Sensing metal ions with DNA building blocks: fluorescent pyridobenzimidazole nucleosides

Rational design of small molecule fluorescent probes for biological applications

Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to "modulate" fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure-property relationships concerning the substituents are discussed in detail with examples for several dye families. We also present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena.

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.

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.

Self-Assembled Cofacial Zinc-Porphyrin Supramolecular Nanocapsules as Tuneable 1 O2 Photosensitizers

We demonstrate the benefits of using cofacial Zn-porphyrins as structural synthons in coordination-driven self-assembled prisms to produce cage-like singlet oxygen (¹ O₂ ) photosensitizers with tunable properties. In particular, we describe the photosensitizing and emission properties of palladium- and copper-based supramolecular capsules, and demonstrate that the nature of the bridging metal nodes in these discrete self-assembled prisms strongly influences ¹ O₂ generation at the Zn-porphyrin centers. The Pd^II -based prism is a particularly robust photosensitizer, whereas the Cu^II self-assembled prism is a dormant photosensitizer that could be switched to a ON state upon disassembly of the suprastructure. Furthermore, the well-defined cavity within the prisms allowed encapsulation of pyridine-based ligands and fullerene derivatives, which led to a remarkable guest tuning of the ¹ O₂ production.

How zinc ions shift and enhance the nucleotide's fluorescence spectra

Zinc–nucleotide complexes in alkaline solutions exhibit strong fluorescence enhancement and red shift, thus enabling an optical discrimination between the nucleotides.

Large-scale detection of metals with a small set of fluorescent DNA-like chemosensors

An important advantage of pattern-based chemosensor sets is their potential to detect and differentiate a large number of analytes with only few sensors. Here we test this principle at a conceptual limit by analyzing a large set of metal ion analytes covering essentially the entire periodic table, employing fluorescent DNA-like chemosensors on solid support. A tetrameric “oligodeoxyfluoroside” (ODF) library of 6561 members containing metal-binding monomers was screened for strong responders to 57 metal ions in solution. Our results show that a set of 9 chemosensors could successfully discriminate the 57 species, including alkali, alkaline earth, post-transition, transition, and lanthanide metals. As few as 6 ODF chemosensors could detect and differentiate 50 metals at 100 μM; sensitivity for some metals was achieved at midnanomolar ranges. A blind test with 50 metals further confirmed the discriminating power of the ODFs.

Pattern-based detection of toxic metals in surface water with DNA polyfluorophores

Heavy metal contamination of water can be toxic to humans and wildlife; thus the development of methods to detect this contamination is of high importance. Here we describe the design and application of DNA-based fluorescent chemosensors on microbeads to differentiate eight toxic metal ions in water. We developed and synthesized four fluorescent 2'-deoxyribosides of metal-binding ligands. A tetramer-length oligodeoxy-fluoroside (ODF) library of 6561 members was constructed and screened for sequences responsive to metal ions, of which seven sequences were selected. Statistical analysis of the response patterns showed successful differentiation of the analytes at concentrations as low as 100 nM. Sensors were able to classify water samples from 13 varied sites and quantify metal contamination in unknown specimens. The results demonstrate the practical potential of bead-based ODF chemosensors to analyze heavy metal contamination in water samples by a simple and inexpensive optical method.

Synthesis of biologically active pyridoimidazole/imidazobenzothiazole annulated polyheterocycles using cyanuric chloride in water

An efficient and mild protocol for rapid access to N-fused polyheterocycles via Pictet–Spengler type 6-endo cyclization by cyanuric chloride in aqueous medium has been developed.

Construction of fluorescence-tunable pyrido-fused benzimidazoles via direct intramolecular C–H amination under transition-metal-free conditions

A mild and efficient synthetic route to fluorescence-tunable pyrido-fused benzimidazole (PBI) scaffolds has been reported.

A new dual functional sensor: highly selective colorimetric chemosensor for Fe3+ and fluorescent sensor for Mg2+

A new artificial receptor 1 was synthesized for the detection of Fe(3+) and Mg(2+) in solution as a colorimetric and fluorescent sensor, respectively. The sensor exhibited highly selective and sensitive recognition towards Fe(3+) in CH(3)CN via color change from colorless to brown. Also it showed a significant fluorescence enhancement (70-fold) towards Mg(2+) in the mixture of solution CH(3)CN/H(2)O (8:2, v/v). The selectivity of either Fe(3+) or Mg(2+) was not interfered by the presence of other metal ions such as Cr(3+), Mn(2+), Co(3+), Ni(2+), Cu(2+), Ag(+), Cd(2+), Pb(2+), Ca(2+) and K(+) ions.

