Lanthanide ion luminescence as a probe of DNA structure. 1. Guanine-containing oligomers and nucleotides

Nucleotide-Based Lanthanide Coordination Polymer Nano-Probe for Turn-On Fluorescence Sensing of Zn2+ in Serum

BACKGROUND

Water-dispersed lanthanide coordination polymers (LCPs) have attracted considerable attention owing to their superiority in bioanalysis. However, so far, most of the reported LCPs, due to the employment of water-insoluble and toxic organic molecules as ligands, are only competent in organic solution or the gaseous phase. Therefore, the construction of a water-dispersed, LCP-based, especially LCP nanoparticle (LCPNP)-based, sensor is still lacking and challenging.

OBJECTIVE

The aim was to obtain a novel and effective LCPNP-based sensor for Zn2+ by simple self-assembly, utilizing water-soluble guanosine monophosphate (GMP) as ligand and Eu3+ as luminescence center, .

METHODS

In aqueous solutions, Eu-GMP NPs were formed via self-assembly reaction between Eu3+ and GMP, and displayed very weak fluorescence due to low energy transfer from GMP to Eu3+ and the rate constant of nonradiactive deactivation of the excited states caused by the O-H vibration of coordinated water molecules. After the introduce of Zn2+, forming Eu-GMP/Zn, very interestingly, an 8-fold fluorescence enhancement was observed due to the removal of coordination water molecules and fluorescence sensitization of Zn2+.

RESULTS

The fluorescence intensity of Eu-GMP NPs at 614 nm showed a linear relationship with the concentration of Zn2+ from 4 to 240 μM with a detection limit of 4 μM. Due to possessing long fluorescence, Eu-GMP showed prominent achievment for application in serum Zn2+ determination.

CONCLUSION

The LCPNP probe exhibited excellent performance for the determination of Zn2+ in serum.

HIGHLIGHTS

For the first time, we developed and designed a kind of water-dispersed, LCPNP-based turn-on fluorescence assay for Zn2+ in serum. High sensitivity and good recoveries were achieved due to long fluorescence life, good water-dispersed behavior, and the turn-on fluorescence response of the LCPNP probe.

Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints

In this contribution we report the high-resolution NMR structure of a recently identified lanthanide-binding aptamer (LnA). We demonstrate that the rigid lanthanide binding by LnA allows for the measurement of anisotropic paramagnetic NMR restraints which to date remain largely inaccessible for nucleic acids. One type of such restraints - pseudocontact shifts (PCS) induced by four different paramagnetic lanthanides - was extensively used throughout the current structure determination study and the measured PCS turned out to be exceptionally well reproduced by the final aptamer structure. This finding opens the perspective for a broader application of paramagnetic effects in NMR studies of nucleic acids through the transplantation of the binding site found in LnA into other DNA/RNA systems.

Eu3+ as a luminescence probe in DNA studies: Structural and conformational implications

Lanthanide ions are widely used as luminescent probes for structural studies of various biomolecules, including DNA. Latest developments of circularly polarized luminescence (CPL) methodology further boosted interest to luminescence techniques. However, an effect of the lanthanide probes themselves on the DNA structure and conformation was investigated only partially and not for all lanthanides. In the present work, we performed a detailed spectroscopic study of Eu³⁺ complexes with native double-stranded DNA and compared them to the relevant complexes with single-stranded DNA. We employed infrared (IR), vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopic methods to investigate Eu³⁺ effect on DNA structure and conformational transitions. It was shown that Eu³⁺ ions can induce significant alteration of the native DNA structure at the concentrations often used in luminescence studies. While no DNA denaturation was observed at these metal ion concentrations, significant unstacking of the base pairs and disordering of the sugar-phosphate backbone, partial appearance of the A-form backbone geometry, and DNA transition into condensed ψ-type form took place. Eu³⁺ binding to single-stranded DNA was more pronounced than the binding to double-stranded DNA. We detected the main Eu³⁺ binding sites and determined the metal ion concentration range in which DNA geometry remains largely unaltered. The results obtained in the current study could be used for tuning the luminescence and CPL structural studies of DNA utilizing Eu³⁺ ions as probes.

