Multiple-pyrene residues arrayed along DNA backbone exhibit significant excimer fluorescence

Kosuge, Momo; Kubota, Mio; Ono, Akira

doi:10.1016/j.tetlet.2004.03.074

Cited by 20 publications

(10 citation statements)

References 23 publications

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“…A properly designed oligonucleotide probe will switch between excimer and monomer emissions depending on the presence of analyte target (free and bound states of the probe). Labeling of the oligonucleotide probe with pyrene can be carried out in a variety of ways, including simple end-labeling via a linker [ 12 , 38 – 40 ], a 2′ sugar modification [ 41 ], attachment of pyrene to the nucleobase [ 42 , 43 ], incorporation of bis-pyrene label [ 44 – 46 ], and by arraying multiple pyrene residues along the DNA backbone [ 47 ].…”

Section: Principles Of Biosensingmentioning

confidence: 99%

Nucleic acid-based fluorescent probes and their analytical potential

2010

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It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.FigureHybridization with a nucleic acid target or affinity interactions with a nonnucleic acid target generate changes in the fluorescence characteristics of a nucleic acid-based fluorescent probe

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Section: Principles Of Biosensingmentioning

confidence: 99%

Nucleic acid-based fluorescent probes and their analytical potential

2010

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“…The addition of K + ions results in the appearance of a new broad excimer band around 480 nm,9 accompanied by quenching of the monomer emission. Interestingly, the weak monomer band at 390 nm lacks the vibronic structure that is probably connected with stacking interactions of the pyrene fluorophore with nucleobases 9e,f. Notably, there is no clear isoemissive point in the system, which suggests a more complex situation than the simple two‐component excimer–monomer equilibrium.…”

mentioning

confidence: 99%

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

et al. 2005

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Ion probes: A potassium‐sensing oligonucleotide with terminal pyrene moieties can be used as a fluorescent probe for the real‐time monitoring of the extracellular concentration of K+ ions under physiological conditions. The excimer emission intensity (b) of the chair‐type quadruplex structure formed depends on the K+ ion concentration (0–200 mm), and differs significantly from that in the absence of potassium (a).

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“…In oligonucleotides covalently attached through a flexible tether to pyrene at the internal phosphate [19], the nucleotide bases [20], and the terminus [21], fluorescence quenching of the pyrene strongly occurs both in the single-stranded and double-stranded forms via migration of an electron between the excited pyrene and the nucleotide bases [22][23][24]. To avoid these disadvantages, several efforts using the pyrene-excimer emission in place of the monomer emission have been made in the development of hybridisation probes [18,[25][26][27]. Because pyrene-excimer emission is less sensitive to quenching by nucleobases than monomer emission, the pyrene-excimerforming probes have been successfully used for DNA and RNA hybridisation assays [27][28][29].…”

Section: Introductionmentioning

confidence: 99%

New Concepts of Fluorescent Probes for Specific Detection of DNA Sequences: Bis-Modified Oligonucleotides in Excimer and Exciplex Detection

Gbaj

Bichenkova

Walsh

et al. 2008

Libyan Journal of Medicine

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The detection of single base mismatches in DNA is important for diagnostics, treatment of genetic diseases, and identification of single nucleotide polymorphisms. Highly sensitive, specific assays are needed to investigate genetic samples from patients. The use of a simple fluorescent nucleoside analogue in detection of DNA sequence and point mutations by hybridisation in solution is described in this study. The 5'-bispyrene and 3'-naphthalene oligonucleotide probes form an exciplex on hybridisation to target in water and the 5'-bispyrene oligonucleotide alone is an adequate probe to determine concentration of target present. It was also indicated that this system has a potential to identify mismatches and insertions. The aim of this work was to investigate experimental structures and conditions that permit strong exciplex emission for nucleic acid detectors, and show how such exciplexes can register the presence of mismatches as required in SNP analysis. This study revealed that the hybridisation of 5'-bispyrenyl fluorophore to a DNA target results in formation of a fluorescent probe with high signal intensity change and specificity for detecting a complementary target in a homogeneous system. Detection of SNP mutations using this split-probe system is a highly specific, simple, and accessible method to meet the rigorous requirements of pharmacogenomic studies. Thus, it is possible for the system to act as SNP detectors and it shows promise for future applications in genetic testing.

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Multiple-pyrene residues arrayed along DNA backbone exhibit significant excimer fluorescence

Cited by 20 publications

References 23 publications

Nucleic acid-based fluorescent probes and their analytical potential

Nucleic acid-based fluorescent probes and their analytical potential

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

New Concepts of Fluorescent Probes for Specific Detection of DNA Sequences: Bis-Modified Oligonucleotides in Excimer and Exciplex Detection

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