Nonradioactive Hybridization Probes Research Articles

Preparation and use of nonradioactive hybridization probes.

AbstractMolecular hybridization is a useful technique for identifying specific target sequences even when they are present as a single copy in a complex population of highly heterogeneous gene sequences. It can be performed either on a solid matrix on which pure DNA (or RNA) is bound (blot hybridization) or on tissue section (in situ hybridization). Until recently, the probes used in hybridization were usually labeled with radioisotopes. However, the short half-life, disposal, and safety problems of radioactive probes stimulated the development of nonradioactive hybridization techniques. In these, the probes are labeled with nonradioactive reporter molecules, which can be haptens, proteins, digoxigenin, biotin, and so forth. These reporter molecules can then be detected by enzyme-labeled antibodies or streptavidin (in the case of biotinylated probes). Of these reporter molecules, biotin and digoxigenin have several advantages over the other because of their small size. Therefore, they minimally interfere with hybridization efficiency. In addition, the high affinity of the binding of biotin and streptavidin (K d =10−15 M) is almost equivalent to covalent bonds. In fact, the biotin system was the first nonradioactive hybridization technique sensitive enough for routine use on blot hybridization (1) and in situ hybridization (2).KeywordsNick TranslationLabel ReactionKlenow FragmentReporter MoleculeMolecular HybridizationThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

The Reactions of H-Phosphonates with Bifunctional Reagents. V. Functionalization of Support-Bound Oligonucleotides and Synthesis of Nonradioactive Hybridization Probesa

Three methods for the functionalization of oligonucleotides with aminoalkyl moieties have been developed and their efficiencies were evaluated in the preparation of non-radioactive hybridization probes. This paper is dedicated to the late Professor Tsujiaki Hata.

Use of oligonucleotide-alkaline phosphatase conjugates as non-radioactive probes for rapid analysis of a proteinase inhibitor gene fromZea mays

Conjugates of oligonucleotides and alkaline phosphatase have been prepared and used as nonradioactive hybridization probes for the study ofPis3 (=MPI) a gene encoding a proteinase inhibitor fromZea mays. Attachment of the alkaline phosphatase was carried out either at the 5′ or 3′ end of two 25-bp oligonucleotides. Sensitivity of each alkaline phosphatase-oligonucleotide probe was assessed using a chemiluminescent substrate for detection of alkaline phosphatase activity. This sensitive method allows the rapid analysis of genomic clones isolated from aZea mays library and the subsequent characterization of the completePis3 gene without the need for construction of restriction maps for the cloned DNA fragments. This general strategy may be valuable for the identification of any gene for which a limited sequence is known and for location of specific DNA sequences that represent a small region within a larger DNA fragment.

Characterization of nonradioactive hybridization probes for detecting infectious bursal disease virus

Reverse transcription followed by the polymerase chain reaction was used to amplify a fragment of infectious bursal disease virus (IBDV) strain P3009 genome. The amplified DNA fragment was annealed into the plasmid pUC18 and used to transform Escherichia coli strain JM109. A clone that contained IBDV-specific nucleotide sequences was selected and designated pC23. The DNA fragment within pC23 was 320 base pairs in length and designated C23. Radiolabeled probes prepared from C23 hybridized to genome segment A of strain P3009 by a northern-blot hybridization assay. Biotin-labeled probes prepared from C23 and pC23 either by using nick translation (designated C23/ NT and pC23/NT, respectively) or by direct introduction of biotin molecules into C23 and pC32 (designated C23/BH and pC23/BH, respectively) were used in the dot blot hybridization assay for detecting IBDV strains. All four biotinylated probes detected three serotype l viruses and one serotype 2 IBDV. However, they did not cross-react with nucleic acids extracted from mockinfected cells or from seven unrelated avian viruses. Probe pC23/BH detected as little as 0.04 ng of IBDV RNA, while the other three probes were less sensitive and detected approximately 1 ng of IBDV RNA. In addition, the probe pC23/ BH detected IBDV RNA in bursa tissues from commercial broiler raising farms following the dot blot hybridization.

Non-radioactive hybridization probes prepared using M13 phage vector and the universal sequencing primer.

