Immunoenzymatic techniques applied to the specific detection of nucleic acids : A review

Numerous enzymatic and chemical methods are now available for the preparation of non-radioactive nucleic acid probes. Labels, such as enzymes, fluorophores, lumiphores can be attached to the nucleic acid probe either by covalent bonds (direct labelling) or by biospecific recognition after hybridization (indirect labelling). The principle of the latter method is based on the use of a hapten-labelled nucleic acid probe which is generally detected by an immunoenzymatic assay. Indirect labelling has several advantages: this procedure uses multienzyme complexes to increase the number of enzyme molecules associated with hybridization and hence provides an increase in detectability; moreover, haptens (biotin, dinitrophenol, acetylaminofluorene analogues, digoxigenin, brominated or sulphonylated pyrimidines) used to label nucleic acid probes are not sensitive to elevated temperatures (42–80°C), extended incubation times (several hours), ddetergent and organic solvents currently required in hybridization techniques.

The application of the immunoenzymatic and related techniques to nucleic acid probing is reviewed, focussing on the strategies of non-radioactive hybridization, hapten-labelling of nucleic acids and methods for the immunodetection of the hybrids.     

Nucleic acid probes in diagnosis of viral diseases of man

Summary With the recent, rapid advances in recombinant DNA technology, it has become possible to consider the use of nucleic acid probes in diagnosis of human viral diseases. Several examples are discussed which employ techniques of dot blot hybridization, sandwich hybridization andin situ hybridization. Typing of viral strains using restriction endonuclease digestion as an epidemiological tool is considered. Finally, the present limitations of molecular hybridization are discussed, and future developments including the production of non-radioactively labeled probes, are assessed.     

Non-isotopic probe labelling: advantages and drawbacks for diagnostic specifications

Nucleic acid probes represent an essential tool for molecular investigation in both basic and applied research. In this last field they are particularly useful for diagnosis or prognosis and even for therapy. In the diagnosis, the nucleic probes theoretically allow to reach a sensitive level of reliability never obtained before. Nevertheless, the use of nucleic probes in diagnosis routine need to respect a drastic schedule of conditions since: nucleic probes have to be perfectly specific. nucleic probes have to be sensitive and to allow the detection of less than 100 femtogram of nucleic acid target in routine. In some cases this threshold has to be less than 1 femtogram (for instance HIV detection cases). Nucleic probes have to be absolutely reliable without risk to obtain false positives or negatives. Complete hybridization results must be obtained fast (within 2 or 3 hours in most cases). Labelling systems of nucleic acids must be non-isotopic. Numerous labelling systems, isotopic or non isotopic, have been described during the last fifteenth years. Since some time, the non-isotopic labelling is allowing to contemplate a widespread diagnostic use of it in daily medical, veterinary and agronomy practice. At the present time, some old labelling systems are ahead and new systems are going to be developed worldwide. The future of nucleic probes for the diagnosis needs to assume the schedule of conditions described above. In addition, uses and results obtained with these probes have to be standardized (what is not done yet). Automation and use of amplification of target nucleic acids must be viewed for some applications.(ABSTRACT TRUNCATED AT 250 WORDS)     

Development and application of a nonradioactive nucleic acid hybridization system for simultaneous detection of four potato pathogens

cDNA clones of potato virus X (PVXcp strain), potato virus Y (PVYo strain), potato leaf roll virus (PLRV) and potato spindle tuber viroid (PSTV) were used separately or combined for the detection of the corresponding RNAs in extracts of infected plants. A general method for the rapid preparation of RNA extracts without use of organic solvents (i.e. phenol) was developed for this purpose. Plant extracts from a range of field, artificially inoculated germplasm genotypes, micro-propagated and protoplast samples, as well as vector insect extracts, were dot-blotted onto nylon or nitrocellulose membranes, subjected to sandwich nucleic acid hybridization with non-labelled specific single-stranded DNA probes followed by a biotin-labelled second step hybridization probe. Each probe was virus-specific but not strain-specific. Healthy or non-related plant extracts developed very faint or no signals. Sensitivity was tested by slot-blot hybridization. Detection levels were between 1.5 to 6 pg of viral nucleic acids and between 20 to 50 times more sensitive than standard double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). The assay developed was tested with material that was prepared for processing in the field (combination of fresh sap with extraction solution) and tested under simple laboratory conditions for detection. It was also successfully employed for screening of germplasm for virus resistance, detection of pathogens in vector insects, plantlets grown in vitro and in more sophisticated quantitative determinations of viral replication in artificially inoculated plants and protoplasts.     

