Seven-color time-resolved fluorescence hybridization analysis of human papilloma virus types

A low density microarray method for the identification of human papillomavirus type 18 variants

We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18's variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings.

Chemiluminescence Energy Transfer Reaction for the On-Line Preparation of Peroxymonocarbonate and Eu(II)−Dipicolinate Complex

In this work, an on-line preparation of peroxymonocarbonate was formed innovatively, which offered a reliable intermediate for further investigation. The forming conditions of on-line peroxymonocarbonate ions were investigated in detail. Meanwhile, the energy transfer chemiluminescent reaction of peroxymonocarbonate and the Eu(II)-dipicolinate complex was studied. Through UV-visible absorption spectra, CL method, ESR spin-trapping technique, and mass spectrum experiments, it can be concluded that peroxymonocarbonate oxidizes Eu(II) to Eu(III), and simultaneously creates radicals. The bond rearrangement within radicals formed the singlet molecular oxygen. The energy originating from the singlet oxygen was accepted by the (Eu(III)dipic)- complex. The excited (Eu(III)dipic)- ions underwent radiative deactivation and emitted the chemiluminescence. The peroxymonocarbonate system was a simple, inexpensive, and relatively nontoxic alternative to other oxidants, and it can be used in a mild, neutral-pH environment.

Progress in Lanthanides as Luminescent Probes

Lanthanides have recently found applications in different fields of biomolecular and medical research. Luminescent lanthanide chelates have created interest mainly due to their unique luminescent properties, such as their long Stokes' shift and exceptional decay times allowing efficient temporal discrimination of background interferences in the assays, such as immunoassays. Recently, new organometallic complexes have been developed giving opportunities to novel applications, in heterogeneous and homogeneous immunoassays, DNA hybridization assays, high-throughput screening as well as in imaging. In addition, encapsulating the chelates into suitable matrix in beads enables the use of new members of lanthanides extending the emission wavelength to micrometer range and decays from a few microseconds to milliseconds. As the luminescence is derived from complicated intra-chelate energy transfer, it also gives novel opportunities to exploit these levels in different types of energy transfer based applications. This review gives a short overview of recent development of lanthanide chelate-labels and discusses in more details of energy levels and their exploitation in new assay formats.

Synthesis, Characterization, and Application of Eu(III), Tb(III), Sm(III), and Dy(III) Lanthanide Chelate Nanoparticle Labels

Preparation and characterization of europium(III), terbium(III), samarium(III), and dysprosium(III) polystyrene nanoparticle labels with lanthanide-specific fluorescence properties has been presented. Emulsion copolymerization of styrene and acrylic acid was used to synthesize uniform-sized nanoparticles approximately 45 nm in diameter. Europium(III) and samarium(III) lanthanides were chelated with 2-naphthoyltrifluoroacetone and trioctylphosphine oxide to dye the spherical particles, whereas terbium(III) and dysprosium(III) chelate complexes contained a newly synthesized ligand, 4-(2,4,6-tridecyloxyphenyl)pyridine-2,6-dicarboxylic acid. The fluorescence properties of the four lanthanides-including a wide Stokes shift, a narrow emission peak, and long fluorescence lifetime-were retained despite the incorporation into the nanoparticles. Furthermore, the nanoparticles, containing more than 1000 lanthanide chelates, were detectable at label concentrations 3 orders of magnitude lower than the corresponding soluble lanthanide chelate labels. The applicability of the labels prepared was demonstrated by a heterogeneous sandwich-type immunoassay for human prostate-specific antigen, where the lowest limits of detection of 1.6, 2.4, 10.1, and 114.2 ng/L were achieved using europium(III), terbium(III), samarium(III), and dysprosium(III) nanoparticles, respectively. The spectral and functional properties of the lanthanide-embedded polystyrene nanoparticles developed here suggest that the technology is applicable for high-sensitivity multicolor assays.

Spectrofluorimetric Determination of Trace Amounts of Europium(III) Ion with Lutetium(III)-Sparfloxacin-Sodium Dodecyl Sulfate Luminescence Enhancement System

A new luminescence-enhancement system based on complex formation between europium and sparfloxacin in the presence of lutetium in a sodium dodecyl sulfate solution has been discovered. By adding a suitable amount of Lu3+ to the Eu-sparfloxacin-sodium dodecyl sulfate system, the luminescence can be enhanced by approximately 5-fold compared with that of the system without Lu3+. Under the optimum conditions, the luminescence intensity of the system is a linear function of the concentration of europium in the range of 1.0 x 10(-10) - 5.0 x 10(-7) mol L(-1). The detection limit of europium is 2.0 x 10(-13) mol L(-1) (S/N = 3). The system was used for the determination of trace amounts of europium in rare earth samples with satisfactory results.

