Quantification of telomerase activity by direct scintillation counting

An improved telomerase assay was developed that allows direct quantification of the enzyme activity by scintillation counting of the labeled telomerase product. The assay measures the incorporation of ³²P-dGTP into telomeric repeats synthesized at the 3′ end of a biotinylated primer. Telomerase reaction product is separated from the reaction mix by streptavidin-coated magnetic beads and counted. The assay can be used for quantitative studies of human telomerase and its inhibitors.     

An interference-free fluorescent assay of telomerase for the high-throughput analysis of inhibitors

We have developed a telomerase assay that can quickly and accurately rank the ability of molecules to inhibit telomerase activity. It is based on the method of Orlando and co-workers which utilizes PicoGreen to detect dsDNA formed during the polymerase chain reaction (PCR) amplification of telomerase products. PCR cycles were optimized to give as linear a signal as possible relative to telomerase products; 96-well streptavidin-coated PCR plates were used to isolate the preamplification telomerase products and to wash inhibitors away before the amplification step. The inhibitor removal step is critical to prevent false positives potentially caused by inhibition of Taq polymerase during amplification. Use of the streptavidin-coated PCR plate allows this step to be done much more rapidly than use of the liquid/liquid extraction adopted by others. We have demonstrated that this assay can correctly order the ability of four inhibitors to inhibit telomerase and reproduce within a factor of two the absolute IC(50) values determined by the more time-consuming direct assay. We have shown that the difference in IC(50) values determined in this assay versus the direct assay can be corrected for by using the standard curve appropriately. Using this method 96 compounds can be assessed in 3-5h.     

Nonradioactive detection of telomerase activity using the telomeric repeat amplification protocol

The telomeric repeat amplification protocol (TRAP) is a two-step process for analyzing telomerase activity in cell or tissue extracts. Recent modifications of this sensitive assay include elimination of radioactivity by using a fluorescently labeled primer instead of a radiolabeled primer. In addition, the TRAP assay has been modified for real-time, quantitative PCR analysis. Here, we describe cost-effective procedures for detection of telomerase activity using a fluorescent-based assay as well as by using real-time PCR. These modified TRAP assays can be accomplished within 4 h (from lysis of samples to analysis of telomerase products).     

Specific binding of telomeric G-quadruplexes by hydrosoluble perylene derivatives inhibits repeat addition processivity of human telomerase

Telomerase is responsible for the immortal phenotype of cancer cells and telomerase inhibition may specifically target cancer cell proliferation. Ligands able to selectively bind to G-quadruplex telomeric DNA have been considered as telomerase inhibitors but their mechanisms of action have often been deduced from a non-quantitative telomerase activity assay (TRAP assay) that involves a PCR step and that does not provide insight on the mechanism of inhibition. Furthermore, quadruplex ligands have also been shown to exert their effects by affecting association of telomere binding proteins with telomeres. Here, we use quantitative direct telomerase activity assays to evaluate the strength and mechanism of action of hydrosoluble perylene diimides (HPDIs). HPDIs contain a perylene moiety and different numbers of positively charged side chains. Side chain features vary with regard to number and distances of the charges. IC₅₀ values of HPDIs were in the low micromolar (0.5–5 μM) range depending on the number and features of the side chains. HPDIs having four side chains emerged as the best compounds of this series. Analysis of primer elongation products demonstrated that at low HPDI concentrations, telomerase inhibition involved formation of telomeric G-quadruplex structures, which inhibited further elongation by telomerase. At high HPDI concentrations, telomerase inhibition occurred independently of G-quadruplex formation of the substrate. The mechanism of action of HPDIs and their specific binding to G-quadruplex DNA was supported by PAGE analysis, CD spectroscopy and ESI-MS. Finally, competition Telospot experiments with duplex DNA indicated specific binding of HPDIs to the single-stranded telomeric substrates over double stranded DNA, a result supported by competitive ESI-MS. Altogether, our results indicate that HPDIs act by stabilizing G-quadruplex structures in single-stranded telomeric DNA, which in turn prevents repeat addition processivity of telomerase.     