Synthesis, characterization and metal ion-sensing properties of two Schiff base derivatives

Two new Schiff base derivatives {2,2'-diphenyl-N,N'-bis(2-pyridylmethylene)biphenyl-4,4'-diamine} (1) and {2,2'-diphenyl-N,N'-bis(salicylidene)biphenyl-4,4'-diamine} (2) were synthesized and characterized by means of elemental analysis, (1)H NMR, FT-IR, and standard spectroscopy techniques. The molecular structure of 2 has been determined by X-ray single crystal analysis. The analyses of fluorescence properties of the compounds revealed that 1 and 2 are both poorly fluorescent and display sensitive fluorescence responses to a panel of 24 monovalent, divalent, and trivalent metal ions in CH(3)CN-DMSO (9:1, v/v). Results with imine 1 showed that Fe(3+), Cu(2+), Zn(2+), Cd(2+), Mn(2+), Zr(4+), Hg(2+), Cr(2+), Pb(2+), Sn(2+), Bi(2+), Al(3+), Ce(3+), La(3+), Sm(3+), Gd(3+), Nd(3+), Eu(3+) and Dy(3+) yields red shifts in emission and increases in intensity. And the greatest spectral changes for imine 2 include enhancements in emission intensity coupled with red shifts (Zr(4+), Sn(2+), Al(3+) and Zn(2+)) and strong quenching (Fe(3+)). The fluorescence enhancement mechanism of 1 and 2 for metal ions is based on: (i) CN isomerization; (ii) chelation-enhanced fluorescence (CHEF) effect; and (iii) excited-state intra/intermolecular proton transfer (ESPT).

Differentiating between fluorescence-quenching metal ions with polyfluorophore sensors built on a DNA backbone

A common problem in detecting metal ions with fluorescentchemosensors is the emission-suppressing effects of fluorescence-quenching metal ions. This quenching tendency makes it difficult to design sensors with turn-on signal, and differentiate between several metal ions that may yield a strong quenching response. To address these challenges, we investigate a new sensor design strategy, incorporating fluorophores and metal ligands as DNA base replacements in DNA-like oligomers, for generating a broader range of responses for quenching metal ions. The modular molecular design enabled rapid synthesis and discovery of sensors from libraries on PEG-polystyrene beads. Using this approach, water-soluble sensors 1-5 were identified as strong responders to a set of eight typically quenching metal ions (Co(2+), Ni(2+), Cu(2+), Hg(2+), Pb(2+), Ag(+), Cr(3+), and Fe(3+)). They were synthesized and characterized for sensing responses in solution. Cross-screening with the full set of metal ions showed that they have a wide variety of responses, including emission enhancements and red- and blue-shifts. The diversity of sensor responses allows as few as two sensors (1 and 2) to be used together to successfully differentiate these eight metals. As a test, a set of unknown metal ion solutions in blind studies were also successfully identified based on the response pattern of the sensors. The modular nature of the sensor design strategy suggests a broadly applicable approach to finding sensors for differentiating many different cations by pattern-based recognition, simply by varying the sequence and composition of ligands and fluorophores on a DNA synthesizer.

Selective sensor for silver ions built from polyfluorophores on a DNA backbone

To explore a new modular metal ion sensor design strategy, fluorophores and ligands were incorporated into short DNA-like oligomers. Compound 1 was found to function as a selective sensor for Ag(+) in aqueous buffer, where low micromolar concentrations of Ag(+) induce a red-shifted, turn-on fluorescence signal. Experiments with HeLa cells show that 1 can penetrate cells and yield a signal for intracellular Ag(+). This suggests a broadly applicable approach to developing sensors for a wide variety of cations.

