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

Blue Long Afterglow and Ultra Broadband Vis-NIR Emission from All-Inorganic Copper-Doped Silver Halide Single Crystals

All-inorganic metal halides with afterglow emission have attracted increasing attention due to their significantly longer afterglow duration and higher stability compared to their organic-inorganic hybrid counterparts. However, their afterglow colors have not yet reached the blue spectral region. Here, we report all-inorganic copper-doped Rb2AgBr3 single crystals with ultralong blue afterglow (>300 s) by modulating defect states through doping engineering. The introduction of copper(I) ions into Rb2AgBr3 facilitates the formation of bromine vacancies, thus increasing the density of trap states available for charge storage and enabling bright, persistent emission after ceasing the excitation. Moreover, cascade energy transfer between distinct emissive centers in the crystals results in ultra-broadband photoluminescence, not only covering the whole white light with near-unity quantum yield but also extending into the near-infrared region. This 'cocktail' of exotic light-emission properties, in conjunction with the excellent stability of copper-doped Rb2AgBr3 crystals, allowed us to demonstrate their implementation to solid-state lighting, night vision, and intelligent anti-counterfeiting.

Ruthenium(II) Polypyridyl Complexes as FRET Donors: Structure- and Sequence-Selective DNA-Binding and Anticancer Properties

Ruthenium(II) polypyridyl complexes (RPCs) that emit from metal-to-ligand charge transfer (MLCT) states have been developed as DNA probes and are being examined as potential anticancer agents. Here, we report that MLCT-emissive RPCs that bind DNA undergo Förster resonance energy transfer (FRET) with Cy5.5-labeled DNA, forming mega-Stokes shift FRET pairs. Based on this discovery, we developed a simple and rapid FRET binding assay to examine DNA-binding interactions of RPCs with diverse photophysical properties, including non-"light switch" complexes [Ru(dppz)₂(5,5'dmb)]²⁺ and [Ru(PIP)₂(5,5'dmb)]²⁺ (dppz = dipyridophenazine, 5,5'dmb = 5,5'-dimethyl-2,2'-bipyridine, PIP = 2-phenyl-imidazo[4,5-f][1,10]phenanthroline). Binding affinities toward duplex, G-quadruplex, three-way junction, and mismatch DNA were determined, and derived FRET donor-acceptor proximities provide information on potential binding sites. Molecules characterized by this method demonstrate encouraging anticancer properties, including synergy with the PARP inhibitor Olaparib, and mechanistic studies indicate that [Ru(PIP)₂(5,5'dmb)]²⁺ acts to block DNA replication fork progression.

Study on the interaction between 4-(1H-indol-3-yl)-2-(p-tolyl)quinazoline-3-oxide and human serum albumin

An organic small-molecular drug, 4-(1H-indol-3-yl)-2-(p-tolyl)quinazoline-3-oxide 1a was synthesized. It was employed to investigate the binding interaction and mechanism with human serum albumin (HSA). The experimental results indicated that the fluorescence quenching of HSA by 1a is a static quenching process and formation 1a-HSA complex. The site competition experiments revealed that the combination of 1a on HSA are hydrophobic interactions in the IIA domain and hydrogen bonds in IIIA domain of HSA, and the hydrophobic interactions of 1a on HSA are stronger than that of hydrogen bonds. These results were also confirmed by molecular docking theoretic analysis and ANS-hydrophobic fluorescent probe experiment. Synchronous fluorescence experiments showed that the polarity of HSA microenvironment was increase in the interaction process of 1a with HSA. The results of binding distance explored indicated that the combination distance between 1a and HSA is 3.63 nm, which is between 0.5R₀ and 1.5R₀, revealing the energy transfer between HSA and 1a is non-radiative. These results are very helpful for people to screen out high efficient indoloquinazoline drugs.