Different approaches for the detection of thrombin by an electrochemical aptamer-based assay coupled to magnetic beads

Different assay formats based on the coupling of magnetic beads with electrochemical transduction were compared here for the detection of thrombin by using a thrombin specific aptamer. By using the thrombin-binding aptamer, a direct and an indirect competitive assay for thrombin have been developed by immobilising the aptamer or the protein, respectively. Moreover, another strategy was based on the direct measurement of the enzymatic product of thrombin captured by the immobilised aptamer. All the assays were developed by coupling the electrochemical transduction with the innovative and advantageous use of magnetic beads.

The assays based on the immobilisation of the protein were not successful since no binding was recorded between thrombin and its aptamer. With the direct competitive assay, when the aptamer was immobilised onto the magnetic beads, a detection limit of 430 nM for thrombin was achieved. A lower detection limit for the protein (175 nM) was instead obtained by detecting the product of the enzymatic reaction catalysed by thrombin. All these assays were finally compared with a sandwich assay which reached a detection limit of 0.45 nM of thrombin demonstrating the best analytical performances.

With this comparison the importance of a deep study on the different analytical approaches for thrombin detection to reach the performances of the best assay configuration has been demonstrated.     

Localized transfection with magnetic beads coated with PCR products and other nucleic acids

The bead transfection method involves binding nucleic acids onto 3-microm-diameter paramagnetic beads, treating the beads with transfection reagent, and using them as scaffolds to direct transfection to individual cells or regions in a population. Typically, PCR products are used because they can be conveniently generated using biotinylated primers and can introduce site-directed mutations, without the need for cloning or plasmid purification. However, the method can be adapted to transfect plasmid DNA or RNA. The magnetic properties of the beads allows magnets to direct the loci of transfection in cell culture; magnetic arrays are built in cell culture chambers to allow multiple parallel transfections on the same microscope coverslip. The PCR reaction and transfection can be carried out in 1 d, and transfection results can be viewed in 24-48 h.     

Use of the polymerase chain reaction and 16S rRNA sequences for the rapid detection of Brochothrix spp. in foods

Oligonucleotide primers were designed against rRNA sequences to give a DNA-based PCR assay for the rapid identification/detection of Brochothrix spp. The PCR products could be confirmed by hybridization to an internal oligonucleotide probe. The method successfully and sensitively detected/identified these organisms in pure cultures but was of limited value as a detection method because the detection sensitivity, in relation to conventional plate counts, varied and the assay sensitivity was reduced in the presence of staphylococci. Furthermore, sensitivity was also lost when the assay was applied directly to meat samples. However, a separation step using a lectin (from Agaricus bisporus ) immobilized on magnetic beads prior to the PCR assay, allowed the direct detection of low numbers (> 10 cfu g^-1) of Brochothrix in meat samples within a working day.     

Microscopic mechanisms influencing the volume amplified magnetic nanobead detection assay

The volume amplified magnetic nanobead detection assay [Str?mberg, M., G?ransson, J., Gunnarsson, K., Nilsson, M., Svedlindh, P., Str?mme, M., 2008. Nano Letters 8, 816-821] was investigated with respect to bead size, bead surface coverage of probe oligonucleotides, bead concentration and rolling circle amplification (RCA) time, with the objective to improve the understanding of the microscopic mechanisms influencing the assay. The most important findings for future biosensor development were the following: (i) small beads exhibit a much reduced tendency to cross-link several RCA products, thus enabling use of both complex magnetisation turn-on and turn-off detection strategies, whereas larger beads only allow for turn-off detection; (ii) small beads exhibit faster immobilisation kinetics, thus reducing the time for diagnostic test completion, and also immobilise in larger numbers than larger beads. Finally, (iii) by demonstrating qualitative dual-target detection of bacterial DNA sequences using 130 and 250nm beads, the bioassay was shown to allow for multiplexed detection.     