Real-time PCR-based system for simultaneous quantification of human papillomavirus types associated with high risk of cervical cancer

We have previously shown that women with a high titer of human papillomavirus type 16 (HPV16) in cervical epithelial cells have an increased risk of developing cervical carcinoma in situ. In order to study the relationship between viral DNA amount and risk of cervical carcinoma for the HPV types most commonly found in cervical tumors, we developed a real-time PCR assay for the detection and quantification of HPV16, -18, -31, -33, -35, -39, -45, -52, -58, and -67. These HPV types are analyzed in two reaction tubes, allowing for independent quantification of three viral types, or groups of viral types, in each reaction. A separate reaction is used for estimating the number of a nuclear single-copy gene and is used to calculate the HPV copy number per genomic DNA equivalent in the sample. The system has a dynamic range from 10(2) to 10(7) HPV copies per assay and is applicable to both fresh clinical samples and DNA extracted from archival samples. Reconstitution experiments, made to mimic infections with several HPV types, shows that individual HPV types can be detected in a mixture as long as they represent 1 to 10% of the main type. The system was evaluated with respect to technical specificity and sensitivity, reproducibility, reagent stability, and sample preparation protocol and then used to analyze clinical samples. This homogeneous assay provides a fast and sensitive way for estimating the viral load of a series of the most frequent oncogenic HPV types in biopsies, as well as cervical smear samples.

Fluorescence in situ hybridization (FISH) on human chromosomes using photoprobe biotin-labeled probes

Fluorescence in situ hybridization (FISH) on human chromosomes in meta- and interphase is a well-established technique in clinical and tumor cytogenetics and for studies of evolution and interphase architecture. Many different protocols for labeling the DNA probes used for FISH have been published. Here we describe for the first time the successful use of Photoprobe biotin-labeled DNA probes in FISH experiments. Yeast artificial chromosome (YAC) and whole chromosome painting (wcp) probes were tested.

Effects of Metallic Silver Particles on Resonance Energy Transfer Between Fluorophores Bound to DNA

We examined the effects of metallic silver island films on resonance energy transfer (RET) between a donor and acceptor bound to double helical DNA. The donor was 4',6-diamidino-2-phenylindole (DAPI) and the acceptor was propidium iodide (PI). Proximity of the labeled DNA to the silver particles resulted in a dramatic increase in RET as seen from the emission spectra and the donor decay times. Proximity to silver particles results in an increase of the Förster distance from 35 Å to an apparent value of 166 Å_. These results suggest a new type of DNA hybridization assays based on RET over distances much longer than the free-space Forster distance.

High-performance real-time quantitative RT-PCR using lanthanide probes and a dual-temperature hybridization assay

We report a time-resolved fluorescence-based, homogeneous approach for multiplex, real-time or end-point detection of PCR products. Signal generation consists of PCR associated digestion of a 5'-labeled oligonucleotide probe, rapid cooling of the reaction mixture, and hybridization of undigested probe oligonucleotides with a complementary, shorter probe that incorporates a quencher at its 3' end. The signal coming from intact fluorescent probe molecules is, thus, quenched. The fluorophores we have used are environmentally sensitive lanthanide chelates. Their signals can be measured in a time-resolved manner that eliminates most of the unspecific fluorescent background. Signal-to-noise ratios are further enhanced by the environmental sensitivity of these chelates; they exhibit a higher fluorescence intensity when free in solution than when coupled to intact probe molecules. Because of the minimal background fluorescence, the signal-to-noise ratios are higher and threshold cycles are lower than those obtained using conventional TaqMan probes. The multiplexing capacity of the assay chemistry is demonstrated through simultaneous amplification and detection of prostate specific antigen (PSA) cDNA and an internal standard mRNA (mmPSA) using probes labeled with terbium and europium. The applicability of the assay chemistry to routine clinical diagnostics is demonstrated through absolute quantification of PSA mRNA in peripheral blood.

Multi-Photon Sensitized Excitation of Near Infrared Emitting Lanthanides

Near infrared (NIR) multi-photon excitation of the NIR-emitting lanthanides neodymium (Nd³⁺) and ytterbium (Yb³⁺) sensitized by a fluorescein-linked chelator was demonstrated. Because tissues display minimal absorbance near the excitation wavelength of 800 nm, and because the lanthanides display long decay times, these results suggest the use of Nd³⁺ and Yb³⁺ as luminescent probes in tissues with multi-photon excitation.

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.

