Polynucleotide sequence analysis by sequential base elimination: 3'-terminus of phage Q-beta RNA.

The nucleotide sequence of a 3'-terminal fragment obtained by ribonuclease T(1) hydrolysis of the ribonucleic acid from bacteriophage Qbeta has been determined by an improved method of sequence analysis which involves sequential removal of bases by periodate oxidation and beta-elimination. The results obtained from ten such oxidation-elimination cycles and from the alkaline hydrolysis of the remaining oligonucleotide indicate that the first 16 nucleotides at the 3'-terminus of this ribonucleic acid have the sequence: -G-C-C-C-U-C-U-C-U-C-C-U-C-C-C-A.

Comparison of RNA terminal sequences of phages f2 and Q-beta: chemical and sedimentation equilibrium studies.

The terminal fragment obtained by hydrolysis with ribonuclease T(1) of the ribonucleic acid from the bacteriophage Qbeta has been isolated and purified. The results of chemical and enzymatic hydrolysis of this fragment and of the intact RNA itself indicate that the fragment has the composition (10 Cp, 4 Up), and that the RNA has the terminal sequence -GP(9 Cp, 4 Up) CpA. These conclusions are supported by the results of an application of the sedimentation-equilibrium method in which the molecular weight of the Qbeta fragment was compared with that of the corresponding fragment from f2 phage RNA for which the terminal sequence, -GpUpUpApCpCpApCpCpCpA had previously been determined.

Analysis of benzo(a)pyrene:DNA adducts formed in cells in culture by immobilized boronate chromatography.

A chromatographic procedure using boronic acid residues linked to a cellulose support [(N-(N'-[m-(dihydroxyboryl)-phenyl]succinamyl)amino]ethyl cellulose), used by Sawicki et al. (Cancer Res., 43: 3212-3218, 1983) for analysis of 7,12-dimethylbenz(a)anthracene:DNA adducts, was modified to allow the analysis of benzo(a)pyrene (BaP):DNA adducts formed in cells in culture. Adducts resulting from reaction of 7 beta, 8 alpha-dihydroxy-9 alpha, 10 alpha-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (anti-BaPDE) contain cis-vicinal hydroxyl groups that complex with the boronic acid residues; adducts resulting from 7 beta, 8 alpha-dihydroxy-9 beta, 10 beta-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (syn-BaPDE) do not. A mixture of [3H]-syn-BaPDE:deoxyguanosine (dGuo) adduct and [14C]-anti-BaPDE:dGuo adduct was completely resolved on a column of boronate:cellulose. Early-passage cultures of Sencar mouse, Syrian hamster, and Wistar rat embryo cells and a culture of a human hepatoma cell line (Hep G2) were exposed to [3H]BaP, and the BaP:DNA adducts were resolved by boronate chromatography and high-performance liquid chromatography. The Hep G2 cells and mouse embryo cells contained two major adducts, a (+)-anti-BaPDE:dGuo adduct and a syn-BaPDE:dGuo adduct. Boronate chromatography permitted the resolution of an additional minor syn-BaPDE:deoxyribonucleoside adduct in the mouse embryo cells. The hamster and rat embryo cells contained a number of major BaP-DNA adducts that were resolved by boronate chromatography followed by high-performance liquid chromatography. The rat embryo cells contained three syn-BaPDE:deoxyribonucleoside adducts and approximately equal amounts of two adducts tentatively identified as dGuo adducts of the (+) and (-) enantiomers of anti-BaPDE. The boronate chromatography-high-performance liquid chromatography procedure improves the separation of the BaP:DNA adducts formed in biological systems and facilitates the identification of the BaP metabolite(s) responsible for the formation of these adducts.

Crystallographic structure of an RNA helix: [U(UA)6A]2.

