Fluorescent nucleoside analogue displays enhanced emission upon pairing with guanine

A Highly Fluorescent Nucleobase Molecular Rotor

Fluorescent base analogs (FBAs) are powerful probes of nucleic acids' structures and dynamics. However, previously reported FBAs exhibit relatively low brightness and therefore limited sensitivity of detection. Here we report the hitherto brightest FBA that has ideal molecular rotor properties for detecting local dynamic motions associated with base pair mismatches. The new trans-stilbene annulated uracil derivative "^tsT" exhibits bright fluorescence emissions in various solvents (ε × Φ = 3400-29 700 cm^-1 M^-1) and is highly sensitive to mechanical motions in duplex DNA (ε × Φ = 150-4250 cm^-1 M^-1). ^tsT is thereby a "smart" thymidine analog, exhibiting a 28-fold brighter fluorescence intensity when base paired with A as compared to T or C. Time-correlated single photon counting revealed that the fluorescence lifetime of ^tsT (τ = 4-11 ns) was shorter than its anisotropy decay in well-matched duplex DNA (θ = 20 ns), yet longer than the dynamic motions of base pair mismatches (0.1-10 ns). These properties enable unprecedented sensitivity in detecting local dynamics of nucleic acids.

Solid-Phase Hybridization Assay for Detection of Mutated Cancer DNA by Fluorescence

We report a straightforward protocol for the detection of mutated DNA extracted from cancer cells. The assay combines a step-wise solid-phase hybridization and a readout by fluorescence emission. We detect a single-nucleotide polymorphism in two human oncogenes, BRAF and EGFR, and reach a limit of the detection of 300 pM by conventional fluorometry. The protocol described herein may be used as a foundation for development of automatic optimized assays capable for detection of mutant DNA and RNA in vitro and in cells.

Pentacyclic adenine: a versatile and exceptionally bright fluorescent DNA base analogue

A highly fluorescent, non-perturbing, pentacyclic adenine analog was designed, synthesized, incorporated into DNA and photophysical evaluated.

Emissive base analogs are powerful tools for probing nucleic acids at the molecular level. Herein we describe the development and thorough characterization of pentacyclic adenine (pA), a versatile base analog with exceptional fluorescence properties. When incorporated into DNA, pA pairs selectively with thymine without perturbing the B-form structure and is among the brightest nucleobase analogs reported so far. Together with the recently established base analog acceptor qA_nitro, pA allows accurate distance and orientation determination via Förster resonance energy transfer (FRET) measurements. The high brightness at emission wavelengths above 400 nm also makes it suitable for fluorescence microscopy, as demonstrated by imaging of single liposomal constructs coated with cholesterol-anchored pA–dsDNA, using total internal reflection fluorescence microscopy. Finally, pA is also highly promising for two-photon excitation at 780 nm, with a brightness (5.3 GM) that is unprecedented for a base analog.

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

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.

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

Most fluorescent nucleoside analogues are quenched when base stacked and some maintain their brightness, but there has been little progress toward developing nucleoside analogues that markedly increase their fluorescence upon duplex formation. Here, we report on the design and synthesis of a new tricyclic cytidine analogue, 8-diethylamino-tC (8-DEA-tC), that responds to DNA duplex formation with up to a 20-fold increase in fluorescent quantum yield as compared with the free nucleoside, depending on neighboring bases. This turn-on response to duplex formation is the greatest of any reported nucleoside analogue that can participate in Watson-Crick base pairing. Measurements of the quantum yield of 8-DEA-tC mispaired with adenosine and, separately, opposite an abasic site show that there is almost no fluorescence increase without the formation of correct Watson-Crick hydrogen bonds. Kinetic isotope effects from the use of deuterated buffer show that the duplex protects 8-DEA-tC against quenching by excited state proton transfer. These results, supported by DFT calculations, suggest a rationale for the observed photophysical properties that is dependent on duplex integrity and the electronic structure of the analogue.

pH-Responsive quencher-free molecular beacon systems containing 2′-deoxyuridine units labeled with fluorene derivatives

pH-Responsive oligodeoxynucleotides only exhibited dramatic increases in fluorescence upon duplex formation with their fully matched target DNAs.