Postsynthetic guanine arylation of DNA by Suzuki-Miyaura cross-coupling

Direct radical addition reactions at the C(8)-site of 2'-deoxyguanosine (dG) can afford C(8)-Ar-dG adducts that are produced by carcinogenic arylhydrazines, polycyclic aromatic hydrocarbons, and certain phenolic toxins. Such modified nucleobases are also highly fluorescent for sensing applications and possess useful electron transfer properties. The site-specific synthesis of oligonucleotides containing the C(8)-Ar-G adduct can be problematic. These lesions are sensitive to acids and oxidants that are commonly used in solid-phase DNA synthesis and are too bulky to be accepted as substrates for enzymatic synthesis by DNA polymerases. Using the Suzuki-Miyaura cross-coupling reaction, we have synthesized a number of C(8)-Ar-G-modified oligonucleotides (dimers, trimers, decamers, and a 15-mer) using a range of arylboronic acids. Good to excellent yields were obtained, and the reaction is insensitive to the nature of the bases flanking the convertible 8-Br-G nucleobase, as both pyrimidines and purines are tolerated. The impact of the C(8)-Ar-G lesion was also characterized by electrospray ionization tandem mass spectrometry, UV melting temperature analysis, circular dichroism, and fluorescence spectroscopy. The C(8)-Ar-G-modified oligonucleotides are expected to be useful substrates for diagnostic applications and understanding the biological impact of the C(8)-Ar-G lesion.

A highly sensitive ratiometric fluorescent probe for Cd2+ detection in aqueous solution and living cells

A ratiometric fluorescent Cd(2+) sensor DBITA which featured the Cd(2+)-induced red-shift of emission (53 nm) and picomolar sensitivity in both aqueous media and living cells was developed.

Synthesis and luminescence properties of a trinucleotide-europium(III) complex conjugate

Two trinucleotide conjugates of the macrocyclic ligand 1,4,7-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane are prepared. One contains only DNA (1) and the second is a chimeric RNA/DNA conjugate (2). The synthetic methodology used to prepare the trinucleotide macrocyclic ligand conjugates is based on the introduction of a convertible nucleoside which has an electrophilic function to facilitate the attachment of any nucleophilic ligand to the 5-position of the 3-nucleoside unit. The convertible nucleoside is first treated with the macrocyclic ligand, 1,4,7,10-tetraazacyclododecane, followed by alkylation of the three remaining amine groups to give a conjugated macrocyclic ligand with three pendent amide groups. Addition of an equivalent of EuCl3 to trinucleotide (1) or (2) yields the complexes Eu(1) and Eu(2), respectively. Studies using time-resolved and steady state direct excitation luminescence spectroscopy show that Eu(III) binds to the macrocyclic moiety in 1 and in 2. The excitation peak frequency for the 7Fo5Do transition and the unexpectedly low number of water ligands in Eu(1) and Eu(2) are consistent with additional interactions of the Eu(III) macrocycle with one of the phosphate diester groups. Studies show that Eu(2) undergoes cleavage at the uridine nucleotide. The unique point of attachment of the macrocyclic complex will enable the preparation of new lanthanide nucleic acid conjugates with useful properties.

Polyfluorophores on a DNA backbone: a multicolor set of labels excited at one wavelength

We recently described the assembly of fluorescent deoxyriboside monomers ("fluorosides") into DNA-like phosphodiester oligomers (oligodeoxyfluorosides or ODFs) in which hydrocarbon and heterocyclic aromatic fluorophores interact both physically and electronically. Here we report the identification of a multicolor set of water-soluble ODF dyes that display emission colors across the visible spectrum, and all of which can be simultaneously excited by long-wavelength UV light at 340-380 nm. Multispectral dye candidates were chosen from a library of 4096 tetramer ODFs constructed on PEG-polystyrene beads using a simple long-pass filter to observe all visible colors at the same time. We resynthesized and characterized a set of 23 ODFs containing one to four individual chromophores and included 2-3 spacer monomers to increase aqueous solubility and minimize aggregation. Emission maxima of this set range from 376 to 633 nm, yielding apparent colors from violet to red, all of which can be visualized directly. The spectra of virtually all ODFs in this set varied considerably from the simple combination of monomer components, revealing extensive electronic interactions between the presumably stacked monomers. In addition, comparisons of anagrams in the set (isomers having the same components in a different sequence) reveal the importance of nearest-neighbor interactions in the emissive behavior. Preliminary experiments with human tumor (HeLa) cells, observing two ODFs by laser confocal microscopy, showed that they can penetrate the outer cellular membrane, yielding cytoplasmic localization. In addition, a set of four distinctly colored ODFs was incubated with live zebrafish embryos, showing tissue penetration, apparent biostability, and no apparent toxicity. The results suggest that ODF dyes may be broadly useful as labels in biological systems, allowing the simultaneous tracking of multiple species by color, and allowing visualization in moving systems where classical fluorophores fail.