Rapid identification of bluetongue virus by nucleic acid hybridization in solution

A liquid phase hybridization format has been adapted for the identification of bluetongue virus (BTV) with respect to serogroup and serotype. In this paper we present experiments which demonstrate the identification of bluetongue virus with respect to both serogroup and serotype. BTV serogroup-specific and BTV serotype 17-specific single-stranded RNA probes labeled with ³⁵S-CTP were used to identify BTV viral nucleic acids in infected cell culture lysates. Cell lysates were prepared for testing by rapid solubilization in a guanidine isothiocyanate/EDTA/dithiothreitol medium. Hybridizations were done in 12.5 μl reaction volumes for 2 h or overnight using nanogram quantities of probe. An RNAse solution was added subsequent to hybridization and incubated for 30 min. TCA-precipitable counts were collected and quantitated by scintillation counting. Specific hybridization signals were obtained in as little as 3 h in assays consisting of uninfected controls, cells infected with different BTV serotypes, and cells infected with a strain of epizootic hemorrhagic disease of deer (EHDV-1). By using asymmetric single-stranded RNA probes we were able to distinguish viral mRNA and viral double-stranded RNA components. We propose this technique as an ancillary or replacement procedure for the confirmation and classification of viral isolates using an appropriate battery of nucleic acid probes. Potential applications and methods of enhancing the technique are discussed.     

Human papillomavirus testing methods

Testing for human papillomavirus (HPV) relies exclusively on techniques of molecular biology using nucleic acid probes. Tests for HPV using nucleic acid probes have been commercially available since the late 1980s, but early tests were cumbersome, involving the use of nucleic acid probes labeled with radioactive phosphorus (32P). These early HPV tests did not achieve widespread use because they did not detect all oncogenic HPV genotypes. The current commercial HPV detection kit, Digene's Hybrid Capture 2 kit, detects virtually all high-risk oncogenic HPV types, as well as most low-risk nononcogenic HPV genotypes. The Hybrid Capture 2 test format is a proprietary nucleic acid hybridization signal amplification system owned by Digene Corporation. Virtually all test formats for DNA sequence analysis are amenable to applications intended to detect and perhaps quantify the various HPV genotypes. These methods can involve direct hybridization with complementary DNA probes, such as Southern blotting or in situ hybridization, signal amplification, such as the Hybrid Capture 2 method or target nucleic acid amplification, most notably the polymerase chain reaction (PCR). Polymerase chain reaction has been used for HPV detection, genotyping, and viral load determination. General or consensus primer-mediated PCR assays have enabled screening for a broad spectrum of HPV types in clinical specimens using a single PCR reaction. Following amplification using consensus primers, individual HPV genotypes are identified using a variety of methods. Using consensus primers in a test format known as real-time quantitative PCR (RQ-PCR), it is possible to generate viral load (concentration) data from reaction curves generated by monitoring PCR reaction kinetics in real time.     

Localization in situ of specific mRNA using thymine-thymine dimerized DNA probes. Sensitive and reliable non-radioactive in situ hybridization

In situ hybridization has been recognized as a powerful technique for localizing specific nucleic acids such as mRNA and viral DNA in individual cells. For in situ hybridization, the use of a non-radioactive probe is considered superior to that of a radioactive one from viewpoints of resolution, probe stability and personal safety. Although various non-radioactive labels are currently available, some interfere with the formation of hybrids and some increase steric hindrance and prevent penetration of the labeled nucleic acid probe into cells and tissues. Recently, we have developed a method using thymine-thymine (T-T) dimerized DNA as a non-radioactive probe. This is simple to make, since it dose not require separation of labeled DNA from unreacted labeling compounds, and T-T dimer will not alter the chemical and physical nature of the probe. In this paper, we describe the tissue processing procedures that are suited for the T-T dimerized DNA probes, and the recent new findings on methodological aspects, particularly the use of synthetic oligodeoxynucleotide probes.     

Detection of dengue-2 viral RNA by reversible target capture hybridization.