CUT&Tag产物回收和建库方法的优化

新兴的染色质靶向切割和标签化(clevage under target and tagment,CUT&Tag)技术利用转座酶在目标蛋白结合的DNA附近进行切割并对切割下的DNA片段进行标签化,通过后续的二代测序可以快速鉴定蛋白质-DNA相互作用,极大的简化了染色质免疫共沉淀测序(chromatin immunoprecipitation sequencing,ChIP-seq)的实验过程。CUT&Tag中转座酶完成标签化后需要DNA回收或其他后处理才能进行建库PCR,不同的回收方法对CUT&Tag结果有着显著的影响。通过建立生物素化转座体-链霉亲和素磁珠体系(streptavidin beads recovery CUT&Tag,srCUT&Tag),可以快速便捷地完成CUT&Tag的产物回收。本文在K562细胞中展开H3K4me3、RNA聚合酶Ⅱ(RNA polymeraseⅡ,RNAPⅡ)、转录因子CTCF和HMGA1的CUT&Tag实验,并利用现有的乙醇沉淀、片段分选(solid-phase reversible immobilization,SPRI)磁珠回收和直接PCR法,以及本研究建立的srCUT&Tag方法对产物进行回收。结果表明,从整体上看,SPRI磁珠回收和srCUT&Tag方法着较高的回收效率,而乙醇沉淀法则回收效率低下。在全部4种CUT&Tag产物回收过程中,SPRI磁珠回收均会损失大部分小于150 bp的产物片段。在CTCF和HMGA1 CUT&Tag产物的回收中,直接PCR法则损失了大部分大于300 bp的片段并与其他回收方法的结果有较大的差别。因此,srCUT&Tag能够比其他三种回收方法提供更多更完整的测序信息。综上所述,新建立srCUT&Tag回收方法相比现有的CUT&Tag产物回收方法能提高建库效率并得到更好的数据质量,为表观遗传学研究提供了更好的技术选择。     

Quantitation of polymerase chain reaction products by hybridization-based assays with fluorescent, colorimetric, or chemiluminescent detection.

In this report two nonradioactive assays for quantitative analysis of polymerase chain reaction (PCR) products are presented. In the first assay, magnetic beads coated with streptavidin were used to capture biotinylated PCR fragments. After hybridization with a hapten-labeled probe, these beads were analyzed either by flow cytometry (method A) or by immunoenzymatic reactions (method B). Using a dilution series of purified PCR products, we consistently found a lower detection limit of 1.5 fmol for method A than the 0.15-fmol limit for method B. In the second assay we used the peroxidase-based enhanced chemiluminescence system in combination with a cooled charge-coupled device camera to quantify PCR fragments that were spotted on membranes. A linear logarithmic response was observed between the amount of light produced within a certain time interval and the number of DNA molecules. With an exposure time of 5 min, a detection limit of 0.15 fmol was found. Longer exposure times did not result in a higher sensitivity. We conclude that the assays are of sufficient sensitivity for application in quantitative PCR strategies. The nonradioactive technology facilitates implementation of these assays in routine settings.     

Advances in quantification and characterization of telomerase activity by the telomeric repeat amplification protocol (TRAP).

The telomeric repeat amplification protocol (TRAP) assay has been used to test telomerase activity in numerous cancer specimens. We describe primers, controls and quantification methods for the TRAP assay to accurately measure the level of telomerase activity in clinical samples. The assay is reliable and reproducible in routine analyses and can be used to estimate the processivity of telomerase activity.     

SYBR Green real-time telomeric repeat amplification protocol for the rapid quantification of telomerase activity

The sensitive telomeric repeat amplification protocol (TRAP) permits telomerase detection in mammalian cell and tissue extracts with very low telomerase activity levels. Unfortunately, conventional TRAP assays require complex post-amplification procedures, such as polyacrylamide gel electrophoresis and densitometry, to measure telomerase products. Therefore, a real-time quantitative TRAP assay (RQ-TRAP) was optimized in the present study and evaluated in comparison with a commercially available quantitative TRAP kit and by monitoring telomerase activity in human hepatocyte cultures, human hepatoma cell lines and telomerase reconstitution experiments. The novel real-time telomerase detection method has many advantages. Other than sample extraction and real-time cycling, no additional time-consuming steps have to be performed for telomerase quantification; reliable and linear telomerase quantification is possible down to single-cell dilutions without the interference of primer-dimer artifacts, and the costs are less. Moreover, the precision is similar to other amplification-based telomerase quantification assays and the results are comparable to data obtained with two commercially available assays. The closed-tube system reduces the risk of carryover contamination and supports high throughput. In conclusion, RQ-TRAP provides a new tool for the rapid and reliable quantification of telomerase activity.     

