Probing the stable G-quadruplex transition using quencher-free end-stacking ethynyl pyrene–adenosine

Seo, Young Jun; Lee, Il Joon; Yi, Jeong Wu; Kim, Byeang Hyean

doi:10.1039/b707278c

Cited by 43 publications

(29 citation statements)

References 27 publications

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“…The resultant color change from blue to green has been used in the detection of G-quadruplex formation. 303 Besides pyrenes, pairs of perylene diimides and thiazole orange 142 have been incorporated into molecular beacons. Strong excitonic interactions between the chromophores result in a red-shifted excimer emission.…”

Section: Properties Of Dna Multichromophoresmentioning

confidence: 99%

DNA-Multichromophore Systems

2012

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Section: Properties Of Dna Multichromophoresmentioning

confidence: 99%

DNA-Multichromophore Systems

2012

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“…121 In the single stranded state these ONs exhibit fluorescence emission at λ em = 451 nm; addition of potassium ions results in a) G-quadruplex formation, b) stacking between pyrene and terminal guanosines, and c) exciplex formation. As a result, red-shifted fluorescence emission is observed (λ em = 485 nm, Fig.…”

Section: Diagnostic Applications Of Pfosmentioning

confidence: 99%

“…18). 121 This is particularly interesting given the recent focus on G-quadruplexes as materials for bottom-up fabrication of nanomaterials. 122 …”

Section: Diagnostic Applications Of Pfosmentioning

confidence: 99%

Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): Tools for fundamental research, diagnostics, and nanotechnology

2011

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Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and materials science. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have motivated development of PFOs for detection of complementary DNA/RNA targets, single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This Review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display distinctive properties such as large fluorescence quantum yields, efficient discrimination of SNPs, and recognition of mixed-sequence double stranded DNA.

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“…G-quadruplexes are prospective tools providing the researcher with the means of manipulating DNA/RNA assemblies in ways not possible using standard nucleotides [ 35 ]. Specific fluorescence properties of pyrene, e.g., an ability to form excimers and a large number of techniques available for its detection, contributed to a great interest in applying pyrene-modified oligonucleotides for G-quadruplexes studies [ 173 , 174 , 175 , 176 , 177 , 178 ].…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

“…Pyrene moiety was introduced into oligonucleotides using modified adenosine ( 8Apy , A Pyrmcm ) [ 173 , 178 , 179 ], modified uridine ( 5Upy ) ( Figure 12 ) [ 177 , 180 ] or non-nucleotidic monomer ( Pyrene-linker , Azo-Pyr ) [ 175 , 176 , 181 ] ( Figure 13 and Figure 31 ).…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

et al. 2017

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In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

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Probing the stable G-quadruplex transition using quencher-free end-stacking ethynyl pyrene–adenosine

Abstract: Pyrene-modified adenosines in the dangling positions of G-rich oligodeoxynucleotides undergo pi-stacking in their G-quadruplex formation, but not in their single strands, which can be characterized by fluorescence lambda(max) changes that occur on stacking.

Cited by 43 publications

References 27 publications

DNA-Multichromophore Systems

DNA-Multichromophore Systems

Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): Tools for fundamental research, diagnostics, and nanotechnology

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

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