A reversible target capture (RTC) sandwich hybridization technique has been developed for the detection of dengue-2 viral RNA. The RTC is a form of sandwich hybridization that utilizes two probes: a poly(dA)-tailed capture probe and a labeled detector probe. Following hybridization of both probes to the analyte in solution, the poly(dA)-tailed capture probe is used to selectively remove the hybrids by capture on oligo(dT)-coated paramagnetic beads. AFter elution from the beads, the presence of specific hybrids is revealed by detection of the labeled probe. After optimization of all parameters by using 32P-labeled probes, digoxigenin was used as a label to preclude the use of radioisotopes. The sensitivity of the developed RTC procedure was determined. The lowest amount of virus detectable in cell culture lysates by using 32P-labeled probes was 20 PFU, while with digoxigenin-labeled probes, 200 PFU was detectable. The RTC procedure also detected dengue-2 virus in infected mosquitoes, both individually and in pools. The RTC has the advantage of being performed directly on crude samples, eliminating the need for phenol extraction and purification of target nucleic acids. These results indicate that the RTC procedure is sensitive, rapid, and easy to perform and that its use in surveillance programs will allow detection of dengue virus in pools of mosquitoes more rapidly than current procedures.     

The peptide nucleic acids, efficient tools for molecular diagnosis (Review)

Peptide nucleic acids (PNAs) are synthetic analogs of DNA that hybridize with complementary DNAs or RNAs with high affinity and specificity, essentially because of an uncharged and flexible polyamide backbone. Originally conceived as ligand for the recognition of double stranded DNA, the unique physico-chemical properties of PNAs have led to the development of a variety of research and diagnostic assays. Initially used as antisense and antigene reagents, the more recent applications of PNA have involved their use as molecular hybridization probes. Thus, sensitive and robust PNA-dependent methods have been designed for developing anti-cancer drugs, modulating PCR reactions, detecting genomic mutation or labelling chromosomes in situ.     

Localization In Situ of Specific mRNA Using Thymine-Thymine Dimerized DNA Probes

In situ hybridization has been recognized as a powerful technique for localizing specific nucleic acids such as mRNA and viral DNA in individual cells. For in situ hybridization, the use of a non radioactive probe is considered superior to that of a radioactive one from viewpoints of resolution, probe stability and personal safety. Although various non-radioactive labels are currently available, some interfere with the formation of hybrids and some increase steric hindrance and prevent penetration of the labeled nucleic acid probe into cells and tissues. Recently, we have developed a method using thymine thymine (TT) dimerized DNA as a nonradioactive probe. This is simple to make, since it dose not require separation of labeled DNA from unreacted labeling compounds, and T-T dimer will not alter the chemical and physical nature of the probe. In this paper, we describe the tissue processing procedures that are suited for the TT dimerized DNA probes, and the recent new findings on methodological aspects, particularly the use of synthetic oligodeoxynucleotide probes. Acta Pathol Jpn 40: 793-807, 1990.     

The peptide nucleic acids (PNAs), powerful tools for molecular genetics and cytogenetics

Peptide nucleic acids (PNAs) are synthetic mimics of DNA in which the deoxyribose phosphate backbone is replaced by a pseudo-peptide polymer to which the nucleobases are linked. PNAs hybridize with complementary DNAs or RNAs with remarkably high affinity and specificity, essentially because of their uncharged and flexible polyamide backbone. The unique physico-chemical properties of PNAs have led to the development of a variety of research assays, and over the last few years, the use of PNAs has proven their powerful usefulness in molecular biology procedures and diagnostic assays. The more recent applications of PNA involve their use as molecular hybridization probes. Thus, several sensitive and robust PNA-dependent methods have been designed for developing antigene and anticancer drugs, modulating PCR reactions, detecting genomic mutation or labelling chromosomes in situ.     

The peptide nucleic acids: a new way for chromosomal investigation on isolated cells?

