Fluorescent Base Analogue Reveals T-HgII-T Base Pairs Have High Kinetic Stabilities That Perturb DNA Metabolism

1H-1,2,3-triazolyl-1,6-naphthyridin-7(6H)-ones as Potential Fluorescent Nucleoside Analogues: Synthesis and Optical Properties

In this article, we present the synthesis and the optical properties of three original molecules as potential fluorescent ribonucleoside analogues incorporating a 1,6-naphthyridin-7(6H)-one scaffold as a fluorescent nucleobase and a 1,2,3-triazole as a linkage. The nucleosides were prepared via a Cu alkyne-azide cycloaddition (CuAAC) reaction between a ribofuranosyl azide and a 4-ethynylpyridine partner. Construction of substituted 1,6-naphthyridin-7(6H)-ones was achieved through two additional steps. Optical property studies were investigated on nucleoside analogues. Powerful fluorescence properties have been evidenced with a remarkable change of emissivity depending on the polarity of the solvent, making these molecules suitable as a new class of artificial fluorescent nucleosides for investigating enzyme binding sites as well as probing nucleic acids. In addition, we are convinced that such analogues could be of great interest in the search for new antiviral or antitumoral drugs based on nucleosides.

A modular aldol approach for internal fluorescent molecular rotor chalcone surrogates for DNA biosensing applications

Fluorescent molecular rotors (FMRs) are critical tools for probing nucleic acid structure and function. Many valuable FMRs have been incorporated into oligonucleotides, although the methods of doing so can be cumbersome. Development of synthetically simple, high yielding modular methods to fine-tune dye performance is crucial to expand the biotechnological applications of oligonucleotides. Herein, we report the utility of 6-hydroxy-indanone (6HI) with a glycol backbone to serve as a handle for on-strand aldehyde capture as a modular aldol approach for site-specific insertion of internal FMR chalcones. Aldol reactions with aromatic aldehydes containing N-donors proceed in high yield to create modified DNA oligonucleotides, which in the duplex match the stability of the fully paired canonical B-form with strong stacking interactions between the planar probe and the flanking base pairs, as evidenced by molecular dynamics (MD) simulations. The FMR chalcones possess remarkable quantum yields (Φ_fl up to 76%) in duplex DNA, coupled with large Stokes shifts (Δν up to 155 nm), light-up emissions (I_rel up to 60-fold) that span the visible region (λ_em 518-680 nm) with brightness up to 17 480 cm^-1 M^-1. The library also contains a FRET pair and dual emission probes, suitable for ratiometric sensing. The ease of aldol insertion coupled with the excellent performance of the FMR chalcones permits their future wide-spread use.

Benzothiazole-substituted 1,3-diaza-2-oxophenoxazine as a luminescent nucleobase surrogate for silver(I)-mediated base pairing

A benzothiazole-substituted derivative (X) of 1,3-diaza-2-oxophenoxazine was evaluated with respect to its ability to engage in Ag(I)-mediated homo base pair formation in two different DNA duplexes. The metal binding was determined by a combination of temperature-dependent UV spectroscopy, CD spectroscopy, and fluorescence spectroscopy, indicating the incorporation of two Ag(I) ions to generate a dinuclear X-Ag(I)₂-X base pair. Interestingly, a luminescence increase was observed upon metal binding. Theoretical luminescence spectra were calculated using time-dependent density functional theory (TDDFT) for all possible Ag(I)-mediated X : X base pair geometries to identify the species responsible for the increase in luminescence. The study shows that even bulky non-planar artificial nucleobases can be applied to form stabilizing metal-mediated base pairs.

Active Uptake and Trafficking of Nucleoside Triphosphates In Vivo

Modified nucleoside triphosphates (NTPs) are powerful probes and medicines, but their anionic character impedes membrane permeability. As such, invasive delivery techniques, transport carriers, or prodrug strategies are required for their in vivo use. Here, we present a fluorescent 2'-deoxyribonucleoside triphosphate "TAMRA-dATP" that exhibits surprisingly high bioavailability in vivo. TAMRA-dATP spontaneously forms nanoparticles in Mg⁺²-containing buffers that are taken into the vesicles of living cells and animals by energy-dependent processes. In cell cultures, photochemical activation with yellow laser light (561 nm) facilitated endosomal escape of TAMRA-dATP, resulting in its metabolic incorporation into DNA in vitro. In contrast, in vivo studies revealed that TAMRA-dATP is extensively trafficked by active pathways into cellular DNA of zebrafish (Danio rerio) and Caenorhabditis elegans where DNA labeling was observed in live animals, even without photochemical release. Metabolic labeling of DNA in whole, living animals can therefore be achieved by simply soaking animals in a buffer containing TAMRA-dATP or a structurally related compound, Cy3-dATP.