Non-radioactive hybridization probes were prepared using the M13 phage vector and the universal sequencing primer. The probe sequence to be used was first cloned into the M13 vector, and the minus strand of the template DNA was then synthesized with the Klenow fragment of E. coli DNA polymerase I in the presence of the biotinylated nucleotide, biotin-11-dUTP, as a label. Resultant DNA was heavily biotinylated, and made up of the entire minus strand of the template DNA. The long tag sequence derived from the M13 vector may increase the sensitivity of the detection. The biotinylated hybrids were visualized with the streptavidin-alkaline phosphatase conjugate and chromogenic substrates. As shown by Southern hybridization, the probe prepared in this way could be used to detect less than 1 pg of target sequence and a single copy gene sequence in human genomic DNA within several hours of signal development.

Synthesis of 5′-oligonucleotide hydrazide derivatives and their use in preparation of enzyme-nucleic acid hybridization probes

A hydrazone-based method for conjugating synthetic nucleic acids and reporter molecules for use as nonradioactive hybridization probes is presented. Oligonucleotides complementary to the hepatitis B virus were derivatized at their 5′ ends with hydrazine or homobi-functional acyl hydrazides. These derivatives reacted facilely with aldehydes to give hydrazones, which were characterized by uv spectroscopy and HPLC. Coupling of aldehyde-modified alkaline phosphatase with carbohydrazide-oligonucleotide derivatives provided a mixture of two enzyme-nucleic acid conjugates in 80–85% yield. The conjugates had a 1:1 and a 2:1 oligonucleotide/enzyme ratio, respectively, and were separated by ion-exchange chromatography. Both conjugates were able to detect 7 amol of target DNA in 1 h, using a colorimetric assay. In contrast, oligonucleotide-horseradish peroxidase conjugates were 40-fold lower in sensitivity of detection.

Synthesis Of Oligodeoxyribonucleotides Containing an Aliphatic Amino Linker Arm at Selected Adenine Bases and Derivatization with Biotin

Abstract The chemical synthesis and characterization of oligodeoxyribonucleotides with a “linker arm” attached to the 8-position of some adenine bases are presented. Derivatizatlon with biotin is described and evaluation of these modified DNA fragments as nonradioactive hybridization probes is briefly discussed.

Nonradioactive hybridization probes prepared by the reaction of biotin hydrazide with DNA

A novel one-step chemical method has been developed for the introduction of biotin into nucleic acids for non-isotopic hybridization. The method is based on the interaction of biotin hydrazide with unpaired cytosine residues. The interaction is catalyzed by sodium bisulfite with an optimum at a buffered pH of about 4.5. The reaction reached its maximum after 24 h incubation at a biotin hydrazide concentration of 10 mg/ml. Using streptavidin-alkaline phosphatase conjugates, the limits for detecting the biotinylated probe, either adsorbed directly to nitrocellulose or hybridized to filter-bound target DNA, were 0.3 and 0.9 pg, respectively. The salience of the approach described here over previously used biotin derivatives is that it is quick (one-step), simple and does not involve any enzymatic or instrument-mediated step to introduce the reporter moiety. In addition, other low- and high-molecular-weight hydrazides (e.g. fluorescent or enzyme hydrazides) can serve as the reporter group. The same procedure may be employed for the single-step biotinylation of free cytidine.

Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin.

A photo-activatable analogue of biotin, N-(4-azido-2-nitrophenyl)-N'-(N-d-biotinyl-3-aminopropyl)-N'-methyl-1,3- propanediamine (photobiotin), has been synthesized and used for the rapid and reliable preparation of large amounts of stable, non-radioactive, biotin-labelled DNA and RNA hybridization probes. Upon brief irradiation with visible light, photobiotin formed stable linkages with single- and double-stranded nucleic acids yielding probes which were purified from excess reagent by 2-butanol extraction and ethanol precipitation. Using single-stranded phage M13 DNA probes chemically labelled with one biotin per 100-400 residues and dot-blot hybridization reactions on nitrocellulose, as little as 0.5 pg (6 X 10(-18) mol) of target DNA was detected colorimetrically by avidin or streptavidin complexes with acid or alkaline phosphatase from three commercial sources. The sensitivity of detection of target RNA in dot-blots and Northern blots was equivalent to that obtained with 32p-labelled DNA probes. Photobiotin was also used for the labelling of proteins with biotin.