Discovery of 2-(2-aminopyrimidin-5-yl)-4-morpholino-N-(pyridin-3-yl)quinazolin-7-amines as novel PI3K/mTOR inhibitors and anticancer agents

In this study, a series of novel 7 or 8-substituted 4-morpholine-quinazoline derivatives was designed and synthesized. Their PI3Kα inhibitory activities, antiproliferative activities against seven cancer cell lines, namely, PC-3, DU145, MCF-7, BT474, SK-BR-3, U937 and A431, were evaluated in vitro. Compound 17f proved to be a potential drug candidate with high PI3Kα inhibition activity (IC50 = 4.2 nM) and good antiproliferative activity. Compound 17f was also tested for its inhibitory activities against other kinases, such as PI3Kβ, PI3Kγ, PI3Kδ and mTOR, its effects on p-Akt (S473) and cell cycle. These results suggested that compound 17f could significantly inhibit the PI3K/Akt/mTOR pathway as a potent PI3K inhibitor and anticancer agent.

TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy

Three 2´-deoxynucleosides containing semi-flexible spin labels, namely (T)A, (U)A and (U)C, were prepared and incorporated into deoxyoligonucleotides using the phosphoramidite method. All three nucleosides contain 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) connected to the exocyclic amino group; (T)A directly and (U)A as well as (U)C through a urea linkage. (T)A and (U)C showed a minor destabilization of a DNA duplex, as registered by a small decrease in the melting temperature, while (U)A destabilized the duplex by more than 10 °C. Circular dichroism (CD) measurements indicated that all three labels were accommodated in B-DNA duplex. The mobility of the spin label (T)A varied with different base-pairing partners in duplex DNA, with the (T)A•T pair being the least mobile. Furthermore, (T)A showed decreased mobility under acidic conditions for the sequences (T)A•C and (T)A•G, to the extent that the EPR spectrum of the latter became nearly superimposable to that of (T)A•T. The reduced mobility of the (T)A•C and (T)A•G mismatches at pH 5 is consistent with the formation of (T)AH(+)•C and (T)AH(+)•G, in which protonation of N1 of A allows the formation of an additional hydrogen bond to N3 of C and N7 of G, respectively, with G in a syn-conformation. The urea-based spin labels (U)A and (U)C were more mobile than (T)A, but still showed a minor variation in their EPR spectra when paired with A, G, C or T in a DNA duplex. (U)A and (U)C had similar mobility order for the different base pairs, with the lowest mobility when paired with C and the highest when paired with T.

Exploring the role of the 5-substituent for the intrinsic fluorescence of 5-aryl and 5-heteroaryl uracil nucleotides: a systematic study

Derivatives of UMP (uridine monophosphate) with a fluorogenic substituent in position 5 represent a small but unique class of fluorophores, which has found important applications in chemical biology and biomolecular chemistry. In this study, we have synthesised a series of derivatives of the uracil nucleotides UMP, UDP and UTP with different aromatic and heteroaromatic substituents in position 5, in order to systematically investigate the influence of the 5-substituent on fluorescence emission. We have determined relevant photophysical parameters for all derivatives in this series, including quantum yields for the best fluorophores. The strongest fluorescence emission was observed with a 5-formylthien-2-yl substituent in position 5 of the uracil base, while the corresponding 3-formylthien-2-yl-substituted regioisomer was significantly less fluorescent. The 5-(5-formylthien-2-yl) uracil fluorophore was studied further in solvents of different polarity and proticity. In conjunction with results from a conformational analysis based on NMR data and computational experiments, these findings provide insights into the steric and electronic factors that govern fluorescence emission in this class of fluorophores. In particular, they highlight the interplay between fluorescence emission and conformation in this series. Finally, we carried out ligand-binding experiments with the 5-(5-formylthien-2-yl) uracil fluorophore and a UDP-sugar-dependent glycosyltransferase, demonstrating its utility for biological applications. The results from our photophysical and biological studies suggest, for the first time, a structural explanation for the fluorescence quenching effect that is observed upon binding of these fluorophores to a target protein.

Two-photon-induced fluorescence of isomorphic nucleobase analogs

Five isomorphic fluorescent uridine mimics have been subjected to two-photon (2P) excitation analysis to investigate their potential applicability as non-perturbing probes for the single-molecule detection of nucleic acids. We find that small structural differences can cause major changes in the 2P excitation probability, with the 2P cross sections varying by over one order of magnitude. Two of the probes, both thiophene-modified uridine analogs, have the highest 2P cross sections (3.8 GM and 7.6 GM) reported for nucleobase analogs, using a conventional Ti:sapphire laser for excitation at 690 nm; they also have the lowest emission quantum yields. In contrast, the analogs with the highest reported quantum yields have the lowest 2P cross sections. The structure-photophysical property relationship presented here is a first step towards the rational design of emissive nucleobase analogs with controlled 2P characteristics. The results demonstrate the potential for major improvements through judicious structural modifications.