The crystallographic structure of the synthetic oligoribonucleotide, U(UA)6A, has been solved at 2.25 A resolution. The crystallographic refinement permitted the identification of 91 solvent molecules, with a final agreement factor of 13%. The molecule is a dimer of 14 base-pairs and shows the typical features of an A-type helix. However, the presence of two kinks causes a divergence from a straight helix. The observed deformation, which is stabilized by a few hydrogen bonds in the crystal packing, could be due to the relatively high (35 degrees C) temperature of crystallization. The complete analysis of the structure is presented. It includes the stacking geometries, the backbone conformation and the solvation.

Formation of MboII vectors and cassettes using asymmetric MboII linkers.

Class-IIS restriction endonucleases such as MboII cleave DNA at a specified distance away from their recognition sequences. This feature was exploited to cleave DNA at previously inaccessible locations by preparing special asymmetric linker/adapters containing the MboII recognition sequence. These could be joined to DNA fragments and subsequently cleaved by MboII. Attachment of a 3' phosphate to one of the two different oligodeoxynucleotides comprising the asymmetric duplex prevented ligation at the improper end of the linker. Plasmids were constructed containing a unique BamHI or BclI site between the recognition and cleavage site of MboII. These sites were used to introduce a foreign fragment into the plasmid at a position permitting MboII to cleave within the newly inserted fragment. Once cleaved at the unique MboII site, another DNA fragment was inserted. DNA was thus inserted at a sequence not previously accessible to specific cleavage by a restriction enzyme. A cassette containing an identifiable marker, the lac operator, between two oppositely oriented MboII/BamHI linkers was made and tested in a random insertion linker mutagenesis experiment.

Silver staining of nucleolar organizer regions in malignant melanoma and melanotic nevi.

The recently described method of staining nucleolar organizer regions (NOR) with colloidal silver nitrate was applied to the paraffin sections of five junctional nevi, 13 compound nevi, seven Spitz nevi, nine cellular blue nevi, 11 dysplastic nevi, seven malignant lentigines, 12 superficial spreading melanomas, and 14 secondary melanomas. There was a significant difference between the pooled silver-NOR (AgNOR) numbers of the 45 benign lesions (mean, 1.22; SD, 0.51) and the 33 melanomas (mean, 9.18; SD, 4.05) by t test analysis (P less than .01). The difference was striking enough to be recognized on casual microscopic examination, suggesting that AgNOR staining may be a useful technique to help separate melanocytic nevi from malignant melanomas.

The effects of progressive formaldehyde fixation on the preservation of tissue antigens.

A wide variety of fresh post-mortem tissues was fixed in 4% formaldehyde for 6 hours, 1, 3, 7, 14 and 30 days to simulate possible fixation schedules in the diagnostic laboratory, before processing through alcohol and chloroform. The immunoreactivity of paraffin-embedded sections to 25 monoclonal and polyclonal antibodies commonly used in tissue diagnosis was tested employing an avidin-biotin-peroxidase technique. There was a distinct fall-off in the staining of many antigens including the lymphocyte antigens LN1, LN2, LN3 and UCHL1 after 3 days of fixation and the intermediate filament proteins vimentin, desmin and neurofilaments failed to be labelled by monoclonal antibodies after 1 day and only variable staining for the cytokeratins was retained. S100 protein, prostate specific antigen, thyroglobulin and carcinoembryonic antigen were more resilient and showed weak staining after 14 days exposure to formaldehyde. Trypsinization improved the staining for cytokeratins, neurofilaments, desmin and Factor VIII-related protein, but for other antigens, the immunoreaction was weaker and background staining was increased. For the effective application of immunohistochemical staining as a diagnostic tool, the duration of formaldehyde fixation should be kept to a minimum and enzyme digestion should only be judiciously employed for selected antigens.

The analogue of thymidine triphosphate containing a methylene group in place of the 5' oxygen can serve as a substrate for reverse transcriptase.

