Efficient methods for attaching non-radioactive labels to the 5' ends of synthetic oligodeoxyribonucleotides

Nonradioactive labeling of synthetic oligonucleotide probes with terminal deoxynucleotidyl transferase

Synthetic oligonucleotides were tailed at the 3' end using terminal deoxynucleotidyl transferase. Nucleotide triphosphates with free primary amines at the end of side chains were compared for their tailing efficiency and/or detection sensitivity, using biotin-11-dUTP as a reference. Free primary amines were tagged with activated biotin or fluorescein isothiocyanate. The probes were then detected with either streptavidin-alkaline phosphatase complex or anti-fluorescein antibodies and alkaline phosphatase-conjugated secondary antibodies. Tailing conditions were optimized and the probes were tested for detection of Escherichia coli ST1a enterotoxin DNA and rotavirus RNA.

Sensitive non-radioactive dot-blot hybridization using DNA probes labelled with chelate group substituted psoralen and quantitative detection by europium ion fluorescence

A new labelling method for cloned DNA probes used in hybridization assays is described. The DNA insert of recombinant plasmid DNA was made partially single-stranded for the labelling reaction by a restriction enzyme digest, followed by a controlled exonuclease III incubation. A thiol-containing psoralen derivative was covalently bound through irradiation with UV-light to the remaining double-stranded region of the plasmid DNA. The psoralen-SH groups were labelled with a large number of metal chelators (diethylentriamine pentaacetic acid, DTPA) using poly-L-lysine as a macromolecular carrier. The main advantage of the labelling procedure is that a high degree of labelling is achieved without modification of the single-stranded DNA hybridizing sequences. The specific hybrids were labelled after filter hybridization with europium ions through the chelating groups of DTPA. The europium ions were quantitatively detected by time-resolved fluorometry. The sensitivity of the assay for target DNA detection was in the low picogram range, comparable to radioactively labelled DNA probes.

Synthesis and application of fluorescent labeled nucleotides to assay DNA damage

A facile method was developed to covalently attach a fluorophore to the 5'-phosphate of a nucleic acid. The procedure, illustrated by coupling 5'-dNmp (N = A,C,G,T) with 5-dimethylaminonaphthalene 1-sulfonyl chloride, commonly known as Dansyl chloride, involves 5'-phosphoramidation with ethylenediamine (EDA) followed by conjugation of the free aliphatic amino group of the phosphoramidate with Dansyl chloride. This method is also applicable to multi-incorporation of fluorescent labels in the nucleic acids. The reaction of 5'-Amp with a polyamine such as poly L-lysine (PLL, mol. wt., 4000) resulted in a phosphoramidate with multiple amino groups, which after isolation and conjugation with fluorescamine gave dAmp with multilabeled fluorophores. A condition was devised to separate the four dansylated mononucleotides of DNA, conjugated via ethylenediamine linker, by reverse phase HPLC. The elution profile could be monitored with a variable wavelength detector at 254 nm and 340 nm corresponding to the absorption of the nucleotides and the dansyl moiety, respectively. The detection limit was 2 nmol at 254 nm. The use of a fluorescence detector enhanced the detection sensitivity to a sub-picomole level (200 fmol). Samples of a DNA model, d(pCpGpTpA) and calf-thymus DNA were digested enzymatically to 5'-mononucleotides and labeled with Dansyl chloride. HPLC analysis of the dansylated digests from these samples, both before and after irradiation, suggests that the combination of enzymatic digestion and fluorescence postlabeling could be a novel approach to assay DNA damage.

The synthesis of protected 5'-amino-2',5'-dideoxyribonucleoside-3'-O-phosphoramidites; applications of 5'-amino-oligodeoxyribonucleotides

Synthetic routes to the four appropriately protected 5'-amino-2',5'-dideoxyribonucleoside-3'-O-(2-cyanoethyl N,N-diisopropylphosphoramidites) have been developed. The structures of all intermediates were confirmed by 13C n.m.r. spectroscopy. These building blocks have been used to prepare 5'-amino-oligodeoxyribonucleotides, which can be coupled to a wide variety of compounds, in particular metal cluster derivatives, but also fluorophores and biotin derivatives, thus generating a variety of very useful probes. Brief mention is made of a tetrairidium cluster derivative of 5'-amino-d[CCGATATCGG], which has been cocrystallised with EcoRV, and will be used for electron microscopy studies.

