G-Quadruplex formation using fluorescent oligonucleotides as a detection method for discriminating AGG trinucleotide repeats

Park, Yoojin; Kim, Ki Tae; Kim, Byeang Hyean

doi:10.1039/c6cc06566j

Cited by 15 publications

(14 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Their quenched emissions were recovered when they met the matched targets [ 46 ]. They also developed a sensitive system for detecting AGG trinucleotide repeats through the formation of intermolecular G-quadruplexes in the presence of added K + ions using a ssODN (5′- U PY GGTT-3′) ( Figure 11 c) [ 47 ]. When this probe interacted with the RNA target sequence (5′-aggaggagga-3′), very strong fluorescence enhancements were observed (44.7-fold increase in fluorescence).…”

Section: Probes Containing a Fluorophore-labeled Basementioning

confidence: 99%

Single-Labeled Oligonucleotides Showing Fluorescence Changes upon Hybridization with Target Nucleic Acids

Hwang

2018

Molecules

View full text Add to dashboard Cite

Sequence-specific detection of nucleic acids has been intensively studied in the field of molecular diagnostics. In particular, the detection and analysis of single-nucleotide polymorphisms (SNPs) is crucial for the identification of disease-causing genes and diagnosis of diseases. Sequence-specific hybridization probes, such as molecular beacons bearing the fluorophore and quencher at both ends of the stem, have been developed to enable DNA mutation detection. Interestingly, DNA mutations can be detected using fluorescently labeled oligonucleotide probes with only one fluorophore. This review summarizes recent research on single-labeled oligonucleotide probes that exhibit fluorescence changes after encountering target nucleic acids, such as guanine-quenching probes, cyanine-containing probes, probes containing a fluorophore-labeled base, and microenvironment-sensitive probes.

show abstract

Section: Probes Containing a Fluorophore-labeled Basementioning

confidence: 99%

Single-Labeled Oligonucleotides Showing Fluorescence Changes upon Hybridization with Target Nucleic Acids

Hwang

2018

Molecules

View full text Add to dashboard Cite

show abstract

“…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%

“…The unique tetrameric assembly of a DNA/RNA duplex bearing a pyrene-modified deoxyadenosine residue at the 5′-end of DNA and a 3′-GAGGG sequence at the 3′-end of the RNA to form the tetra-duplex complex was studied in [ 178 ]. A simple and sensitive system for detecting RNA AGG trinucleotide repeats through the formation of intermolecular G-quadruplexes using a fluorescent oligonucleotide was developed [ 177 ].…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2017

View full text Add to dashboard Cite

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.

show abstract

“…In a recent study, we developed a novel technique to recover the formation of damaged G4s, using pyrene-conjugated guanine tracts (PyG3) [11]. PyG3 forms (3 + 1) intermolecular G4 structures by replacing damaged guanine bases [13], significantly stabilizing intermolecular G4 formation by stacking of pyrene moieties to form G-quartets [11]. Therefore, the conjugation of suitable G4 ligands to short guanine-rich oligonucleotides can be considered as a general strategy for restoring G4 structures containing base lesions.…”

Section: Introductionmentioning

confidence: 99%

Design and Properties of Ligand-Conjugated Guanine Oligonucleotides for Recovery of Mutated G-Quadruplexes

et al. 2018

View full text Add to dashboard Cite

The formation of a guanine quadruplex DNA structure (G4) is known to repress the expression of certain cancer-related genes. Consequently, a mutated G4 sequence can affect quadruplex formation and induce cancer progression. In this study, we developed an oligonucleotide derivative consisting of a ligand-containing guanine tract that replaces the mutated G4 guanine tract at the promoter of the vascular endothelial growth factor (VEGF) gene. A ligand moiety consisting of three types of polyaromatic hydrocarbons, pyrene, anthracene, and perylene, was attached to either the 3′ or 5′ end of the guanine tract. Each of the ligand-conjugated guanine tracts, with the exception of anthracene derivatives, combined with other intact guanine tracts to form an intermolecular G4 on the mutated VEGF promoter. This intermolecular G4, exhibiting parallel topology and high thermal stability, enabled VEGF G4 formation to be recovered from the mutated sequence. Stability of the intramolecular G4 increased with the size of the conjugated ligand. However, suppression of intermolecular G4 replication was uniquely dependent on whether the ligand was attached to the 3′ or 5′ end of the guanine tract. These results indicate that binding to either the top or bottom guanine quartet affects unfolding kinetics due to polarization in DNA polymerase processivity. Our findings provide a novel strategy for recovering G4 formation in case of damage, and fine-tuning processes such as replication and transcription.

show abstract

G-Quadruplex formation using fluorescent oligonucleotides as a detection method for discriminating AGG trinucleotide repeats

Cited by 15 publications

References 32 publications

Single-Labeled Oligonucleotides Showing Fluorescence Changes upon Hybridization with Target Nucleic Acids

Single-Labeled Oligonucleotides Showing Fluorescence Changes upon Hybridization with Target Nucleic Acids

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

Design and Properties of Ligand-Conjugated Guanine Oligonucleotides for Recovery of Mutated G-Quadruplexes

Contact Info

Product

Resources

About