The thymidine 5'-triphosphate analogue containing a methylene group in place of the 5' oxygen atom can be prepared using modifications of published procedures and can substitute for the natural thymidine triphosphate in chain extension reactions catalyzed by Moloney-MLV reverse transcriptase. Using rabbit beta-globin mRNA as the template together with an appropriate primer, the enzyme readily makes full-length DNA transcripts in which all thymidine 5' oxygen atoms have been replaced with methylene groups. In sequence analyses using the partial depurination procedure, the analogue DNA transcript produces electrophoretic gel patterns identical with those of the corresponding natural DNA transcript. Experiments on second strand synthesis using the four regular triphosphates show that the analogue DNA transcript, like the natural transcript, can serve as a template. The two DNA duplexes (natural/natural and analogue/natural) formed by these reactions produce similar electrophoretic cleavage patterns when treated with either of the endonucleases HaeIII and EcoRI. However, further studies on template properties indicate that, while the enzyme makes a full-length product when using the analogue substrate with a natural DNA strand as template, it appears unable to use the analogue transcript as template with the analogue triphosphate as substrate during second strand synthesis. Preliminary experiments have also been carried out with a DNA polymerase. No products are detected reactions using Taq polymerase with PCR protocols containing the analogue triphosphate as the only source of thymidine.

A new, rapid, microwave-stimulated method of staining melanocytic lesions.

A new and sensitive method of staining melanocytic lesions is described. Tissue sections covered by a solution of colloidal silver nitrate are exposed to microwaves for 45 sec in a domestic oven to produce clean, crisp staining of melanocytes and melanoma cells, often showing long delicate dendritic cell processes. The staining technique does not stain other pigments or argyrophilic tissues and is shown to be more sensitive than the standard Masson-Fontana procedure.

A new method for sequence analysis of oligodeoxyribonucleotides.

The structure of an oligodeoxyribonucleotide may be determined by a simple two-dimensional separation on a polyethyleneimine-cellulose thin layer sheet. Chromatography in the first dimension fractionates by chain length a nested set of fragments that are generated by subjecting the oligomer to partial spleen phosphodiesterase degradation and then labelling their non-common ends with 32P using polynucleotide kinase. A subsequent in situ treatment with nuclease Bal 31 produces labelled mononucleotides, and these are identified by chromatography in the second dimension. Since the method does not identify the 3' terminal nucleotide, a convenient procedure involving 3' end labelling followed by enzymatic digestion to monomers has been developed for this purpose. This approach to sequence analysis also has the advantage of permitting assignment of the identity and location of any modified or unusual bases within the oligonucleotide.

Anomalous hairpin formation in an oligodeoxyribonucleotide.

An accurate method for deriving molar absorptivity-temperature profiles applied to a set of single-stranded oligodeoxyribonucleotides shows that the undecamer CGAGTTTGACGp exists in a hairpin conformation involving Watson-Crick base pairing between the two terminal CG dinucleotides. The hairpin, which has a transition midpoint of 40 degrees C in 0.115 M Na+, is unusually stable in comparison with previously reported hairpins. A non-linear least squares analysis of the undecamer's profile in terms of a two-state equilibrium model indicates that the hairpin-to-coil transition occurs with an enthalpy change about twice that expected if only combinations of Watson-Crick base-paired stacking interactions are considered. The analogous hairpin structure (containing an identical CG/CG stem) assignable to the complementary strand CGTCAAACTCGp does not form above 0 degrees C. Measurements on the two undecamers indicate that variation in non Watson-Crick interactions within the loops of two similar hairpins can produce a difference in stability of at least 2.2 kcal/mol (25 degrees C, 0.115 M Na+), roughly equal to the amount contributed to a double helix by a 5'-CG-3'/5'-CG-3' base-paired stacking interaction.

"Single Addition" substrates for the synthesis of specific oligoribonucleotides with polynucleotide phosphorylase. Synthesis of 2'-(alpha-methoxyethy) nucleoside 5'-diphosphates.

