Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop

Dembska, Anna; Juskowiak, Bernard

doi:10.1016/j.saa.2015.06.041

Cited by 18 publications

(13 citation statements)

References 27 publications

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“…The final conclusion is that elongation of i-motifs ends leading to formation a duplex blunt end should enable arrangement of pyrene moieties that promote formation of fluorescent excimer. This idea has been further developed by us [40]. …”

Section: Discussionmentioning

confidence: 99%

Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene

2015

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Cytosine-rich nucleic acids undergo pH-stimulated structural transitions leading to formation of an i-motif architecture at an acidic pH. Thus, i-motifs are good foundation for designing simple pH-sensitive fluorescent probes. We report here steady-state and time-resolved fluorescence studies of pyrene-labeled probes based on RET sequence: C4GC4GC4GC4TA (RET21), AC4GC4GC4GC4TA (RET21A) and C4GC4GC4GC4T (RET20). Comparative studies with single-and double-labeled i-motif probes were carried out. For each probe, we have measured fluorescence spectra and decays for emission wavelength of 390 nm over a wide range of pH (from 4.0 to 8.0). Effect of the oligonucleotide sequence and the number of pyrene labels on the spectral characteristics of probes were discussed.

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Section: Discussionmentioning

confidence: 99%

Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene

2015

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“…Light-up systems based on molecular beacons (MBs), i.e., structured pyrene-modified oligonucleotide probes, are powerful tools for sensitive fluorescence detection of a broad spectrum of different targets [ 66 , 85 , 92 , 93 , 94 , 95 , 96 , 97 ]. Originally, MBs are oligonucleotides forming a stem-loop-structure and labeled by a fluorescent group and a quencher at opposite ends of the probe to display an on/off output pattern [ 98 ].…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

“…Due to the remarkable property of pyrene fluorophores to form excimers and exciplexes with pronounced changes in output fluorescence signals, pyrene-modified MBs have been well developed. To obtain MBs with improved emission characteristics and specificity, several interesting design decisions have been proposed (see, for instance, [ 29 , 30 , 66 , 85 , 92 , 94 , 95 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 ]; some of them are illustrated in Figure 9 ), among them are excimer-forming MBs containing a quencher (for instance, types MB1a [ 85 , 100 , 105 ], MB1b [ 105 ], MB1c and MB1d [ 100 ], and MB2 [ 30 ]) and numerous quencher-free MBs (for instance, types MB3 [ 66 ], MB4 [ 94 ], MB5 [ 29 , 101 ], MB6 [ 109 ], MB7 [ 106 , 108 ], and MB8 [ 107 ]), including systems that utilize γ-cyclodextrin or hybridization chain reaction-mediated signal amplification (types MB9 [ 95 , 111 ] and MB10 [ 104 ]).…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

“…These compact structures are often found in human telomeric DNA and regulatory regions of eukaryotic chromosomes [ 182 ], therefore the probing of i-motif structures is of particular importance. Several fluorescent probes for sensing of i-motif transitions based on pyrene-modified oligonucleotides have been proposed [ 92 , 110 , 183 , 184 , 185 , 186 , 187 , 188 , 189 , 190 ].…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

“…Dembska and Juskowiak have reported the dual pyrene-functionalized molecular beacons as pH-sensitive fluorescent probes [ 92 , 110 ]. These probes consist of a C-rich pH-sensitive domain (C 4 GC 4 GC 4 GC 4 TA) in their loops.…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

See 2 more Smart Citations

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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A pH-responsive activatable aptamer probe for targeted cancer imaging based on i-motif-driven conformation alteration

Yan

Shi

et al. 2016

Sci. China Chem.

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Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop

Cited by 18 publications

References 27 publications

Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene

Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene

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

A pH-responsive activatable aptamer probe for targeted cancer imaging based on i-motif-driven conformation alteration

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