Interplay between Förster and Dexter Energy Transfer Rates in Isomeric Donor-Bridge-Acceptor Systems

The ability to direct the flow of excitons enable molecular systems to perform highly advanced functions. Intramolecular energy transfer in donor-bridge-acceptor systems can occur by different mechanisms, and the ability to control the excited state energy pathways depends on the capacity to favor one process over another. Here, we show an anticorrelation between the rates of Förster and Dexter types of energy transfer in two isomeric donor-bridge-acceptor systems. Both dyads display intramolecular Förster triplet-to-singlet and Dexter triplet-to-triplet energy transfers. However, as the bridge-acceptor connection point changes, the rate of one energy transfer process increases at the same time as the other one decreases, allowing us to control the energy flow direction. This work shows how rational design can be used to tune excited state energy pathways in molecular dyads, which is of importance for advanced functions such as multiplicity conversion in future molecular materials.

Multi-spectroscopic approaches and molecular simulation research of the intermolecular interaction between the angiotensin-converting enzyme inhibitor (ACE inhibitor) benazepril and bovine serum albumin (BSA)

Benazepril, a common ACE inhibitor, widely used in the treatment of arterial hypertension and congestive heart failure. In this study, We evaluated the characteristics of the interaction between benazepril and BSA under the simulated physiological condition (pH7.4) through various spectroscopic and molecular docking methods. Fluorescence and absorption spectroscopy results showed benazepril quenched the intrinsic fluorescence of BSA through a combined dynamic and static quenching mechanism. The number of binding sites (n) and the binding constant (K_b) of benazepril-BSA complex were circa 1 and 6.81×10³M^-1 at 298K, respectively, indicating that the binding affinity between benazepril and BSA was moderate. The displacement experiments confirmed that benazepril binding to the site I of BSA, which was quite in accordance with molecular docking. The values of the Gibbs free energy (ΔG⁰), enthalpic change (ΔH⁰) and entropic change (ΔS⁰) were negative, verifying that van der Waals force and hydrogen bonding interaction played a predominant roles in the process of spontaneous bonding. Furthermore, a slight change of the conformation in BSA upon benazepril interaction was proved through SF, 3-DF and FTIR spectroscopy results.

Thiazole- and selenazole-comprising high-affinity inhibitors possess bright microsecond-scale photoluminescence in complex with protein kinase CK2

A previously disclosed protein kinase (PK) CK2-selective inhibitor 4-(2-amino-1,3-thiazol-5-yl)benzoic acid (ATB) and its selenium-containing counterpart (ASB) revealed remarkable room temperature phosphorescence when bound to the ATP pocket of the protein kinase CK2. Conjugation of these fragments with a mimic of CK2 substrate peptide resulted in bisubstrate inhibitors with increased affinity towards the kinase. Attachment of the fluorescent acceptor dye 5-TAMRA to the conjugates led to significant enhancement of intensity of long-lifetime (microsecond-scale) photoluminescence of both sulfur- and selenium-containing compounds. The developed photoluminescent probes make possible selective determination of the concentration of CK2 in cell lysates and characterization of CK2 inhibitors by means of time-gated measurement of photoluminescence.

Interaction of Flavonoids from Woodwardia unigemmata with Bovine Serum Albumin (BSA): Application of Spectroscopic Techniques and Molecular Modeling Methods

Phytochemical investigation on the methanol extract of Woodwardia unigemmata resulted in the isolation of seven flavonoids, including one new flavonol acylglycoside (1). The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis and comparison of literature data. The multidrug resistance (MDR) reversing activity was evaluated for the isolated compounds using doxorubicin-resistant K562/A02 cells model. Compound 6 showed comparable MDR reversing effect to verapamil. Furthermore, the interaction between compounds and bovine serum albumin (BSA) was investigated by spectroscopic methods, including steady-state fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular docking approach. The experimental results indicated that the seven flavonoids bind to BSA by static quenching mechanisms. The negative ΔH and ΔS values indicated that van der Waals interactions and hydrogen bonds contributed in the binding of compounds 2–6 to BSA. In the case of compounds 1 and 7 systems, the hydrophobic interactions play a major role. The binding of compounds to BSA causes slight changes in the secondary structure of BSA. There are two binding sites of compound 6 on BSA and site I is the main site according to the molecular docking studies and the site marker competitive binding assay.