2-Trifluoromethyl-6-mercurianiline Nucleotide, a Sensitive 19F NMR Probe for Hg(II)-mediated Base Pairing

A 2-trifluoromethylaniline C-nucleoside was synthesized, incorporated in the middle of an oligonucleotide, and mercurated. The affinity of the mercurated oligonucleotide toward complementary strands placing each of the canonical nucleobases opposite to the organomercury nucleobase analogue was examined by ultraviolet (UV), circular dichroism (CD), and 19F NMR spectroscopy analyses. According to the UV melting profile analysis, the organomercury nucleobase analogue showed increased affinities in the order T > G > C > A. The CD profiles indicated the typical B-type helix in each case. The 19F resonance signal proved sensitive for the local environmental changes, showing clearly distinct signals for the duplexes with different opposing nucleobases. Furthermore, valuable information on the mercurated oligonucleotide and its binding to complementary strands at varying temperature could be obtained by 19F NMR spectroscopy.

Towards polymerase-mediated synthesis of artificial RNA–DNA metal base pairs

Polymerase-mediated synthesis of RNA-DNA metal base pairs.

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

Phenoxazine pseudonucleotides in DNA i-motifs allow precise profiling of small molecule binders by fluorescence monitoring

The lack of high throughput screening (HTS) techniques for small molecules that stabilize DNA iMs limits their development as perspective drug candidates. Here we showed that fluorescence monitoring for probing the effects of ligands on the iM stability using the FAM-BHQ1 pair provides incorrect results due to additional dye-related interactions. We developed an alternative system with fluorescent phenoxazine pseudonucleotides in loops that do not alter iM unfolding. At the same time, the fluorescence of phenoxazine residues is sensitive to iM unfolding that enables accurate evaluation of ligand-induced changes of iM stability. Our results provide the basis for new approaches for HTS of iM ligands.

Covalently Mercurated Molecular Beacon for Discriminating the Canonical Nucleobases

A highly nucleobase-discriminating metalated nucleoside analogue, 3-fluoro-2-mercuri-6-methylaniline, was incorporated into an oligonucleotide molecular beacon. Fluorescence emission spectra were measured after the addition of four different complementary strands, in which the nucleobase opposite the metalated analogue varies. The fluorescence results showed a clear binding selectivity at room temperature, in the order G>T>C>A. The selectivity is based on the different affinities between the metalated nucleoside analogue and the canonical nucleobases. The synthesized probe is capable of robust discrimination between the two purine as well as the two pyrimidine bases by fluorescence at room temperature, and more sophisticated temperature analysis allows clear separation of every canonical nucleobase. The probe would, hence, be a suitable method for the detection of single nucleotide polymorphisms.

Stable Hg(II)-mediated base pairs with a phenanthroline-derived nucleobase surrogate in antiparallel-stranded DNA

Metal-mediated base pairs involving artificial nucleobases have emerged as a promising means for the site-specific functionalization of nucleic acids with metal ions. In this context, a GNA-appended (GNA: glycol nucleic acid) nucleoside analogue containing the artificial nucleobase 1H-imidazo[4,5-f][1,10]phenanthroline (P) has already been applied successfully in a variety of homo- and heteroleptic metal-mediated base pairs, mainly involving Ag(I) ions. Herein, we report a thorough investigation of the Hg(II)-binding properties of P when incorporated into antiparallel-stranded DNA duplexes. The artificial nucleobase P is able to form Hg(II)-mediated homoleptic base pairs of the type P-Hg(II)-P with a [2 + 2] coordination environment. In addition, the heteroleptic P-Hg(II)-T pair was investigated. The addition of a stoichiometric amount of Hg(II) to a duplex comprising either a P:P pair or a P:T pair stabilizes the DNA duplex by 4.3 °C and 14.5 °C, respectively. The P-Hg(II)-T base pair, hence, represents the most stabilizing non-organometallic Hg(II)-mediated base pair reported to date. The formation of the Hg(II)-mediated base pairs was investigated by means of temperature-dependent UV spectroscopy and CD spectroscopy.

Light-Induced Formation of Thymine-Containing Mercury(II)-Mediated Base Pairs

By applying caged thymidine residues, DNA duplexes were created in which Hg^II‐mediated base pair formation can be triggered by irradiation with light. When a bidentate ligand was used as the complementary nucleobase, an unprecedented stepwise formation of different metal‐mediated base pairs was achieved.

Concerted dynamics of metallo-base pairs in an A/B-form helical transition

Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-Hg^II-T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-Hg^II-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-Hg^II-(N4)C base pairs and greater A-form characteristics. Ten-fold different ¹J coupling constants (¹⁵N,¹⁹⁹Hg) are observed for (N3)C-Hg^II (114 Hz) versus (N4)C-Hg^II (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-Hg^II-T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding Hg^II, demonstrating that C-Hg^II-T has unique switching potential in DNA-based materials and devices.