The development of nucleic acid analogues has become an important feature due to the potential use of this new biomolecular tool in genetic diagnostics and investigations. Among all the synthetic oligonucleotides designed, the peptide nucleic acids (PNA) constitute a remarkable class of nucleic acid mimics, with important physico-chemical properties which have been exploited to develop a wide range of powerful biomolecular tools, including molecular probes, biosensors and anti-gene agents. New applications of PNA involve their use as hybridization probes, and consequently the PNA technology is now developing within the field of in situ hybridization techniques. Recent studies have reported the successful use of centromeric PNA probes on human lymphocytes, sperm as well as on isolated oocytes and blastomeres. Muticolour PNA protocols have been described for the specific identification of several human chromosomes. These data show that PNA could become a powerful complement to fluorescence in situ hybridization (FISH) for in situ chromosomal investigation, especially on isolated cells. The present paper gives an overview of the properties of PNA and the assays exploiting PNA technology in molecular genetics and cytogenetics.     

Measles virus nucleic acid sequences in human brain

We constructed a measles virus genomic recombinant DNA library, and used clones coding for portions of the viral P, M and H proteins to probe for measles virus nucleic acid sequences in post-mortem multiple sclerosis, SSPE and control brains. By dot blot hybridization, the probes detected measles virus nucleic acid sequences in as little as 3 nanograms of total RNA extracted from measles virus-infected cells and also in highly diluted RNA extracted from SSPE brain, but did not detect measles virus sequences in RNA extracted from 11 multiple sclerosis or 8 control brains, even at a 1 000-fold higher concentration of RNA. By in situ hybridization, these probes detected measles virus nucleic acid sequences in virtually every cell and the surrounding neuropile of SSPE brain, but again did not detect such sequences in multiple sclerosis or control brains. Our findings using these highly specific probes confirm that measles virus is found in SSPE brains and indicate that measles virus genome is unlikely to be present in multiple sclerosis or normal brains.     

Diagnosis of psittacine beak and feather disease (PBFD) viral infection, avian polyomavirus infection, adenovirus infection and herpesvirus infection in psittacine tissues using DNA in situ hybridization

The evaluation of the usefulness of DNA probes in a diagnostic setting to identify nuclear inclusions in selected viral infections (psittacine beak and feather disease viral infection, avian polyomavirus infection, adenovirus infection and Pacheco's parrot disease) is reported. A DNA in situ hybridization method was used to detect viral nucleic acid in sections of paraffin-embedded tissues coming from birds naturally and/or experimentally infected. It is concluded that DNA probes used for polyomavirus (FN-19) and adenovirus (FN-23) are able to identify nucleic acid of each virus in the cells with nuclear inclusions, and when used for psittacine beak and feather disease virus (FN-8), and Pacheco's parrot disease virus (FN-49) are able to detect viral nucleic acid in cells with or without inclusions.     

DNA hybridization: comparison of liquid and solid phase formats

In nucleic acid hybridization an oligo- or polynucleotide probe is allowed to anneal to its complementary strand which possibly is present in the sample. This offers an extremely specific way to identify and quantify given genes and thus, for instance, given microbes. The annealing reaction is, however, slow since the reactants are present at very low concentrations and the diffusion rate of DNA is slow. To overcome this problem high concentrations of probe are used in order to "drive" the reaction in a pseudo-first order fashion. As a result a positive hybridization is easily masked by the large excess of unreacted probe molecules, unless a powerful fractionation system is used which removes the free probes. A frequently used method is to immobilize the nucleic acids of the sample on a solid support which then after the reaction is easy to wash. The solid support introduces, however, a diffusion barrier which significantly reduces the reaction rate. Thus kinetically solution phase reactions are preferable to solid phase ones. In this communication a test format is described in which the advantages of both solid and solution phase assays are combined. Two probes are used, one carrying a detectable label (the detector probe) and the other an affinity moiety, e.g. biotin (the capture probe). After hybridization in solution a sandwich hybrid is formed in which the target nucleic acid is annealed to the two probes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Radioactive and enzymatic cloned cDNA probes for bovine enteric coronavirus detection by molecular hybridization