Key Structural Elements of Unsymmetrical Cyanine Dyes for Highly Sensitive Fluorescence Turn-On DNA Probes

Unsymmetrical cyanine dyes, such as thiazole orange, are useful for the detection of nucleic acids with fluorescence because they dramatically enhance the fluorescence upon binding to nucleic acids. Herein, we synthesized a series of unsymmetrical cyanine dyes and evaluated their fluorescence properties. A systematic structure-property relationship study has revealed that the dialkylamino group at the 2-position of quinoline in a series of unsymmetrical cyanine dyes plays a critical role in the fluorescence enhancement. Four newly designed unsymmetrical cyanine dyes showed negligible intrinsic fluorescence in the free state and strong fluorescence upon binding to double-stranded DNA (dsDNA) with a quantum yield of 0.53 to 0.90, which is 2 to 3 times higher than previous unsymmetrical cyanine dyes. A detailed analysis of the fluorescence lifetime revealed that the dialkylamino group at the 2-position of quinoline suppressed nonradiative decay in favor of increased fluorescence quantum yield. Moreover, these newly developed dyes were able to stain the nucleus specifically in fixed HeLa cells examined by using a confocal laser-scanning microscope.

Bichromophoric dyes for wavelength shifting of dye-protein fluoromodules

Dye-protein fluoromodules consist of fluorogenic dyes and single chain antibody fragments that form brightly fluorescent noncovalent complexes. This report describes two new bichromophoric dyes that extend the range of wavelengths of excitation or emission of existing fluoromodules. In one case, a fluorogenic thiazole orange (TO) was attached to an energy acceptor dye, Cy5. Upon binding to a protein that recognizes TO, red emission due to efficient energy transfer from TO to Cy5 replaces the green emission observed for monochromophoric TO bound to the same protein. Separately, TO was attached to a coumarin that serves as an energy donor. The same green emission is observed for coumarin-TO and TO bound to a protein, but efficient energy transfer allows violet excitation of coumarin-TO, versus longer wavelength, blue excitation of monochromophoric TO. Both bichromophores exhibit low nanomolar KD values for their respective proteins, >95% energy transfer efficiency and high fluorescence quantum yields.

PIM kinase-responsive microsecond-lifetime photoluminescent probes based on selenium-containing heteroaromatic tricycle

Microsecond-lifetime binding-responsive organic photoluminescent probes for PIM kinases were developed based on selenium-comprising heteroaromatic tricycle.

Intermolecular interaction of prednisolone with bovine serum albumin: spectroscopic and molecular docking methods

The intermolecular interaction of prednisolone with bovine serum albumin (BSA) was studied using fluorescence, circular dichroism (CD) and molecular docking methods. The experimental results showed that the fluorescence quenching of the BSA at 338 nm by prednisolone resulted from the formation of prednisolone-BSA complex. The number of binding sites (n) for prednisolone binding on BSA was approximately equal to 1. Base on the sign and magnitude of the enthalpy and entropy changes (ΔH(0)=-149.6 kJ mol(-1) and ΔS(0)=-370.7 J mol(-1)K(-1)) and the results of molecular docking, it could be suggested that the interaction forces were mainly Van der Waals and hydrogen bonding interactions. Moreover, in the binding process of BSA with prednisolone, prednisolone molecule can be inserted into the hydrophobic cavity of subdomain IIIA (site II) of BSA. The distance between prednisolone and Trp residue of BSA was calculated as 2.264 nm according to Forster's non-radiative energy transfer theory.

"Light Switch" Effect Upon Binding of Ru-dppz to Water-Soluble Conjugated Polyelectrolyte Dendrimers

We report the "light switch" effect of [Ru(bpy)2(dppz)](2+) (where bpy = 2,2'-bipyridine and dppz = dipyrido[3,2-a:2',3'-c] phenazine, Ru-dppz) in the presence of anionic conjugated polyelectrolyte dendrimers (CPDs). The metal-to-ligand charge-transfer luminescence from Ru-dppz is efficient in the presence of CPD because the complex is shielded from water by binding to the hydrophobic dendrimer core.

