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Review
. 2018 Jan 8;23(1):124.
doi: 10.3390/molecules23010124.

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

Gil Tae Hwang  1
Affiliations
Review

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

Gil Tae Hwang. Molecules. .

Abstract

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.

Keywords: DNA; fluorescent probes; fluorophore; nucleic acids chemistry; oligonucleotides; single-nucleotide polymorphism.

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Conflict of interest statement

The author declares no conflicts of interest.

Figures

Figure 1
Figure 1
MB probe.
Figure 2
Figure 2
(a) Guanine-quenching probe and (b) Guanine-dequenching probe.
Figure 3
Figure 3
(a) YO-linked probe and (b) TO-linked probe.
Figure 4
Figure 4
(a) Principle of FIT-probes; (b) TO-PNA conjugate; and (c) TO-, YO-, MO-, and JO-PNA conjugates.
Figure 5
Figure 5
(a) Oligonucleotide conjugates of 5-deazaflavin (dFl) and flavin (Fl) and (b) single-base bulge formation of a 3-MI-containing oligonucleotide.
Figure 6
Figure 6
(a) BPP, NPP, MDA, and MDI, (b) Chpp, and (c) boPhpC.
Figure 7
Figure 7
(a) Tricyclic base-linked acyclonucleoside, P and N, and (b) tricyclic cytidine analog 8-DEA-tC.
Figure 8
Figure 8
Tricyclic cytidine analogs, Cf, tCo, β-tc, and α-tc.
Figure 9
Figure 9
HyBeacon probe.
Figure 10
Figure 10
(a) 5-Phenylethynyluridine and (b) pyrenylethynyl derivatives.
Figure 11
Figure 11
(a) APY and UPY, (b) APy-labeled probe, and (c) probe for agg trinucleotide repeats.
Figure 12
Figure 12
(a) 2′-Deoxyuridines labeled with FL derivatives and (b) Total discrimination factors for the OND4(UF) probes relative to those of ssDNAs and mismatched dsDNAs.
Figure 13
Figure 13
Working mechanism of quencher-free linear beacon systems.
Figure 14
Figure 14
BDF probes.
Figure 15
Figure 15
(a) Furan- or thiophene-modified pyrimidines and (b) incorporation of ribonucleoside triphosphate.
Figure 16
Figure 16
ESF probes.
Figure 17
Figure 17
pH-sensitive probes. (a) 7-hydroxycoumarin; (b) BIQA; and (c) UAF and UDAF.
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