Enzymatic incorporation of emissive pyrimidine ribonucleotides

The enzymatic incorporation of a series of emissive pyrimidine analogues into RNA oligonucleotides is explored. T7 RNA polymerase is challenged with accepting three non-natural, yet related, triphosphates as substrates and incorporating them into diverse RNA transcripts. The three ribonucleoside triphosphates differ only in the modification of their uracil nucleus and include a thieno[3,2-d]pyrimidine nucleoside, a thieno[3,4-d]pyrimidine derivative, and a uridine containing a thiophene ring conjugated at its 5-position. All thiophene-containing uridine triphosphates (UTPs) get incorporated into RNA oligonucleotides at positions that are remote to the promoter, although the yields of the transcripts vary compared with the transcript obtained with only native triphosphates. Among the three derivatives, the 5-modified UTP is found to be the most "polymerase-friendly" and is well accommodated by T7 RNA polymerase. Although the fused thiophene analogues cannot be incorporated next to the promoter region, the 5-modified non-natural UTP gets incorporated near the promoter (albeit in relatively low yields) and even in multiple copies. Labeling experiments shed light on the mediocre incorporation of the fused analogues, suggesting the enzyme frequently pauses at the incorporation position. When incorporation does take place, the enzyme fails to elongate the modified oligonucleotide and yields aborted transcripts. Taken together, these results highlight the versatility and robustness, as well as the scope and limitation, of T7 RNA polymerase in accepting and incorporating reporter nucleotides into modified RNA transcripts.

Design, synthesis and anti-HIV integrase evaluation of 4-oxo-4H-quinolizine-3-carboxylic acid derivatives

4-Oxo-4H-quinolizine-3-carboxylic acid derivatives bearing sulfamido, carboxylamido, benzimidazole and benzothiazole substituents have been designed and synthesized. The structures of these new compounds were confirmed by ¹H-NMR, ¹³C- NMR, IR and ESI (or HRMS) spectra. Compounds were screened for possible HIV integrase inhibitory activity.

Design and synthesis of a caged Zn2+ probe, 8-benzenesulfonyloxy-5-N,N-dimethylaminosulfonylquinolin-2-ylmethyl-pendant 1,4,7,10-tetraazacyclododecane, and its hydrolytic uncaging upon complexation with Zn2+

8-Benzenesulfonyloxy-5- N,N-dimethylaminosulfonylquinolin-2-ylmethyl-pendant cyclen (BS-caged-L(4), BS = benzenesulfonyl) was designed and synthesized as a "caged" derivative of a previously described Zn(2+) fluorophore, 8-hydroxy-5- N,N-dimethylaminosulfonylquinolin-2-ylmethyl-pendant cyclen (L(4)) (cyclen = 1,4,7,10-tetraazacyclododecane). In the absence of metal ions and in the dark, BS-caged-L(4) (10 microM) showed negligible fluorescence emission at pH 7.4 (10 mM HEPES with I = 0.1 (NaNO3)) and 25 degrees C (excitation at 328 nm). Addition of Zn(2+) induced an increase in the UV/vis absorption of BS-caged-L(4) (10 microM) at 258 nm and a significant increase in fluorescence emission at 512 nm. These responses are results from the formation of Zn(H-1L(4)) by the hydrolysis of the sulfonyl ester at the 8-position of the quinoline unit promoted by the Zn(2+)-bound HO(-). Improvement of cell membrane permeation in comparison with L(4) is also described.

Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue

This article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tC(O), is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tC(O) is thoroughly characterized with respect to its photophysical properties and structural performance in single- and double-stranded oligonucleotides. The lowest energy absorption band at 360 nm (epsilon = 9000 M(-1) cm(-1)) is dominated by a single in-plane polarized electronic transition and the fluorescence, centred at 465 nm, has a quantum yield of 0.3. When incorporated into double-stranded DNA, tC(O) shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tC(O), on average, the brightest DNA-incorporated base analogue so far reported. Furthermore, it base pairs exclusively with guanine and causes minimal perturbations to the native structure of DNA. These properties make tC(O) a promising base analogue that is perfectly suited for e.g. photophysical studies of DNA interacting with macromolecules (proteins) or for determining size and shape of DNA tertiary structures using techniques such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET).