Synthesis of oligodeoxyribonucleotide with aliphatic amino or phosphate group at the 5' end by the phosphotriester method on a polystyrene support

Lipophilic protecting groups mTrNH(CH2)n X (mTr:monomethoxytrityl, X = NH,O,S, n = 2,3,4,6) were attached to the 5'-phosphoryl group of 3'-O-protected thymidine. When the diamine derivatives (X = NH2) were used, the time course of the stability of mTr groups on the amino group and the phosphoramidate linkage with 80% aq. AcOH was measured. It was found that the mTr group was removed from the amino group rapidly and that the phosphoramidate linkage was more stable. It's stability depended upon the length of the CH2 linker. Oligonucleotides with an aliphatic amino group at their 5'-ends were synthesized by the phosphotriester method on a polystyrene support using protected nucleotides with P-O or P-S linkages. In the case of product with a P-S linkage, 5'-O-phosphorylated nonadecanucleotide was also prepared by I2-H2O treatment.

Introduction of 5'-terminal functional groups into synthetic oligonucleotides for selective immobilization

Oligodeoxyribonucleotides terminating in a 5'-primary amine group are synthesized using solid-phase supported phosphoramidite chemistry. The 5'-terminal amine group in the deprotected oligomers is further derivatized with either succinic anhydride to give 5'-carboxylic acid or with dithiobis(succinimidylpropionate) followed by treatment with dithioerythritol to produce 5'-thiol-terminated oligonucleotides. The 5'-thiol-terminated oligonucleotides are selectively immobilized on solid supports containing either p-chloromercuribenzoate or 2,2'-dithiobis(5-nitropyridine) activated thiol groups.

Colorimetric-detected DNA sequencing

A sensitive, colorimetric method for visualizing the band pattern of DNA sequencing reaction is described. The enzymatic incorporation of radioactive nucleotides commonly used for the band detection is replaced by biotin conjugated to the 5'-terminus of a synthetic oligonucleotide by chemical synthesis. The oligonucleotide so labeled is used as a primer for dideoxy DNA sequencing in a primer extension reaction. The products of the sequencing reactions are analyzed on a denaturing polyacrylamide gel using the direct blotting electrophoresis technique. This technique makes it possible to transfer the band pattern during the electrophoresis onto an immobilizing matrix, on which it is made visible by an enzymatic reaction in less than 3 h. This biotin-based detection method is so sensitive that the sequencing reactions can be performed under the same conditions and concentrations as those for the radioactive detection.

Hybridization histochemistry

The location of gene expression by hybridization histochemistry is being applied in many areas of research and diagnosis. The aim of this technique is to detect specific mRNA in cells and tissues by hybridization with a complementary DNA or RNA probe. Requirements for optimal specificity, sensitivity, resolution and speed of detection may not all be encompassed in one simple technique suitable for all applications, thus appropriate procedures should be selected for specific objectives. With reference to published procedures and our own extensive experience, we have evaluated fixatives, probes, labels and other aspects of the technique critical to the preservation and hybridization in situ of mRNA and detection and quantitation of hybrids.

Efficient methods for attachment of thiol specific probes to the 3'-ends of synthetic oligodeoxyribonucleotides

Methodology is described for the synthesis of DNA oligomers containing a free 3'-thiol group which can be selectively crosslinked with a wide variety of probes. This chemistry is compatible with both phosphotriester and phosphoramidite solid phase chemistry. Moreover, the sulphydryl group is introduced into the 3'-nucleoside solid support linkage prior to oligonucleotide synthesis. Consequently, no additional coupling steps are required after oligonucleotide synthesis, and isolation of the 3'-thiol oligonucleotide requires only one additional deprotection step. Cross-linking of the thiol-containing oligonucleotide to a fluorescent probe was carried out with high selectivity, in high yield, and under mild conditions.

Covalent attachment of oligonucleotides to solid supports

Coupling efficiencies for the covalent attachment of oligonucleotides (17-29 bases in length) to solid supports derivatized with alkyl-amino and -carboxylic functionalities have been determined. Attachment efficiencies of 60-80% were obtained for coated long-chain alkylamino controlled pore glass (CPG) supports. Similar efficiencies of immobilization were observed for carboxyl-bearing supports, which additionally exhibited lower levels of non-covalent binding. The extent of terminally linked oligonucleotide was determined to be 50-55% of the overall attachment in the carbodiimide-mediated coupling reaction of a 5'-aminohexyl phosphoramidate derivative of a 29-mer to Sephacryl carboxyl support. While lower overall efficiencies of attachment were obtained in the reaction with Sephacryl N-hydroxysuccinimide-activated carboxyl support, greater than 80% of this coupling results in end-attached oligonucleotides.