Europium (III) as a Circularly Polarized Luminescence Probe of DNA Structure

We report as a proof-of-concept the first application of circularly polarized luminescence (CPL) measured with a Raman optical activity (ROA) spectrometer to differentiate several DNA structures without need of sensitizing complexes. The ROA/CPL approach provides sufficiently high CPL intensity to use hydrated Eu³⁺ ions, thus avoiding DNA structural changes associated with binding of sensitizers and overcoming the sensitizer quenching issue. We showed that deoxyguanosine monophosphate (dGMP), single- and double-stranded DNA provide different CPL spectra, which could be used for their discrimination. Our results demonstrate that ROA/CPL method is a promising approach to measure CPL spectra of complex biomolecules when the use of sensitizers is not possible. The method can be extended to other biomolecules, such as proteins, lipids, sugars, etc.

Application of lanthanide luminescence in probing enzyme activity

Enzymes play critical roles in the regulation of cellular function and are implicated in numerous disease conditions. Reliable and practicable assays are required to study enzyme activity, to facilitate the discovery of inhibitors and activators of enzymes related to disease. In recent years, a variety of enzyme assays have been devised that utilise luminescent lanthanide(iii) complexes, taking advantage of their high detection sensitivities, long luminescence lifetimes, and line-like emission spectra that permit ratiometric and time-resolved analyses. In this Feature article, we focus on recent progress in the development of enzyme activity assays based on lanthanide(iii) luminescence, covering a variety of strategies including Ln(iii)-labelled antibodies and proteins, Ln(iii) ion encapsulation within defined peptide sequences, reactivity-based Ln(iii) probes, and discrete Ln(iii) complexes. Emerging approaches for monitoring enzyme activity are discussed, including the use of anion responsive lanthanide(iii) complexes, capable of molecular recognition and luminescence signalling of polyphosphate anions.

Luminescence sensitization of Tb3+-DNA complexes by Ag. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017;180:85-90. [PMID: 28279827 DOI: 10.1016/j.saa.2017.03.001]

Terbium ions (Tb³⁺) with unique photophysical properties have been utilized to develop biosensors with low background and high sensitivity. In this study, the Ag⁺-sensitized luminescence of Tb³⁺-DNA complexes was uncovered. The luminescence of Tb³⁺-DNA complexes could be enhanced by more than 30 times in the presence of Ag⁺, when Tb³⁺ was bound with poly(G) and poly(T) whereas not with other homopolymers. This research confirmed that the sensitization resulted from the interaction of Ag⁺ with certain bases involved in DNA, not just with the reported certain G-quadruplex sequence. The coordination of Ag⁺ to guanine and thymine bases was expected to increase their rigidities, form Tb³⁺-DNA-Ag⁺ ternary structures, and thus enhance energy transfer from guanine and thymine to Tb³⁺. These findings benefit the development of sensitive luminescence probes for various nucleic acids-related targets.

Enhanced DNA sensitized Tb3+ luminescence in organic solvents for more sensitive detection

DNA-sensitized Tb³⁺ luminescence spectroscopy is a powerful method for probing nucleic acids and developing biosensors. Its performance in organic solvents has yet to be explored. In this study, Tb³⁺ luminescence with nucleosides, nucleotides and DNA oligonucleotides in various organic solvents is studied. Tb³⁺ emission with single nucleotides is quenched up to 88% in dimethyl formamide (DMF), while its emission with nucleosides is enhanced. For the four 15-mer DNA homopolymers, the strongest absolute emission enhancement was achieved with C₁₅. Similar emission properties are observed in other solvents including DMF, DMSO, acetonitrile methanol, ethanol, isopropanol and ethylene glycol. A few DNAzymes are tested as random DNA sequences all showing 1.4-6.9-fold emission enhancement in ethanol. A previously reported optimized sequence in water (G₃T)₅ is further enhanced by the solvents. Using this sequence, a detection limit of 5.5 nm Hg²⁺ is achieved in 25% ethanol solution. A similar Hg²⁺ sensitivity is also observed in a lake water mixed with ethanol. Luminescence lifetime is longer in DMF than in water. This study indicates that DNA-sensitized Tb³⁺ luminescence can be measured in water miscible solvents and most likely, with even stronger emission than that in water.

Turn-on fluorescence detection of ciprofloxacin in tablets based on lanthanide coordination polymer nanoparticles

Metal–organic coordination polymers (MOCPs) have emerged as a new family of functional nanomaterials.