Forced Intercalation (FIT)-Aptamers

Aptamers are oligonucleotide sequences that can be evolved to bind to various analytes of interest. Here, we present a general design strategy that transduces an aptamer-target binding event into a fluorescence readout via the use of a viscosity-sensitive dye. Target binding to the aptamer leads to forced intercalation (FIT) of the dye between oligonucleotide base pairs, increasing its fluorescence by up to 20-fold. Specifically, we demonstrate that FIT-aptamers can report target presence through intramolecular conformational changes, sandwich assays, and target-templated reassociation of split-aptamers, showing that the most common aptamer-target binding modes can be coupled to a FIT-based readout. This strategy also can be used to detect the formation of a metallo-base pair within a duplexed strand and is therefore attractive for screening for metal-mediated base pairing events. Importantly, FIT-aptamers reduce false-positive signals typically associated with fluorophore-quencher based systems, quantitatively outperform FRET-based probes by providing up to 15-fold higher signal to background ratios, and allow rapid and highly sensitive target detection (nanomolar range) in complex media such as human serum. Taken together, FIT-aptamers are a new class of signaling aptamers which contain a single modification, yet can be used to detect a broad range of targets.

Highly sensitive and selective mercury sensor based on mismatched base pairing with dioxT

A highly selective and sensitive sensor for mercury was designed based on a new fluorescent nucleobase, dioxT. Its metal-sensing ability was investigated using mismatched dioxT-T and dioxT-C base pairing. The sensor exhibited a high sensitivity (quenching efficiency, 80%, 1 : 1 binding mode) and selectivity upon the addition of mercury ions.

Synthesis and Enzymatic Incorporation of a Responsive Ribonucleoside Probe That Enables Quantitative Detection of Metallo-Base Pairs

Synthesis of a highly responsive fluorescent ribonucleoside analogue based on a 5-methoxybenzofuran uracil core, enzymatic incorporation of its triphosphate substrate into RNA transcripts, and its utility in the specific detection and estimation of Hg²⁺-ion-mediated metallo-base pair formation in DNA–RNA and RNA–RNA duplexes are described.

Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing

The rational design of fluorescent nucleoside analogues is greatly hampered by the lack of a general method to predict their photophysics, a problem that is especially acute when base pairing and stacking change fluorescence. To better understand these effects, a series of tricyclic cytidine (tC and tC^O ) analogues ranging from electron-rich to electron-deficient was designed and synthesized. They were then incorporated into oligonucleotides, and photophysical responses to base pairing and stacking were studied. When inserted into double-stranded DNA oligonucleotides, electron-rich analogues exhibit a fluorescence turn-on effect, in contrast with the electron-deficient compounds, which show diminished fluorescence. The magnitude of these fluorescence changes is correlated with the oxidation potential of nearest neighbor nucleobases. Moreover, matched base pairing enhances fluorescence turn-on for the electron-rich compounds, and it causes a fluorescence decrease for the electron-deficient compounds. For the tC^O compounds, the emergence of vibrational fine structure in the fluorescence spectra in response to base pairing and stacking was observed, offering a potential new tool for studying nucleic acid structure and dynamics. These results, supported by DFT calculations, help to rationalize fluorescence changes in the base stack and will be useful for selecting the best fluorescent nucleoside analogues for a desired application.

A novel helper qPCR system for platinum detection via Pt-DNA coordination

A novel real-time polymerase chain reaction (qPCR) platform for the simple and robust detection of platinum is described for the first time. Compared with conventional qPCR, a helper template, which is related to the active template for performing qPCR, was introduced in our helper qPCR system. Several guanine (G) bases were introduced in the helper template to obtain a platinum-responsive on/off switch based on G-Pt-G coordination. Because of the helper template, a slight change in platinum concentration would significantly change the signal in the qPCR. This novel helper qPCR technique easily detects platinum with high sensitivity (1 ng/mL) and selectivity over other metal ions. Therefore, it will be a promising technique for the detection of platinum in biomedical and environmental samples.

Rox-DNA Functionalized Silicon Nanodots for Ratiometric Detection of Mercury Ions in Live Cells