Protein-induced long lifetime luminescence of nonmetal probes

Time-resolved luminometry-based assays have great potential for measurements in complicated biological solutions and living cells as the measured signal can be easily distinguished from nanosecond lifetime background fluorescence of organic compounds and autofluorescence of cells. In the present study we discovered that binding of a thiophene- or a selenophene-containing heteroaromatic moiety (luminescence donor) to the purine-binding pocket of a protein kinase (PK) induces long lifetime photoluminescence signal that is largely intensified through efficient energy transfer to a fluorescent dye present in close proximity to the luminescence donor. The developed ARC-Lum probes possessing 19-266 μs luminescence lifetime when associated with the target kinase can be used for determination of activity of basophilic PKs, characterization of inhibitors of PKs, and as cAMP sensors. An ARC-Lum probe was also used for the determination of kinetic parameters of inhibitor binding to the catalytic subunit of protein kinase A (PKAc). Effective real-time monitoring of the activation of PKA by Forskolin and the displacement of an ARC-Lum probe from its complex with PKA by inhibitor H89 was performed in live cells. The discovered phenomenon, protein-induced long lifetime luminescence of aromatic probes is very likely to occur with all PKs and many other proteins.

Photophysical characterization of a FRET system using tailor-made DNA oligonucleotide sequences

We have carried out a detailed photophysical study of the FRET D/A pair consisting of a carbostyril donor and a Ru(II)bathophenanthroline complex acceptor in double-stranded synthetic DNA. Altogether 13 different double-stranded 30 base pair DNAs showing small incremental differences in the distances between donor and acceptor were synthesized. Using the fluorescence of the donor as well as of the acceptor, D/A separations were determined and compared to those derived from a well-established model for DNA distance calculations. The model calculations and anisotropy studies revealed that the donor can nearly be seen as a free rotator allowing the application of the established FRET data evaluation.

Long wavelength fluorescence lifetime standards for front-face fluorometry

With the increased development and use of fluorescence lifetime-based sensors, fiber optic sensors, fluorescence lifetime imaging microscopy (FLIM), and plate and array readers, , calibration standards are essential to ensure the proper function of these devices and accurate results. For many devices that utilize a "front face excitation" geometry where the excitation is nearly coaxial with the direction of emission, scattering-based lifetime standards are problematic and fluorescent lifetime standards are necessary. As more long wavelength (red and near-infrared) fluorophores are used to avoid background autofluorescence, the lack of lifetime standards in this wavelength range has only become more apparent . We describe an approach to developing lifetime standards in any wavelength range, based on Förster resonance energy transfer (FRET). These standards are bright, highly reproducible, have a broad decrease in observed lifetime, and an emission wavelength in the red to near infrared making them well suited for the laboratory and field applications as well. This basic approach can be extended to produce lifetime standards for other wavelength regimes.

Dopamine 5 receptor mediates Ang II type 1 receptor degradation via a ubiquitin-proteasome pathway in mice and human cells

Hypertension is a multigenic disorder in which abnormal counterregulation between dopamine and Ang II plays a role. Recent studies suggest that this counterregulation results, at least in part, from regulation of the expression of both the antihypertensive dopamine 5 receptor (D5R) and the prohypertensive Ang II type 1 receptor (AT1R). In this report, we investigated the in vivo and in vitro interaction between these GPCRs. Disruption of the gene encoding D5R in mice increased both blood pressure and AT1R protein expression, and the increase in blood pressure was reversed by AT1R blockade. Activation of D5R increased the degradation of glycosylated AT1R in proteasomes in HEK cells and human renal proximal tubule cells heterologously and endogenously expressing human AT1R and D5R. Confocal microscopy, Förster/fluorescence resonance energy transfer microscopy, and fluorescence lifetime imaging microscopy revealed that activation of D5R initiated ubiquitination of the glycosylated AT1R at the plasma membrane. The regulated degradation of AT1R via a ubiquitin/proteasome pathway by activation of D5R provides what we believe to be a novel mechanism whereby blood pressure can be regulated by the interaction of 2 counterregulatory GPCRs. Our results therefore suggest that treatments for hypertension might be optimized by designing compounds that can target the AT1R and the D5R.