Paramagnetic decoration of DNA origami nanostructures by Eu³⁺ coordination

The folding of DNA into arbitrary two- and three-dimensional shapes, called DNA origami, represents a powerful tool for the synthesis of functional nanostructures. Here, we present the first approach toward the paramagnetic functionalization of DNA origami nanostructures by utilizing postassembly coordination with Eu(3+) ions. In contrast to the usual formation of toroidal dsDNA condensates in the presence of trivalent cations, planar as well as rod-like DNA origami maintain their shape and monomeric state even under high loading with the trivalent lanthanide. Europium coordination was demonstrated by the change in Eu(3+) luminescence upon binding to the two DNA origami. Their natural circular dichroism in the Mg(2+)- and Eu(3+)-bound state was found to be very similar to that of genomic DNA, evidencing little influence of the DNA origami superstructure on the local chirality of the stacked base pairs. In contrast, the magnetic circular dichroism of the Mg(2+)-bound DNA origami deviates from that of genomic DNA. Furthermore, the lanthanide affects the magnetic properties of DNA in a superstructure-dependent fashion, indicative of the existence of superstructure-specific geometry of Eu(3+) binding sites in the DNA origami that are not formed in genomic DNA. This simple approach lays the foundation for the generation of magneto-responsive DNA origami nanostructures. Such systems do not require covalent modifications and can be used for the magnetic manipulation of DNA nanostructures or for the paramagnetic alignment of molecules in NMR spectroscopy.

Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids

Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb(3+)). Single-stranded oligonucleotides greatly enhance the Tb(3+) emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb(3+)/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb(3+), producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb(3+)/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb(3+)/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36±1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.

Significant FRET between SWNT/DNA and rare earth ions: a signature of their spatial correlations

Significant acceleration of the photoluminescence (PL) decay rate was observed in water solutions of two rare earth ions (REIs), Tb and Eu. We propose that the time-resolved PL spectroscopy data are explained by a fluorescence resonance energy transfer (FRET) between the REIs. FRET was directly confirmed by detecting the induced PL of the energy acceptor, Eu ion, under the PL excitation of the donor ion, Tb, with FRET efficiency reaching 7% in the most saturated solution, where the distance between the unlike REIs is the shortest. Using this as a calibration experiment, a comparable FRET was measured in the mixed solution of REIs with single-wall nanotubes (SWNTs) wrapped with DNA. From the FRET efficiency of 10% and 7% for Tb and Eu, respectively, the characteristic distance between the REI and SWNT/DNA was obtained as 15.9 ± 1.3 Å, suggesting that the complexes are formed because of Coulomb attraction between the REI and the ionized phosphate groups of the DNA.

Luminescence study of G-quadruplex formation in the presence of Tb3+ ion

The interactions of Tb3+ with the quadruplex-forming oligonucleotide bearing human telomeric repeat sequence d(G(3)T(2)AG(3)T(2)AG(3)T(2)AG(3)), (htel21), have been studied using luminescence spectroscopy and circular dichroism (CD). Enhanced luminescence of Tb3+, resulting from energy transfer from guanines, indicated encapsulation of Tb3+ ion in the central cavity of quadruplex core. The ability of lanthanide ions (Eu3+ and Tb3+) to mediate formation of quadruplex structure has been further evidenced by the fluorescence energy transfer measurements with the use of oligonucleotide probe labeled with fluorescein and rhodamine FRET partners, FAM-htel21-TAMRA. The CD spectra revealed that Tb3+/htel21 quadruplex possesses antiparallel strand orientation, similarly as sodium quadruplex. Tb3+ binding equilibria have been investigated in the absence and the presence of competing metal cations. At low Tb3+ concentration (8 microM) Tb3+/htel21 quadruplex stability is very high (5 x 10(6) M(-1)) and stoichiometry of 5-7 Tb3+ ions per one quadruplex molecule is observed. Luminescence and CD titration experiments suggested that the cavity of quadruplex accommodates two Tb3+ ions and the remaining Tb3+ ions bind probably to TTA loops of quadruplex. Higher concentration of Tb3+ (above 10 microM) results in the excessive binding of Tb3+ ions that finally destabilizes quadruplex, which undergoes transformation into differently organized assemblies. Such assemblies (probably possessing multiple positive charge) exhibit kinetic stability, which is manifested by a very slow kinetics of displacement of Tb3+ ion by competing cations (Li+, Na+, K+).