Emerging role of p53, bcl-2 and telomerase activity in Egyptian breast cancer patients

Apoptotic cell death represents an important mechanism for the precise regulation of cell numbers, and a defense mechanism against tumor cells. Both bcl-2 and mutant p53 gene products have been involved in apoptotic pathways. On the other hand, cell proliferation capacity and tumorgenesis have been controlled by telomerase. The purpose of our study is to assess the prognostic significance of additional markers implicated in apoptosis and tumorgenesis. Fifty-one fresh tissue samples of primary breast carcinoma and 26 tissue samples of benign breast lesions were included in this study. Expression of bcl-2 in cell lysates and mutant p53 protein in nuclear fraction were measured by Oncogene Science EIA procedures. Telomerase activity was analyzed using the Telomerase-PCR-ELISA based on the TRAP (telomerase repeat amplification protocol) method. On the same specimens, steroid hormone receptors (ER and PgR) were measured in cytosol fraction using Abbott EIA assays. In addition, information regarding surgical-pathological features of the tumor was obtained. Univariate and Multivariate analysis was done to identify variables predictive of poor prognosis. Significant expression of bcl-2, mutant p53 proteins and relative telomerase activity were observed in malignant cases when compared to benign ones. Univariate analysis revealed significant association in the level of both mutant p53 and relative telomerase activity with tumor size and disease recurrence. Moreover, telomerase activity was significantly expressed in late stages than early ones. Multivariate analysis revealed that bcl-2, mutant p53, telomerase activity, PgR and age were independent prognostic factors. Among a panel of molecular genetic factors investigated, mutant p53 and relative telomerase activity were strongly associated with disease recurrence; hence they exert a significant prognostic role in breast cancer.     

Coupled-enzyme and direct assays for uroporphyrinogen III synthase activity in human erythrocytes and cultured lymphoblasts: Enzymatic diagnosis of heterozygotes and homozygotes with congenital erythropoietic porphyria

Rapid and reproducible assays for uroporphyrinogen III synthase (URO-S; EC 4.2.1.75) have been developed and used to determine the enzymatic activity in human erythrocytes and cultured lymphoid cells. In the coupled-enzyme assay, porphobilinogen was first converted to hydroxymethylbilane, the natural substrate for URO-S, by hydroxymethylbilane synthase which was conveniently obtained from heat-treated erythrocyte lysates. In the direct assay, synthetic hydroxymethylbilane was used as substrate. In both assays, the uroporphyrinogen reaction products were oxidized to their respective uroporphyrin isomers, which were then resolved and quantitated by reversed-phase high-pressure liquid chromatography. Both assays were optimized for pH, substrate concentration, and linearity with time and protein concentration. The mean URO-S activities in normal human erythrocyte lysates determined by the coupled-enzyme and direct assays were 7.41 ± 1.35 and 7.64 ± 1.73 units/mg protein, respectively. In normal human cultured lymphoid cells, the mean activities were 13.7 ± 1.39 and 17.6 ± 1.15 units/mg protein for the coupled-enzyme and direct assays, respectively. In four families with congenital erythropoietic porphyria, both assays reliably identified the markedly decreased URO-S activities in erythrocytes and cultured lymphoid cells from affected homozygotes and the half-normal activities in these sources from obligate heterozygotes. The coupled-enzyme assay was easier to perform and was suited for clinical diagnostic assays and for monitoring enzyme purification procedures, while the direct assay, which required substrate preparation and technical dexterity, was best for kinetic studies of URO-S.     

Use of magnetic beads in selection and detection of biotoxin aptamers by electrochemiluminescence and enzymatic methods.