Rab4 and Rab11 coordinately regulate the recycling of angiotensin II type I receptor as demonstrated by fluorescence resonance energy transfer microscopy

The recycling of G-protein-coupled receptors (GPCR) to the cell surface after internalization plays an important role in the regulation of overall GPCR activity. The angiotensin II type I receptor (AT1R) belongs to class B GPCRs that recycle slowly back to the cell surface. Previous studies have proposed that Rab11 controls the recycling of AT1R; however, recent reports show that Rab4, a rapid recycling regulator, co-localizes also with internalized AT1R. Different from the subcellular co-localization provided by fluorescence microscopy, fluorescence resonance energy transfer (FRET) microscopy provided the spatial relationship of AT1R with Rab4 and Rab11 in the nanometer-range proximity during the entire course of AT1R recycling. During the early recycling stage, internalized AT1Rs were mainly associated with Rab4 in the cytoplasm. During the mid-recycling stage, AT1Rs were associated with both Rab4 and Rab11 in the perinuclear compartments. However, during the late-recycling stage, AT1Rs were mainly associated with Rab11, both in the perinuclear compartments and the plasma membrane. Co-immunoprecipitation data confirmed these dynamic associations, which were disrupted by silencing of either the Rab4 or Rab11 gene. Based on these observations, we propose a Rab4 and Rab11 coordinated model for AT1R recycling.

Homogeneous TR-FRET High-Throughput Screening Assay for Calcium-Dependent Multimerization of Sorcin

A homogeneous high-throughput screening method based on time-resolved fluorescence resonance energy transfer (TR-FRET) for the measurement of calcium-dependent multimerization of an EF-hand protein, sorcin, is described. The assay is based on a specific sorcin binding peptide conjugated either with an intrinsically highly fluorescent europium chelate (donor) or an Alexa Fluor 700 fluorophore (acceptor). Addition of calcium results in multimerization of sorcin, allowing several peptides to bind simultaneously to the epitopes of the multimeric protein complex, and the proximity of peptides labeled either with donor or acceptor label results in fluorescence resonance energy transfer between the 2 labels. When no calcium is present, the protein remains in a monomer form, and thus no FRET can take place. In the optimized assay construct, the assay was performed in 45 min, and a more than 20-fold signal-to-background ratio was achieved. The reversibility of sorcin multimerization was shown by chelating free calcium with ethylenediamine tetraacetic acid (EDTA). The developed homogeneous assay can be used in screening molecules that either inhibit or enhance multimerization of sorcin, and the assay format is applicable to various noncompetitive high-throughput screening assays detecting protein multimerization reactions. ( Journal of Biomolecular Screening 2007:842-848)

Luminescent metal-ligand complexes as probes of macromolecular interactions and biopolymer dynamics

The knowledge of microsecond dynamics is important for an understanding of the mechanism and function of biological systems. Fluorescent techniques are well established in biophysical studies, but their applicability to probe microsecond timescale processes is limited. Luminescent metal-ligand complexes (MLCs) have created interest mainly due to their unique luminescent properties, such as the exceptionally long decay times and large fundamental anisotropy values, allowing examination of microsecond dynamics by fluorescence methods. MLC properties also greatly simplify instrumentation requirements and enable the use of light emitting diode excitation for time-resolved measurements. Recent literature illustrates how MLC labels take full advantage of well developed fluorescence techniques and how those methods can be extended to timescales not easily accessible with nanosecond probes. MLCs are now commercially available as reactive labels which give researchers access to methods that previously required more complex approaches. The present paper gives an overview of the applications of MLC probes to studies of molecular dynamics and interactions of proteins, membranes and nucleic acids.

Fluorometric investigation of the interaction between methylene blue and human serum albumin

The interaction between methylene blue (MB) and human serum albumin (HSA) was investigated by fluorescence spectroscopy and UV-vis absorbance spectroscopy. In the mechanism discussion, it was proved that the fluorescence quenching of HSA by MB is a result of the formation of MB-HSA complex and electrostatic interactions play a major role in stabilizing the complex. The Stern-Volmer quenching constant K(SV) and corresponding thermodynamic parameters DeltaH, DeltaG and DeltaS were calculated. Binding studies concerning the number of binding sites n and apparent binding constant Kb were performed by fluorescence quenching method. The distance r between the donor (HSA) and the acceptor (MB) was obtained according to fluorescence resonance energy transfer (FRET). Wavelength shifts in synchronous fluorescence spectra showed the conformation of HSA molecules is changed in the presence of MB.