Anomalously high cooperativity of oligodeoxycytidylic acid for luminescence resonance energy transfer to lanthanide ions

The luminescence of terbium(III) and europium(III) through luminescence resonance energy transfer from mononucleotides and oligodeoxynucleotides is examined. Among mononucleotides, dGMP gives the strongest luminescence of terbium(III), while dTMP and dCMP yield a luminescence intensity of europium(III) that is larger than the other two cases. In the homodeoxydecamers, decadeoxycytidylic acid (dC10) produces the highest intensity for both metals. The anomalously large cooperativity of dC10 is explained by the easiness of deformation of the helical structure to bind lanthanide ions, and a circular dichroism study supports this explanation.

Enhanced Emission Induced by FRET from a Long-Lifetime, Low Quantum Yield Donor to a Long-Wavelength, High Quantum Yield Acceptor

We report observation of high quantum yield, long-lifetime fluorescence from a red dye BO-PRO-3 excited by resonance energy transfer (RET). The acceptor fluorescence was highly enhanced upon binding to the donor-labeled DNA. A ruthenium complex (Ru) was chosen as a donor in this system because of its long fluorescence lifetime. Both donor and acceptor were non-covalently bound to DNA. Emission from the donor-acceptor system (DA) at wavelengths exceeding 600 nm still preserves the long-lifetime component of the Ru donor, retaining average fluorescence lifetimes in the range of 30-50 ns. Despite the low quantum yield of the Ru donor in the absence of acceptor, its overall quantum yield of the DA pair was increased by energy transfer to the higher quantum yield acceptor BO-PRO-3. The wavelength-integrated intensity of donor and acceptor bound to DNA was many-fold greater than the intensity of the donor and acceptor separately bound to DNA. The origin of this effect is due to an efficient energy transfer from the donor, competing with non-radiative depopulation of the donor excited state. The distinctive features of DA complexes can be used in the development of a new class of engineered luminophores that display both long lifetime and long-wavelength emission. Similar DA complexes can be applied as proximity indicators, exhibiting strong fluorescence of adjacently located donors and acceptors over the relatively weak fluorescence of separated donors and acceptors.

Long-wavelength long-lifetime luminophores

We describe a new approach to making luminophores that display long emission wavelengths, long decay times, and high quantum yields. These luminophores are covalently linked pairs with a long-lifetime resonance-energy-transfer donor and a long-wavelength acceptor. The donor was a ruthenium (Ru) metal-ligand complex. The acceptor was the Texas Red. The donor and acceptor were covalently linked by polyproline spacers. The long-lifetime donor results in a long-lived component in the acceptor decay, which is due to RET. Importantly, the quantum yield of the luminophores approaches that of the higher quantum yield acceptor, rather than the lower quantum yield typical of metal-ligand complexes. The emission maxima and decay time of such tandem luminophores can be readily adjusted by selection of the donor, acceptor, and distance between them. Luminophores with these useful spectral properties can also be donor-acceptor pairs brought into close proximity by some biochemical association reaction. Luminophores with long-wavelength emission and long lifetimes can have numerous applications in biophysics, clinical diagnostics, DNA analysis, and drug discovery.

On the possibility of long-wavelength long-lifetime high-quantum-yield luminophores

We describe an approach to creating a new class of luminophores which display both long wavelength emissions exceeding 600 nm and long lifetimes. These luminophores are based on resonance energy transfer (RET) from a long lifetime donor to a short lifetime but long wavelength acceptor. We demonstrated the possibility of obtaining these desirable spectral properties using donors and acceptors noncovalently bound to DNA. The donor was a ruthenium (Ru) metal-ligand complex in which one of the diimine ligands intercalated into double-helix DNA. The acceptors were either nile blue, TOTO-3, or TO-PRO-3. Upon binding of the acceptor to donor-labeled DNA, we found that the acceptor quantum yield was remarkably enhanced so that the wavelength-integrated intensities of the donor and acceptor bound to DNA were many-fold greater than the intensity of the donor and acceptor alone when separately bound to DNA. The origin of this effect is efficient energy transfer from the donor. Under these conditions the effective overall quantum yield approaches that of the acceptor. Importantly, the increased quantum yield can be obtained while maintaining usefully long apparent acceptor lifetimes of 30 to 80 ns. The effect of an increased quantum yield from a low quantum yield donor may find use in assays to detect macromolecular binding interactions. These results suggest the synthesis of covalently linked donor-acceptor pairs with the desirable spectral properties of long wavelength emission, high quantum yield, and moderately long lifetimes for gated detection.

