Polymerase chain reaction detection limits

A variation on the theme of conventional assay uses both lanthanide-labeled and biotin-labeled single strands to form split probes for sequence of target strands (Figure 12).120 When both of these bind to DNA, the complex binds (via the biotin residue) to a surface functionalized with streptavidin, immobilizing the europium and allowing assay to be carried out. This approach is already very sensitive to DNA sequence, since both sequences must match to permit immobilization of the lanthanide, but can be made even more sensitive by using PCR (the polymerase chain reaction) to enhance the concentration of DNA strands. In this way, initial concentrations corresponding to as few as four million molecules can be detected. This compares very favorably with radioimmunoassay detection limits. 

Antibody-based detection methods include immuno-cytochemistry, which gives qualitative data but has very good spatial resolution. Radioimmunoassays provide a quantitative measure of release or content. One of the major limitations of all antibody-based methods is the potential for cross-reactivity among the many peptides. For example, some of the most sensitive gastrin antisera also detect CCK, since the peptides share a common COOH-terminal tetrapeptide sequence. Methods for detection of the mRNAs encoding neuropeptides include Northern blots, which provide quantitative data and information on splice variants, but lack fine anatomical resolution. The more commonly used polymerase chain reaction, which can be quantitative but often is used in a more qualitative manner, provides great sensitivity. Alternatively, in situ hybridization preserves anatomical relationships and can be used to obtain both qualitative and quantitative data. 

The traditional microbiological methods are very time consuming and sometimes limited concerning their interpretation. For that reason fast analysis methods as well as automated methods have been developed the latter are often used in specialised microbiological laboratories. During the last few years more and more modern biotechnological methods have been implemented into quality control, for example the enzyme-linked immunosorbent assay or more recently the polymerase chain reaction, which allows the detection of very specific microorganisms. 

Conventionally, the variants are characterized by coamplification with wild-type sequences using reverse transcription polymerase chain reaction (RT-PCR). However, this approach focuses on small regions of the known wild-type mRNA. Because of this threshold detection, spliced transcripts expressed at low levels may fall below the threshold of detection. To avoid this and other limitations of the conventional RT-PCR technique, the targeted amplification method can be used (Poola et al., 2000). This method involves the targeted amplification of the alternatively spliced molecules as separate gene populations using specific primers designed for the alternative splice junctions, without coamplification of wild-type molecules. 

Eig. 5. Several endpoint detection methods were compared for the detection of immuno-polymerase chain reaction (IPCR) amplificate from a direct IPCR (Fig. 3A) of mouse-IgG. Although all IPCR/DNA-detection combinations were able to improve the detection limit of a comparable enzyme-linked immunosorbent assays (ELISA) of approximately 10 amol IgG in a 30-fL sample volume, several differences were observed in actual detection limit, and the linearity of the concentration/signal ratio dependent on the DNA quantification was applied. Best results were obtained for PCR-ELISA (see also Fig. 6) in combination with fluorescence- or chemiluminescence-generating substrates (b, c). With photometric substrates (d) or gel electrophoresis and subsequent spot densitometry (a), a 10-fold decrease in sensitivity was observed. In addition to the more sigmoid curve in gel electrophoresis, an enhanced overall error of 20% compared to 13% in PCR-ELISA was observed for two independent assays. The simple addition of a double-strand sensitive intercalation marker to the PCR-amplificate and measurement in a fluorescence spectrometer further decreased sensitivity (e) and appears therefore to be unsuited for IPCR amplificate quantification. (Figure modified according to references 37 and 65.)... 

Detection with a microchip is primarily through LIF, since this is eashy implemented with the planar configuration of the microchip (Figure 5-10). Limits of detection for fluorescein-like fluors have been easily demonstrated at the 10 M level and pushed as low as 10 M—a mass detection limit of a few hundred molecules. This allows for detection, for example, of polymerase chain reaction (PCR)-amplified DNA fragments at a level that competes with P-autoradiography jffom Southern blots. Typical microchip separation times are around 50 to 200 seconds. 

In the absence of an unambiguous history of ricin exposure, the preferred diagnostic method is specific immunoassay of ricin in serum, respiratory secretions, or other clinical samples associated with poisoning. Most of the methods described for ricin detection are experimental or are under development. The CDC and the Federal Laboratory Response Network have the capability to detect ricin in environmental specimens using validated polymerase chain reaction (PCR) tests and time-resolved immunofluorescence assays, with cell-based bioassays to confirm ricin activity. The U.S. Department of Defense has produced experimental field immunoassays, but commercial distribution of field test kits currently is limited. 

Related mRNAs encoding various proteins can be detected by different types of in situ hybridization. For this method, the number of specific mRNAs detectable per tumor sample is limited. However, the advantage of in situ hybridization is the same as in immunohistochemistry where the morphology of the tumor is still visible. Specific mRNA-species can be detected by northern blot, nuclease protection assay or reverse transcription (RT) combined with polymerase chain reaction (PCR). Using the modern real-time PCR protocols, reliable quantification of PCR targets is possible. A more complex approach is possible by using the micro-array technology, where hundreds or even more of mRNAs can be detected simultaneously in a semi-quantitative fashion. 

Yon, KO., Klinz, M. et al. (1998) Limitations of the reverse-transcription-polymerase chain reaction method for the detection of carcinoembryonic antigenpositive tumor cells in peripheral blood. Clin Cancer Res, 4, 2141-2146. 

Limitations of specific reverse-transcriptase polymerase chain reaction markers in the detection of metastases in the lymph nodes and blood of breast cancer patients. J Clin Oncol, 16, 2632-2640. 

The use of animal antibodies to detect antigens is highly effective but it involves the use of animals, complex separations, and has a variety of limitations. Starting around 1990 a new method for detection and separation of substances, including amino acids, proteins, and pharmaceuticals, was developed based on synthetic nucleic acids termed aptomers aptos = "to fit"). Aptomers are DNA or RNA molecules that bind with high specificity to certain molecules. Their application depends upon many principles described earlier in this book chromatography, combinatorial chemistry, and the polymerase chain reaction (PCR) technique. 

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