Transforming growth factor-beta : biology and clinical relevance

Transforming growth factor-beta is a pleiotropic growth factor that has enthralled many investigators for approximately two decades. In addition to many reports that have clarified the basic mechanism of transforming growth factor-beta signal transduction, numerous laboratories have published on the clinical implication/application of transforming growth factor-beta . To name a few, dysregulation of transforming growth factor-beta signaling plays a role in carcinogenesis, autoimmunity, angiogenesis, and wound healing. In this report, we will review these clinical implications of transforming growth factor-beta .

Dynamics of Supercoiled and Linear pBluescript II SK(+) Phagemids Probed with a Long-lifetime Metal-ligand Complex

We extended the measurable time scale of DNA dynamics to microsecond using [Ru(phen)(2)(dppz)](2+)(phen = 1,10-phenanthroline, dppz=dipyrido[3,2-a:2',3'-c]phenazine)(RuPD) , which displays a mean lifetime near 500 ns. To evaluate the usefulness of this luminophore (RuPD) for probing nucleic acid dynamics, its intensity and anisotropy decays when intercalated into supercoiled and linear pBluescript (pBS) II SK(+) phagemids were examined using frequency-domain fluorometry with a blue light-emitting diode (LED) as the modulated light source. The mean lifetime for the supercoiled phagemids (<tau> = 489.7 ns) was somewhat shorter than that for the linear phagemids (<tau> = 506.4 ns), suggesting a more efficient shielding from water by the linear phagemids. The anisotropy decay data also showed somewhat shorter slow rotational correlation times for supercoiled phagemids (997.2 ns) than for the linear phagemids (1175.6 ns). The slow and fast rotational correlation times appear to be consistent with the bending and torsional motions of the phagemids, respectively. These results indicate that RuPD can have applications in studies of both bending and torsional dynamics of nucleic acids.

DNA dynamics in RecA-DNA filaments: ATP hydrolysis-related flexibility in DNA

RecA-catalyzed DNA recombination is initiated by a mandatory, high-energy form of DNA in RecA-nucleoprotein filaments, where bases are highly unstacked and the backbone is highly unwound. Interestingly, only the energetics consequent to adenosine triphosphate (ATP) binding, rather than its hydrolysis, seems sufficient to mediate such a high-energy structural hallmark of a recombination filament. The structural consequence of ATP hydrolysis on the DNA part of the filament thus remains largely unknown. We report time-resolved fluorescence dynamics of bases in RecA-DNA complexes and demonstrate that DNA bases in the same exhibit novel, motional dynamics with a rotational correlation time of 7-10 ns, specifically in the presence of ATP hydrolysis. When the ongoing ATP hydrolysis of RecA-DNA filament is "poisoned" by a nonhydrolyzable form of ATP (ATPgammaS), the motional dynamics cease and reveal a global motion with a rotational correlation time of >20 ns. Such ATP hydrolysis-induced flexibility ensues in single-stranded as well as double-stranded bases of RecA-DNA filaments. These results suggest that the role of ATP hydrolysis is to induce a high level of backbone flexibility in RecA-DNA filament, a dynamic property that is likely to be important for efficient strand exchanges in ATP hydrolysis specific RecA reactions. It is the absence of these motions that may cause high rigidity in RecA-DNA filaments in ATPgammaS. Dynamic light scattering measurement comparisons of RecA-ss-DNA filaments formed in ATPgammaS vs that of ATP confirmed such an interpretation, where the former showed a complex of larger (30 nm) hydrodynamic radius than that of latter (12-15 nm). Taken together, these results reveal a more dynamic state of DNA in RecA-DNA filament that is hydrolyzing ATP, which encourage us to model the role of ATP hydrolysis in RecA-mediated DNA transactions.