Multiphoton Ligand-Enhanced Excitation of Lanthanides

We describe multiphoton excitation of the lanthanides europium (Eu³⁺) and terbium (Tb³⁺) when these ions are complexed with nucleic acids, proteins, and fluorescent chelators. In all cases excitation occurs by multiphoton absorption of the sensitizers. For the nucleotide GDP and an oligonucleotide with several guanines, the sensitized emission of Tb³⁺ excited at 776 nm indicated a three-photon process. For Tb³⁺ bound to the wild-type troponin C and a single tryptophan mutant (26W), excitation at 794 nm was also close to a three-photon process. For lanthanide chelators containing various sensitizers, we observed three-photon excitation in the case of methyl anthranilate, a mixuture of two- and three-photon excitation for carbostyril 124, and a two-photon process with a coumarin derivative. In the case of coumarin-sensitized emission of Eu³⁺ varied from a two- to a three-photon process at wavelengths ranging from 780 to 880 nm. The sensitized luminescence also shows significantly higher photostability compared to the fluorescence from the organic fluorophores alone. These results suggest the use of multiphoton-induced sensitized lanthanide fluorescence in biochemistry and cellular imaging.

DNA enzymes

The past year has seen a coming-of-age in DNA enzyme research. Far from being laboratory curiosities, the activities of new DNA enzymes have broadened the known catalytic repertoire of nucleic acid enzymes, provided valuable insights into different mechanistic possibilities open to nucleic acid catalysts, and explored the importance for catalysis of native functionalities within DNA and RNA, as well as of a diversity of extrinsic cofactors. Thus, the first amino acid cofactor-utilizing DNA enzyme has been described, as well as DNA enzymes that cleave RNA without the assistance of any external cofactor. On the practical side, the most efficient RNA-cleaving nucleic acid enzyme described to date is a DNA enzyme.

Determination of internuclear angles of DNA using paramagnetic-assisted magnetic alignment

Paramagnetic ions have been used to assist the magnetic alignment of DNA. The anisotropy of the binding sites is sufficient to give rise to significant alignment of the DNA with the observed proton-carbon dipolar couplings spanning a 70-Hz range. The dipolar couplings have been used to determine the positions of the axial and rhombic alignment axes. The positions of the alignment axes relative to the positions of the binding sites of the paramagnetic europium ions have also been determined.

Lanthanide probes for a phosphodiester-cleaving, lead-dependent, DNAzyme

Lanthanides are useful probes for studying metal ion interactions in biological systems. The trivalent cations of the lanthanide metals are unique in that their ionic radii and the first pKa values of bound water molecules vary monotonically along the period. In addition, the europium and terbium cations have the useful property that their luminescence is enhanced when bound to nucleic acids. We have found that lanthanide ions can function as effective co-factors for a lead-dependent, phosphodiester-cleaving catalytic DNA (DNAzyme). We used the unique properties of the lanthanide co-factors to study the metal binding site as well as the catalytic mechanism of the DNAzyme. The catalyzed lanthanide-mediated cleavage occurred at neutral pH and at room temperature, with multiple turnovers of substrate. A range of lanthanide ions could act as co-factors, but differentially, with the smaller lanthanides (Tb, Tm, Lu) being the most effective. The rate of cleavage of the phosphodiester did not vary linearly with either the ionic radius or the first pKa of lanthanide-coordinated water molecules. The DNAzyme appeared to use only a single bound lanthanide ion as co-factor. Luminescence spectroscopy with terbium revealed the importance of the 2' hydroxyl group at the cleavage site in lanthanide ion binding, and the substrate molecule alone appeared to generate substantially the catalytically relevant metal-binding site. This model system demonstrated further the utility of complexing lanthanide ions directly to DNA molecules for catalytic purposes. The use of lanthanide ions also provides a means for investigating the metal ion binding sites of nucleic acid enzymes in general.