Summary Genomic RNA of F15 strain bovine enteric coronavirus (BECV) was cloned inE. coli. Three clones (174, 160, PG 78), selected in the cDNA library, including a large portion of the nucleocapsid (N), matrix (M) and peplomeric (S) protein genes, were used as probes for a slot blot hybridization assay. Two probe labelling techniques were compared, radiolabelling with³²P and enzymatic labelling through covalent linkage to peroxidase and chemiluminescence detection. The radioactive probe 174 detected as little as 1 to 3 pg of viral RNA, while the less sensitive enzymatic probe could not reveal more than 100 pg of RNA. No significant detection amplification was achieved when a mixture of the three probes was used. Probe 174 allowed specific identification for BECV. No hybridization was noticed either with rotaviruses or even with other antigenically unrelated members of the familyCoronaviridae such as transmissible gastroenteritis virus. The test proved valid for detection of BECV in the supernatant of infected HRT-18 cells: genomic RNA could be detected after direct spotting of samples, but prior nucleic acid extraction after proteinase K treatment improved virus detection. BECV diagnosis in faecal samples using enzymatic probe was compared with conventional diagnostic methods.     

High prevalence of latently present cytomegalovirus in arterial walls of patients suffering from grade III atherosclerosis.

The presence of cytomegalovirus (CMV) nucleic acids was demonstrated in arterial walls of patients with grade III and with maximally grade I atherosclerosis by dot blot and in situ DNA hybridization and by polymerase chain reaction (PCR) using probes and primers derived from immediate early (IE) and late (L) genomic regions. The presence of the complete viral genome could be demonstrated by both dot blot DNA hybridization and PCR. IE mRNA but not L mRNA could be demonstrated by in situ DNA hybridization, indicating the presence of latent CMV in the human arterial wall. By PCR 90% of the samples obtained from atherosclerotic patients were shown to contain viral nucleic acids as compared to 53% of patients with maximally grade I atherosclerosis, thus substantiating a role for this virus in the pathogenesis of atherosclerosis.     

In situ hybridization: an optimised detection protocol for a biotinylated DNA probe renders it more sensitive than a comparable 35S-labelled probe

The development of a highly sensitive biotinylated in situ hybridization protocol using egg drop syndrome virus infection of domestic fowl as a model is described. This protocol incorporates the use of a monoclonal antibody to biotin as the initial step in a peroxidase-based detection system. The detection of viral nucleic acid in formalin-fixed, paraffin-embedded sections using biotinylated and 35S-labelled probes is compared to the detection of viral antigen by immunocytochemistry. Biotinylated probes detected more positive cells than 35S-labelled probes and were more specific. Biotinylated probes detected more positive cells than immunocytochemistry.     

Cellular localization of cytomegalovirus nucleic acids in guinea pig salivary glands by in situ hybridization

In situ hybridization with guinea pig cytomegalovirus (CMV) DNA probes was used to detect guinea pig CMV nucleic acid sequences in salivary glands during the course of infection. Optimum conditions for detection of guinea pig CMV gene sequences at the cellular level were determined. The technique of nucleic acid hybridization was compared to antigen detection and histologic examination for cellular localization of guinea pig CMV during acute and chronic infection. Tissue sections fixed for 1 h in 4% paraformaldehyde demonstrated darker specific staining and contained significantly larger numbers of cells positive for guinea pig CMV nucleic acids and antigens than sections fixed longer and in other fixatives. The method of in situ hybridization detected more guinea pig CMV infected cells than did routine histological evaluation. Histologically normal salivary gland duct cells as well as cells bearing typical inclusions were found to contain guinea pig CMV nucleic acids. Guinea pig CMV nucleic acids were also detected although less frequently in cells outside of the ducts. These results suggest that in situ hybridization allows for the detection of histologically inapparent guinea pig CMV infections at the cellular level.     

Detection of human immunodeficiency virus type 1 by using the polymerase chain reaction and a time-resolved fluorescence-based hybridization assay.

The polymerase chain reaction (PCR) has many potential applications in the field of nucleic acid diagnostics. In particular, it has been successfully applied to the detection of pathogens present in low copy numbers such as the human immunodeficiency virus type 1. Here we describe a time-resolved fluorescence-based hybridization assay which, combined with the PCR, offers an extremely sensitive method for the detection of nucleic acids. In this assay format, the PCR is run by standard procedures and the subsequent hybridization reaction is carried out in solution by using two oligonucleotide probes, one biotinylated and one labeled with europium (Eu3+). The sandwich hybrids are then collected onto a streptavidin-coated microtitration well, and the bound Eu3+ is measured in a time-resolved fluorometer. This assay is rapid, user friendly, and quantitative and lends itself to automation. The application of this assay to the detection of human immunodeficiency virus type 1 is described.