Flow-injection chemiluminescence study of Ce(IV)-Na2SO3-Tb(III)-fluoquinolone antibiotic system with DNA

A novel flow injection chemiluminescence (CL) system is developed to determine DNA. According to the fact that DNA linearly quenches the CL intensity of Ce(IV)-Na(2)SO(3)-Tb(III)-fluoquinolone antibiotic (FLUQ) system, DNA concentration is determined. The calibration graphs are linear in the range of 0.04-10 microg/ml (for both natural and denatured DNA), and the 3sigma limits of detection are 7.8 ng/ml (natural DNA) and 9.5 ng/ml (denatured DNA). According to fluorescence spectrum and CL spectrum, and through studying the reaction of Ce(IV)-Na(2)SO(3)-Tb(III)-FLUQ with nucleotides and bases, we conclude that DNA counteracts the energy transfer from FLUQ to Tb(III), and this function is related to both bases and phosphate groups in DNA.

Lengthening of fluorescence lifetimes in self-organized metal-organic assemblies

Resonance energy transfer from tris(2,2'-bipyridyl)ruthenium (II) ([Ru(bpy)3](2+)) to nile blue A is demonstrated in aqueous solution in the presence of sodium dodecyl sulfate (SDS). At SDS concentrations below the critical micelle concentration, aggregates that permit energy transfer between these dyes at optically dilute (10 microM) concentrations with nearly 100% efficiency are formed. The disparity between the lifetimes of the donor and acceptor results in the lengthening of the photoluminescence lifetime of the sensitized emission observed from nile blue A. Time-resolved luminescence measurements confirm that the long-lived components of the emission originate from sensitized acceptor emission.

Real-time background suppression during frequency domain lifetime measurements

We describe real time background suppression of autofluorescence from biological samples during frequency domain or phase modulation measurements of intensity decays. For these measurements the samples were excited with a train of light pulses with widths below 1 ps. The detector was gated off for a short time period of 10 to 40 ns during and shortly after the excitation pulse. The reference signal needed for the frequency domain measurement was provided by a long-lifetime reference fluorophore which continues to emit following the off-gating pulse. Both the sample and the reference were measured under identical optical and electronic conditions avoiding the need for correction of the photomultiplier tube signal for the gating sequence. We demonstrate frequency domain background suppression using a mixture of short- and long-lifetime probes and for a long-lifetime probe in human plasma with significant autofluorescence.

Dynamics of supercoiled and relaxed pTZ18U plasmids probed with a long-lifetime metal-ligand complex

[Ru(bpy)2(dppz)](2+) (bpy = 2,2'-bipyridine, dppz = dipyrido- [3,2-a:2',3'-c]phenazine) (RuBD), a long-lifetime metalligand complex, displays favorable photophysical properties. These include long lifetime, polarized emission, but no significant fluorescence from the complex that is not bound to DNA. To show the usefulness of this luminophore (RuBD) for probing the bending and torsional dynamics of nucleic acids, its intensity and anisotropy decays when intercalated into supercoiled and relaxed pTZ18U plasmids were examined using frequency-domain fluorometry with a blue light-emitting diode (LED) as the modulated light source. The mean lifetimes for the supercoiled plasmids (< tau > = 148 ns) were somewhat shorter than those for the relaxed plasmids (< tau > = 160 ns). This suggests that the relaxed plasmids were shielded more efficiently from water. The anisotropy decay data also showed somewhat shorter slow rotational correlation times for supercoiled plasmids (288 ns) than for the relaxed plasmids (355 ns). The presence of two rotational correlation times suggests that RuBD reveals both the bending and torsional motions of the plasmids. These results indicate that RuBD can be useful for studying both the bending and torsional dynamics of nucleic acids.