Synthesis and enzymatic incorporation of a fluorescent pyrimidine ribonucleotide

A detailed protocol for the synthesis of a fluorescent pyrimidine ribonucleoside analogue and its enzymatic incorporation into an RNA strand by transcription reactions is described. Furan-modified ribonucleoside triphosphate is synthesized in two steps with an overall yield of 33%. Incorporation of the triphosphate into an RNA oligomer occurs with nearly 225-fold amplification over the amount of the DNA template. Bacterial rRNA decoding site (known as the A-site) derived from this fluorescently modified ssRNA positively signals a binding event upon interaction with aminoglycoside antibiotics, its cognate ligands. The total time for the synthesis of ribonucleoside triphosphate is approximately 6 days, and that for the incorporation of the nucleoside triphosphate and purification of the fluorescently labeled RNA approximately 40 h.

Exploring the limits of DNA size: naphtho-homologated DNA bases and pairs

A new design for DNA bases and base pairs is described in which the pyrimidine bases are widened by naphtho-homologation. Two naphtho-homologated deoxyribosides, dyyT (1) and dyyC (2), were synthesized and could be incorporated into oligonucleotides as suitably protected phosphoramidite derivatives. The deoxyribosides were found to be fluorescent, with emission maxima at 446 and 433 nm, respectively. Studies with single substitutions of 1 and 2 in the natural DNA context revealed exceptionally strong base stacking propensity for both. Sequences containing multiple substitutions of 1 and 2 paired opposite adenine and guanine were subsequently mixed and studied by several analytical methods. Data from UV mixing experiments, FRET measurements, fluorescence quenching experiments, and hybridizations on beads suggest that complementary "doublewide DNA" (yyDNA) strands may self-assemble into helical complexes with 1:1 stoichiometry. Data from thermal denaturation plots and CD spectra were less conclusive. Control experiments in one sequence context gave evidence that yyDNA helices, if formed, are preferentially antiparallel and are sequence selective. Hypothesized base pairing schemes are analogous to Watson-Crick pairing, but with glycosidic C1'-C1' distances widened by over 45%, to ca. 15.2 A. The possible self-assembly of the double-wide DNA helix establishes a new limit for the size of information-encoding, DNA-like molecules, and the fluorescence of yyDNA bases suggests uses as reporters in monomeric and oligomeric forms.

Synthesis and site-specific incorporation of a simple fluorescent pyrimidine

We describe procedures for the synthesis of a fluorescent pyrimidine analog and its site-specific incorporation into a DNA oligomer. The 5'-protected and 3'-activated nucleoside 4 is synthesized in three steps with an overall yield of 40%. Site-specific incorporation into a DNA oligomer occurs with greater than 88% coupling efficiency. This isosteric fluorescent DNA analog can be used to monitor denaturation of DNA duplexes via fluorescence and can positively detect the presence of abasic sites in DNA duplexes. The total time for synthesis of the phosphoramidite 4 is about 75 h, whereas the total time for site-specific incorporation of nucleoside 2 into an oligonucleotide and purification of the corresponding oligonucleotide is about 114 hours.

Model Systems for Fluorescence and Singlet Oxygen Quenching by Metalloporphyrins

Next-generation photodynamic therapy agents will minimize extraneous phototoxicity by being active only at the target site. To this end, we have developed a model system to systematically investigate the excited-state quenching ability of a number of metalloporphyrins. Central metal ions that prefer four-coordinate, square planar orientations (Ag(II), Cu(II), Ni(II), Pd(II), and Zn(II)) were used. Porphyrin dimers based on 5-(4-aminophenyl)-10,15,20-triphenylporphyrin and comprising both a free base porphyrin and a metalloporphyrin covalently linked through a five-carbon alkyl chain were synthesized. The fluorescence and singlet oxygen quantum yields for the dimers were probed at 630 and 650 nm, respectively, resulting in the excitation of only the free base porphyrin and allowing a comparison of the quenching efficacy of each central metal ion. These results demonstrate that metalloporphyrins can serve as efficient quenchers, and may be useful in the design of novel light-activated therapeutic agents.