The synthesis of protected 5'-mercapto-2',5'-dideoxyribonucleoside-3'-O-phosphoramidites; uses of 5'-mercapto-oligodeoxyribonucleotides

The syntheses of the four novel, base protected 5'-(S-triphenylmethyl)mercapto-2',5'-dideoxyribonucleoside-3 '-O-(2-cyanoethyl N,N-diisopropylphosphoramidites) are described. These compounds have been used to prepare 5'-(S-triphenylmethyl) mercapto-oligodeoxyribonucleotides, which are readily purified by reversed phase h.p.l.c., owing to the highly lipophilic trityl group. After cleavage of the S-trityl group by silver or mercuric ions, the free thiol moiety can be coupled to a wide variety of reagents, generating very useful probes. Fluorescent labelled 5'-mercapto-oligodeoxyribonucleotides are being used for automated DNA sequencing without radioactivity, and heavy metal labelled 5'-mercapto-oligonucleotides will be used in X-ray crystallography.

Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oligodeoxyribonucleotides

A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino groups. Fluorescein isothiocyanate coupled to these compounds gives oligonucleotide probes carrying multiple fluorescein labels. These compounds have a free 5'-hydroxy group enabling additional 5'- end radioactive labelling for evaluation of their hybridization characteristics. It was found that oligonucleotides carrying a long (11 atom) linker arm to the fluorescein hybridize more efficiently to mRNA than those carrying a short (4 atom) arm. The long linker arm derivatives are comparable to underivatized oligonucleotides in hybridizing to mRNA.

Immobilization of DNA via oligonucleotides containing an aldehyde or carboxylic acid group at the 5' terminus

A general method for the immobilization of DNA through its 5'-end has been developed. A synthetic oligonucleotide, modified at its 5'-end with an aldehyde or carboxylic acid, was attached to latex microspheres containing hydrazide residues. Using T4 polynucleotide ligase and an oligonucleotide splint, a single stranded 98mer was efficiently joined to the immobilized synthetic fragment. After impregnation of the latex microspheres with the fluorescent dye, Nile Red and attachment of an aldehyde 16mer, 5 X 10(5) bead-DNA conjugates could be detected with a conventional fluorimeter.

The synthesis of oligonucleotides containing a primary amino group at the 5'-terminus

Oligonucleotides containing a primary amino group at their 5'-termini have been prepared and further derivatised with amino specific probes. The sequence required is prepared using standard solid phase phosphoramidite techniques and an extra round of synthesis is then performed with N-monomethoxytrityl-0-methoxydiisopropylaminophosphinyl 3-aminopropan(1)ol. After cleavage from the resin, removal of the phosphate and base protecting groups and purification gives a monomethoxytrityl-NH(CH2)3PO4-oligomer. The monomethoxytrityl group can be removed with acetic acid to give the desired amino containing oligomer. The amino group can be further derivatised with amino specific probes yielding fluorescent or biotinylated oligonucleotide products.

Molecular diagnosis of infectious diseases by nucleic acid hybridization

Diagnostic microbiology has traditionally relied on the cultivation of an infecting agent in an in vitro system. However, the limitations of these methods have led to the development of alternative, molecular techniques which can detect specific microbial proteins or nucleic acids directly in body fluids. One such method, nucleic acid hybridization, has many attractive features including the potential for high sensitivity and specificity, the detection of a chemically stable analyte and the use of uniform reagents. Nucleic acid hybridization reactions have been used to detect a variety of microbial pathogens in assay formats using extracted nucleic acids or tissue sections. However, wider application of these techniques is limited by the fact that current methods employ radioisotopically labelled probes and cumbersome assay procedures. Solutions to these problems have been sought by the development of non-radioactive hybridization techniques which utilize enzymatic detection methods and by the development of rapid hybridization assays performed in solution. Further improvements in labelling techniques, assay formats and enzymatic detection methods should allow for the wider application of nucleic acid hybridization reactions in diagnostic microbiology.