Synthesis and optical behaviors of 6-seleno-deoxyguanosine

We have developed a simple method to synthesize 6-seleno-2'-deoxyguanosine (^SedG) by selectively replacing the 6-oxygen atom with selenium. This selenium-atom-specific modification (SAM) alters the optical properties of the naturally occurring 2'-deoxyguanosine (dG). Unlike the native dG, the UVabsorption of ^SedG is significantly influenced by the pH of the aqueous solution. Moreover, ^SedG is fluorescent at the physiological pH and exhibits pH-dependent fluorescence in aqueous solutions. Furthermore, ^SedG has noticeable fluorescence in non-aqueous solutions, indicating its sensitivity to environmental changes. This is the first time a fluorescent nucleoside by single-atom alteration has been observed. Fluorescent nucleosides modified by a single atom have great potential as molecular probes with minimal perturbations to investigate nucleoside interactions with proteins, such as membrane-transporter proteins.

Oligodeoxynucleotides containing multiple thiophene-modified isomorphic fluorescent nucleosides

5-(Thien-2-yl)-2'-deoxyuridine, an isomorphic fluorescent nucleoside analogue, was incorporated into multiple positions within single stranded oligodeoxynucleotides. With minimal impact on duplex stability and overall structure, oligonucleotides containing three identical isomorphic fluorescent nucleosides in alternating or neighboring positions display enhanced, sequence-dependent on-signals for either duplex formation or dissociation.

Highly efficient quencher-free molecular beacon systems containing 2-ethynyldibenzofuran- and 2-ethynyldibenzothiophene-labeled 2'-deoxyuridine units

We have prepared two fluorescent DNA probes--UDBF and UDBT, containing 2-ethynyldibenzofuran and 2-ethynyldibenzothiophene moieties, respectively, covalently attached to the base dU--and incorporated them in the central positions of oligodeoxynucleotides (ODNs) so as to develop new types of quencher-free linear beacon probes and investigate the effect of functionalization of the fluorene scaffold on the photophysical properties of the fluorescent ODNs. The ODNs containing adenine flanking bases (FBs) displayed a selective fluorescence "turn-off" response to mismatched targets with guanine bases; this suggests that these probes could be used as base-discriminating fluorescent nucleotides. On the other hand, we observed a "turn-on" response to matched targets when the UDBF and UDBT units of ODNs containing pyrimidine-based FBs were positioned opposite the four natural nucleobases. In particular, an ODN incorporating UDBT and cytosine FBs has potential use in single-nucleotide polymorphism typing.

A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers

Cy3B is an extremely bright and stable fluorescent dye, which is only available for coupling to nucleic acids post-synthetically. This severely limits its use in the fields of genomics, biology and nanotechnology. We have optimized the synthesis of Cy3B, and for the first time produced a diverse range of Cy3B monomers for use in solid-phase oligonucleotide synthesis. This molecular toolkit includes phosphoramidite monomers with Cy3B linked to deoxyribose, to the 5-position of thymine, and to a hexynyl linker, in addition to an oligonucleotide synthesis resin in which Cy3B is linked to deoxyribose. These monomers have been used to incorporate single and multiple Cy3B units into oligonucleotides internally and at both termini. Cy3B Taqman probes, Scorpions and HyBeacons have been synthesized and used successfully in mutation detection, and a dual Cy3B Molecular Beacon was synthesized and found to be superior to the corresponding Cy3B/DABCYL Beacon. Attachment of Cy3, Cy3B and Cy5 to the 5-position of thymidine by an ethynyl linker enabled the synthesis of an oligonucleotide FRET system. The rigid linker between the dye and nucleobase minimizes dye–dye and dye–DNA interactions and reduces fluorescence quenching. These reagents open up new future applications of Cy3B, including more sensitive single-molecule and cell-imaging studies.

Synthesis and photophysical properties of biaryl-substituted nucleos(t)ides. Polymerase synthesis of DNA probes bearing solvatochromic and pH-sensitive dual fluorescent and 19F NMR labels

The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.