we used a FRET pair labeled Hg II binding DNA and monitored metal induced folding in the presence of various cations. While non-specific electrostatically mediated folding can be very significant, at each tested salt condition, Hg II induced folding was still observed with a similar sensitivity. We also studied the biophysical meaning of the acceptor/donor fluorescence ratio that allowed us to explain the experimental observations. Potential solutions for this ionic strength problem have been discussed. For example, probes designed to signaling the formation of double-stranded DNA showed a lower dependency on ionic strength.3

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“…Importantly, such DNA units could be combined, covalently, or by hybridization, as independent functional modules to form molecular complexes with intended synergy functions. Thus, DNA would be a versatile scaffold to construct molecular devices for analyzing not only nucleic acids, but also other varieties of species in aqueous solution, such as metal ions, [60][61][62][63] proteins, [64][65][66] and other physiologically active substances. 67,68 8 References…”

Section: Resultsmentioning

confidence: 99%

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

Ihara

Mukae

2007

ANAL. SCI.

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Much effort has focused on methods for detecting various genetic differences in individuals, including single nucleotide polymorphisms (SNPs). SNP can be characterized as a substitution, insertion, or deletion at a single base position on a DNA strand. There is expected to be on average one SNP for every 1000 bases of the human genome, and some variations located in genes are suspected to alter both the protein structure and the expression level. Therefore, highly sensitive techniques with a simple procedure would be desirable for a high-throughput screening of millions of SNPs widely dispersed throughout the human genome. In this short review, we consider recently reported unique techniques for genotyping in a homogeneous solution, and organize them in terms of the chemical and physical processes accelerated on DNA.

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A Pyrene‐Labeled G‐Quadruplex Oligonucleotide as a Fluorescent Probe for Potassium Ion Detection in Biological Applications

Cited by 177 publications

References 25 publications

Light-switching excimer probes for rapid protein monitoring in complex biological fluids

Light-switching excimer probes for rapid protein monitoring in complex biological fluids

Metal‐Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications

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

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