Systematic evolution of ligands by exponential enrichment (SELEX) was used to develop DNA ligands (aptamers) to cholera whole toxin and staphylococcal enterotoxin B (SEB). Affinity selection of aptamers was accomplished by conjugating the biotoxins to tosyl-activated magnetic beads. The use of magnetic beads reduces the volumes needed to perform aptamer selection, thus obviating alcohol precipitation and allowing direct PCR amplification from the bead surface. Following five rounds of SELEX, 5'-biotinylated aptamers were bound to streptavidin-coated magnetic beads and used for the detection of ruthenium trisbypyridine [Ru(bpy)3(2+)]-labeled cholera toxin and SEB by an electrochemiluminescence methodology. A comparison of control (double-stranded) aptamer binding was made with aptamers that were heat denatured at 96 degrees C (single-stranded) and allowed to cool (conform) in the presence of biotoxin-conjugated magnetic beads. Results suggest that control aptamers performed equally well when compared to heat-denatured DNA aptamers in the cholera toxin electrochemiluminescence assay and a colorimetric microplate assay employing peroxidase-labeled cholera toxin and 5'-amino terminated aptamers conjugated to N-oxysuccinimide-activated microtiter wells. Interestingly, however, in the SEB electrochemiluminescence assay, double-stranded aptamers exceeded the performance of single-stranded aptamers. The detection limits of all aptamer assays were in the low nanogram to low picogram ranges.     

Microarray TRAP--a high-throughput assay to quantitate telomerase activity

Telomeric repeat amplification protocol (TRAP)--a sensitive, PCR-based assay to detect telomerase activity was quintessential to the evaluation of telomerase role in telomere maintenance, cell proliferation, tumour development, and cell immortalization. The assay, however, suffers from many limitations. The most significant are: lack of telomerase activity quantification, changes of the enzyme activity product size and/or ratio, and complex post-amplification procedures which limit the assay throughput. Here we report the development of the microarray TRAP (MTRAP) assay which combines advantages of microarray technology with a modified TRAP assay. The MTRAP was designed and optimized on rice cell suspension telomerase extract to enable telomerase specific, reliable, and linear quantification in high throughput mode, with sensitivity comparable to those of radioisotope-based TRAP assays. The MTRAP has a built-in system guaranteeing the amplification of telomerase activity products unchanged in length and/or ratio and built-in control for false negatives. Thus, our MTRAP assay provides new reliable tool for experiments requiring massive quantitation of telomerase activity.     

Assay of intercellular adhesiveness using cell-coated Sephadex beads as collecting particles.

A simple, rapid and precise method, based on a previous method, for measuring relative rates of intercellular adhesion is described. DEAE-Sephadex beads were treated with nitrocellulose in order to allow cells to grow on their surfaces. Balb/c 3T3 and Balb/c 3T12 cells were used to characterize the assay. They formed confluent cell layers on nitrocellulose-treated DEAE-Sephadex. These cell-coated beads were employed to collect 32P-labelled cells from single cell suspensions. Since they formed statistically uniform, large collecting surfaces, the collection of labelled cells was markedly improved as compared to the original assay. The cell-coated beads collected a large percentage of the labelled cells in a short time. The percentage of cells collected was independent of the concentration of labelled cells in the assay mixture, and the collection was linear for approximately 60 min. The variability between replicate assays was usually +/- 5%. The assay allows the rapid and precise determination of intercellular adhesion in large numbers of individual samples. These features make it useful to screen for effects of different treatments on intercellular adhesions.     

Rapid, femtomolar bioassays in complex matrices combining microfluidics and magnetoelectronics

A significant challenge for all biosensor systems is to achieve high assay sensitivity and specificity while minimizing sample preparation requirements, operational complexity, and sample-to-answer time. We have achieved multiplexed, unamplified, femtomolar detection of both DNA and proteins in complex matrices (including whole blood, serum, plasma, and milk) in minutes using as few as two reagents by labeling conventional assay schemes with micrometer-scale magnetic beads, and applying fluidic force discrimination (FFD). In FFD assays, analytes captured onto a microarray surface are labeled with microbeads, and a controlled laminar flow is then used to apply microfluidic forces sufficient to preferentially remove only nonspecifically bound bead labels. The density of beads that remain bound is proportional to the analyte concentration and can be determined with either optical counting or magnetoelectronic detection of the magnetic labels. Combining FFD assays with chip-based magnetoelectronic detection enables a simple, potentially handheld, platform capable of both nucleic acid hybridization assays and immunoassays, including orthogonal detection and identification of bacterial and viral pathogens, and therefore suitable for a wide range of biosensing applications.