A ratiometric fluorescent sensor for mercury ions (Hg²⁺) has been constructed via covalent functionalization of silicon nanodot (SiND) with Hg²⁺-specific 6-carboxy-X-rhodamine (Rox)-tagged DNA. For the Rox-DNA functionalized SiND, the red fluorescence of Rox can be quenched by the blue-emitting SiND in the presence of Hg²⁺ due to structural change in DNA, which serves as the response signal. Meawhile, the fluorescence of SiND is insensitive to Hg²⁺ and acts as the reference signal. The wavelength difference in the optimal emission peak is as large as 190 nm between SiND (422 nm) and Rox (612 nm), which can efficaciously exclude the interference of the two emission peaks, and facilitates dual-color visualization of Hg²⁺ ions. The biofunctionalization of SiND improves the acid-base stability of SiND significantly, which is favorable for its application in the intracellular environment. Accordingly, a sensitive, simple, precise and rapid method for tracing Hg²⁺ was proposed. The limit of detection and precision of this method for Hg²⁺ was 9.2 nM and 8.8% (50 nM, n = 7), respectively. The increase of Hg²⁺ concentration in the range of 10-1500 nM was in accordance with linearly increase of the I₄₂₂/ I₆₁₂ ratio. As for practical application, the recoveries in spiked human urine and serum samples were in the range of 81-107%. Moreover, this fluorescent nanosensor was utilized to the ratiometric detection of Hg²⁺ in HeLa cells.

HgII binds to C-T mismatches with high affinity

Binding reactions of HgII and AgI to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1H NMR. Unlike AgI, HgII exhibited stoichiometric, site-specific binding of C-T mismatches. The on- and off-rates of HgII binding were approximately 10-fold faster to C-T mismatches (kon ≈ 105 M-1 s-1, koff ≈ 10-3 s-1) as compared to T-T mismatches (kon ≈ 104 M-1 s-1, koff ≈ 10-4 s-1), resulting in very similar equilibrium binding affinities for both types of 'all natural' metallo base pairs (Kd ≈ 10-150 nM). These results are in contrast to thermal denaturation analyses, where duplexes containing T-T mismatches exhibited much larger increases in thermal stability upon addition of HgII (ΔTm = 6-19°C), as compared to those containing C-T mismatches (ΔTm = 1-4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C-HgII-T base pairs, our results demonstrate that fluorescent nucleobase analogs enable highly sensitive detection and characterization of metal-mediated base pairs - even in situations where metal binding has little or no impact on the thermal stability of the duplex.

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.

Fluorescence Regulation of Copper Nanoclusters via DNA Template Manipulation toward Design of a High Signal-to-Noise Ratio Biosensor

Because of bioaccumulation of food chain and disability of biodegradation, concentration of toxic mercury ions (Hg²⁺) in the environment dramatically varies from picomolar to micromolar, indicating the importance of well-performed Hg²⁺ analytical methods. Herein, reticular DNA is constructed by introducing thymine (T)-Hg²⁺-T nodes in poly(T) DNA, and copper nanoclusters (CuNCs) with aggregate morphology are prepared using this reticular DNA as a template. Intriguingly, the prepared CuNCs exhibit enhanced fluorescence. Meanwhile, the reticular DNA reveals evident resistance to enzyme digestion, further clarifying the fluorescence enhancement of CuNCs. Relying on the dual function of DNA manipulation, a high signal-to-noise ratio biosensor is designed. This analytical approach can quantify Hg²⁺ in a very wide range (50 pM to 500 μM) with an ultralow detection limit (16 pM). Besides, depending on the specific interaction between Hg²⁺ and reduced l-glutathione (GSH), this biosensor is able to evaluate the inhibition of GSH toward Hg²⁺. In addition, pollution of Hg²⁺ in three lakes is tested using this method, and the obtained results are in accord with those from inductively coupled plasma mass spectrometry. In general, this work provides an alternative way to regulate the properties of DNA-templated nanomaterials and indicates the applicability of this way by fabricating an advanced biosensor.

Fluorescent nucleobases as tools for studying DNA and RNA

Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.

Metal-Mediated Base Pairs: From Characterization to Application

The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.

DNA Aptamer-Target Binding Motif Revealed Using a Fluorescent Guanine Probe: Implications for Food Toxin Detection

DNA aptamers are single-stranded oligonucleotides that are generated by an in vitro selection method to bind targets with high affinity and specificity. Understanding molecular recognition by DNA aptamers is of fundamental importance in the development of biosensor applications. The small molecule ochratoxin A (OTA) is a fungal-derived food toxin, and OTA DNA aptamers have been established for the development of rapid detection platforms required for food safety. One such OTA aptamer (OTAA) is a guanine-rich DNA oligonucleotide that folds into an antiparallel G-quadruplex (GQ) upon OTA binding, although structural details of the GQ fold and its interaction with OTA are currently unknown. In the present study, the fluorescent nucleobase analogue, 8-thienyl-2'-deoxyguanosine (ThdG), was inserted into various G sites of OTAA to determine the probe impact on GQ folding and OTA binding affinity. Our results suggest that OTAA contains three lateral (l) loops connecting two stacked G-tetrads with an anticlockwise loop progression to afford a -(lll) GQ topology. The phenolic ring system of OTA undergoes π-stacking interactions with the G-tetrads of OTAA. Our results also demonstrate aptamer sites that can be modified with ThdG to afford a fluorescent light-up signal upon OTA binding.