Time-resolved fluorometry in end-point and real-time PCR quantification of nucleic acids

Two time-resolved fluorescence-based methods for nucleic acid quantification are described and their results are compared. Both methods use an exogenous internal standard to eliminate errors arising from different steps of the assay. The first method is a competitive end-point assay, where the standard competes for the same primers with the actual target sequence, prostate-specific antigen (PSA) cDNA. The standard and target are quantified in a dual-label plate hybridization with lanthanide-labelled probes after a fixed number of PCR cycles. The second method is based on real-time monitoring of PCR and on the use of a novel homogeneous signal generation principle that relies on the use of a 5'-->3' exonucleolytic DNA polymerase and a probe labelled with an environment sensitive, stable and fluorescent lanthanide chelate. In this assay, a non-competitive, exogenous internal standard is used. Both assays have a wide linear range (50-5 x 10(6) and 10-5 x 10(7) input PSA cDNA molecules for the end-point and real-time assays, respectively) and there is a strong correlation between the results obtained with the two assays (r = 1.0). Being somewhat faster to perform, the real-time format is better suited for assays that require high throughput.

Fluorescence techniques: shedding light on ligand-receptor interactions

The ability of organisms, or individual cells, to react to external chemical signals, which are detected and transduced by cell-surface receptors, is crucial for their survival. These receptors are the targets of the majority of clinically used medicines. Combinatorial genetics can provide almost unlimited numbers of mutant receptor proteins and combinatorial chemistry can produce large libraries of potential therapeutic compounds that act on these membrane receptors. What is missing for the fundamental understanding of receptor function and for the discovery of new medicines are efficient procedures to screen both ligand-receptor interactions and the subsequent functional consequences. Ultrasensitive fluorescence spectroscopic approaches, in combination with efficient labelling protocols, offer enormous possibilities for highly parallel functional bioanalytics at the micro- and nanometer level.

Molecular genetic applications of streptavidin-coated manifold supports

Practical problems of handling large numbers of samples limit the application of molecular genetic procedures in clinical settings and in research. In the present review we describe a multipronged manifold support, coated with streptavidin, that offers distinct advantages in preparative and diagnostic applications. In order to increase the surface available on the manifold, porous Sepharose particles conjugated with streptavidin were attached to the plastic support. This procedure increased the surface by almost three orders of magnitude, permitting sufficient streptavidin to be coupled to the support for most routine applications. The manifold supports have been used for sample preparation and in a number of genetic assays, including allele discrimination assays and DNA sequencing, In all these assay formats the manifold supports allow large numbers of samples to be processed in parallel.

Color multiplexing hybridization probes using the apolipoprotein E locus as a model system for genotyping

Fluorescent hybridization probes were multiplexed for color genotyping of the apolipoprotein E locus using model oligonucleotide targets. Fluorescence resonance energy transfer was observed during adjacent hybridization of 3'-fluorescein-labeled "donor" probes paired with 5'-labeled "acceptor" probes with different emission spectra reporting at codons 112 and 158. The acceptor dyes emitted at either 640 nm (LightCycler Red 640) or 705 nm (LightCycler Red 705) and were monitored with a LightCycler, a thermal cycler with an integrated fluorimeter. The color of the acceptor dye identified each site and the characteristic melting temperatures of the fluorescein-labeled probes identified single base changes within each codon. Color compensation of temperature-dependent spectral overlap was applied to completely separate each channel. Competition between the probes and the complementary strand for the target sequence decreased resonance energy transfer, indicating an advantage of single-stranded target. Hybridization probes of the same length, but different GC content are T(m) shifted by the same amount during A:C mismatch duplex melting. Genotyping was optimal at both sites if melting curve analysis was preceded by a slow (1 degrees C/s) annealing phase. Although each site preferred different concentrations of Mg(2+) and target strand for optimal genotyping, conditions for multiplexing were found. This method, along with an appropriate amplification technique, should allow real-time multiplex genotyping from genomic DNA.

Homogeneous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes

Multiplex polymerase chain reaction amplification and genotyping by fluorescent probe melting temperature (Tm) was used to simultaneously detect multiple variants in the hereditary hemochromatosis gene. Homogenous real-time analysis by fluorescent melting curves has previously been used to genotype single base mismatches; however, the current method introduces a new probe design for fluorescence resonance energy transfer and demonstrates allele multiplexing by Tm for the first time. The new probe design uses a 3'-fluorescein-labeled probe and a 5'-Cy5-labeled probe that are in fluorescence energy transfer when hybridized to the same strand internal to an unlabeled primer set. Two hundred and fifty samples were genotyped for the C282Y and H63D hemochromatosis causing mutations by fluorescent melting curves. Multiplexing was performed by including two primer sets and two probe sets in a single tube. In clinically defined groups of 117 patients and 56 controls, the C282Y mutation was found in 87% (204/234) of patient chromosomes, and the relative penetrance of the H63D mutation was 2.4% of the homozygous C282Y mutation. Results were confirmed by restriction enzyme digestion and agarose gel electrophoresis. In addition, the probe covering the H63D mutation unexpectedly identified the A193T polymorphism in some samples. This method is amenable to multiplexing and has promise for scanning unknown mutations.