Dynamics of supercoiled and linear pTZ18U plasmids observed with a long-lifetime metal-ligand complex

The metal-ligand complex, [Ru(bpy)2(dppz)]2+ (bpy = 2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine) (Ru-BD), was used as a spectroscopic probe for studying nucleic acid dynamics. The Ru-BD complex displays a long lifetime of over 100 ns and a molecular light switch property upon DNA binding due to shielding of its dppz ligand from water. To further show the usefulness of this luminophore (Ru-BD) for probing DNA dynamics, we examined its intensity and anisotropy decays when intercalated into supercoiled and linear pTZ18U plasmids using frequency-domain fluorometry with a light-emitting diode (LED) as the modulated light source. Compared to the supercoiled plasmids with an average intensity decay time of 120.8 ns at 25 degrees C, we obtained somewhat longer lifetimes for the linear plasmids ((tau) = 141.4 ns at 25 degrees C), suggesting a more efficient shielding from water by the linear plasmids. The anisotropy decay data also showed longer rotational correlation times for the linear plasmids (495 and 35 ns at 25 degrees C) as compared to the supercoiled plasmids (412 and 27 ns at 25 degrees C). The slow and fast rotational correlation times appear to be consistent with the bending and torsional motions of the plasmids, respectively. The anisotropy values were quite similar, although the values of the supercoiled plasmids were slightly higher in both the steady-state and anisotropy decay measurements. These results indicate that Ru-BD can be applied in the study of both bending and torsional dynamics of nucleic acids.

DNA dynamics: a fluorescence resonance energy transfer study using a long-lifetime metal-ligand complex

Fluorescent probes bound to DNA typically display nanosecond decay times and reveal only nanosecond motions. We extend the time range of measurable DNA dynamics using [Ru(bpy)2(dppz)]2+ (bpy=2,2'-bipyridine, dppz=dipyrido[3,2-a:2',3'-c]phenazine) (RuBD) which displays a mean lifetime near 90 ns. To test the usefulness of RuBD as a probe for diffusive processes in calf thymus DNA, we compared the efficiencies of fluorescence resonance energy transfer (FRET) using three donors which display lifetimes near 5 ns for acridine orange (AO), 22 ns for ethidium bromide (EB) and 92 ns for RuBD, with nile blue (NB) as the acceptor. The Forster distances for AO-NB, EB-NB and RuBD-NB donor-acceptor pairs were 42.3, 52.3, and 30.6 A, respectively. All three donors showed dramatic decreases in fluorescence intensities and more rapid intensity decays with increasing NB concentrations. The intensity decays of AO and EB in the presence of varying concentrations of NB were satisfactorily described by the one-dimensional FRET model without diffusion (Blumen and Manz, 1979). In the case of the long-lifetime donor RuBD, the experimental phase and modulation somewhat deviated from the recovered values computed from this model. The recovered NB concentrations and FRET efficiencies from the model were slightly larger than the expected values, however, the recovered and expected values did not show a significant difference. Thus, it is suggested that the lifetime of RuBD is too short to measure diffusive processes in calf thymus DNA.

Lateral diffusion coefficients in membranes measured by resonance energy transfer and a new algorithm for diffusion in two dimensions

We describe measurements of lateral diffusion in membranes using resonance energy transfer. The donor was a rhenium (Re) metal-ligand complex lipid, which displays a donor decay time near 3 micros. The long donor lifetime resulted in an ability to measure lateral diffusion coefficient below 10(-8) cm(2)/s. The donor decay data were analyzed using a new numerical algorithm for calculation of resonance energy transfer for donors and acceptors randomly distributed in two dimensions. An analytical solution to the diffusion equation in two dimensions is not known, so the equation was solved by the relaxation method in Laplace space. This algorithm allows the donor decay in the absence of energy transfer to be multiexponential. The simulations show that mutual lateral diffusion coefficients of the donor and acceptor on the order of 10(-8) cm(2)/s are readily recovered from the frequency-domain data with donor decay times on the microsecond timescale. Importantly, the lateral diffusion coefficients and acceptor concentrations can be recovered independently despite correlation between these parameters. This algorithm was tested and verified using the donor decays of a long lifetime rhenium lipid donor and a Texas red-lipid acceptor. Lateral diffusion coefficients ranged from 4.4 x 10(-9) cm(2)/s in 1,2-dimyristoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (DMPG) at 10 degrees C to 1.7 x 10(-7) cm(2)/s in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) at 35 degrees C. These results demonstrated the possibility of direct measurements of lateral diffusion coefficients using microsecond decay time luminophores.