Controlling the Fluorescence of Benzofuran‐Modified Uracil Residues in Oligonucleotides by Triple‐Helix Formation

Abstract

We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).

7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein

“…A second method is to label DNAs by incorporating fluorescent nucleoside analogues. Several attempts toward establishing in vivo applications have been made using microenvironmentsensitive fluorescent nucleosides, [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24] for which fluorescence intensities correlate with physicochemical properties such as viscosity of the local environment. Binding between proteins and the fluorescent DNA changes the microenvironment, thereby altering the fluorescence of the nucleosides.…”

Novel Signal-Enhancing Approaches for Optical Detection of Nucleic Acids—Going beyond Target Amplification

“…Remarkably, metal nanoclusters can detect natural nucleic acids, such as cancer related mRNAs, directly in living cells [31]. Finally, the use of so-called environmentally sensitive modified nucleosides and nucleotides also offers exciting opportunities for the specific detection of nucleic acids [32][33][34][35][36]. The distinguishing feature of these is enhanced fluorescence upon a change in the local microenvironment.…”

“…They were able to achieve this owing to the environmentally sensitive intramolecular charge transfer (ICT) between the nucleobase and naphthalene moieties [33]. Other successful examples of environmentally sensitive modified nucleosides include light-up probes for the detection of triplex formation and polarity sensitive probes [34][35][36]. One particularly useful mechanism involves introducing intramolecular conformational changes at the bond between the attached modifications and nucleobase [34,35].…”

“…Other successful examples of environmentally sensitive modified nucleosides include light-up probes for the detection of triplex formation and polarity sensitive probes [34][35][36]. One particularly useful mechanism involves introducing intramolecular conformational changes at the bond between the attached modifications and nucleobase [34,35]. This makes modified nucleosides attractive objects of study with a high potential in diagnostics and structural studies of biomolecules.…”

Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design

“…Fluorescent base analogues (FBAs) are intrinsically fluorescent molecules which overcome some of the disadvantages of external probes by mimicking the shape and hydrogen-bonding ability of the natural nucleobases 9 10 11 12 13 14 15 16 17 18 19 20 21 . FBAs can be incorporated into nucleic acids chemically 14 15 21 , and in many cases enzymatically by DNA or RNA polymerases 22 23 .…”