A number of synthetic methods for the preparation of the 2-O-(alpha-methoxyethyl) derivatives of the 5-diphosphates of adenosine, cytidine, guanosine, and uridine have been studied in order to provide nucleotide substrates that can be applied to the synthesis of specific oligoribonucleotides using polynucleotide phosphorylase. The reaction of nucleoside 5-diphosphates with methyl vinyl ether for a limited time produces low yields of the corresponding 2-O-(alpha-methoxyethyl) derivatives because the rate of methoxyethylation of the 3-hydroxyl groups. A study of the rates of acidic hydrolysis of alpha-methoxyethyl groups in the 2 and 3 positions of nucleosides and nucleotides has been made, and the results obtained form the basis of a more efficient method for the synthesis of the blocked nucleoside diphosphates. The method involves the reaction of nucleoside 5-diphosphates with methyl vinyl ether to give the corresponding 2,3-di-O-(alpha-methoxyethyl)nucleoside 5-diphosphates, and exploits the fact that, in the acidic hydrolysis of these derivatives, the rate of removal of the 3-methoxyethyl group is about twice that of the group in the 2 position. Alternative syntheses were based on the phosphorylation of methoxyethylated nucleosides and nucleotides. The derivatives, 2-O- and 2,3-di-O-(alpha-methoxyethyl)uridine, were prepared by the methoxyethylation of 3,5-di-O-acetyluridine and 5-O-acetyluridine followed by removal of the acetyl groups. The corresponding guanosine derivatives were made by the synthetic routes: (i) guanosine leads to O-2,O-3,O-5,N-2-tetrabenzoylguanosine leads to 2-N-benzoylguanosine leads to O3-acetyl-N-2,O5-dibenzoylguanosine leads to 2-O-(alpha-methoxyethyl)guanosine, and (ii) 2,3-O-isopropylideneguanosine leads to N-2,O5-diacetyl-2,3-O-isopropylideneguanosine leads to N-2,O-5-diacetylguanosine leads to 2,3-di-O-(alpha-methoxyethyl)guanosine. These methoxyethylated nucleosides were converted to the corresponding 5-phosphates by reaction with cyanoethyl phosphate and dicyclohexylcarbodiimide, and then to the corresponding 5-diphosphates by subsequent reaction with 1,1-carbonyldiimidazole and inorganic phosphate.

Cytokeratin and vimentin intermediate filament proteins in benign and neoplastic prostatic epithelium.

Prostatic samples from 30 hyperplastic prostates and 61 prostatic adenocarcinomas were examined for vimentin and cytokeratins. The co-expression of cytokeratins and vimentin was found in all benign prostatic epithelium and in 83% of adenocarcinomas. Benign prostatic epithelium showed vimentin intermediate filaments distinctively distributed in the basal regions and as paranuclear sheaves along the long axis of the cell. This pattern of vimentin staining was seen in adenocarcinomas with low Gleason scores, whereas high-grade tumours showed intense diffuse perinuclear staining.

Esterification of terminal phosphate groups in nucleic acids with sorbitol and its application to the isolation of terminal polynucleotide fragments.

The exposure of mono- and polynucleotides to 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide and high concentrations of sorbitol results in the esterification of their monosubstituted phosphate groups. The presence of the sorbitol moiety permits these derivatives to bind strongly at pH 8.7 to columns of chromatographic supports containing the dihydroxyboryl group and to be subsequently released by elution with buffers at pH 5.5. The procedure constitutes a method for the isolation of polynucleotide fragments arising from the terminals of nucleic acids. A new method for the preparation of the chromatographic supports involves the synthesis of the 1,3-propanediol cyclic ester of m-[[3-(N-succinimidoxycarbonyl)propanoyl]amino]benzeneboronic acid and its condensation with aminoethylcellulose or amino-ethylpolyacrylamide. The reagent is readily prepared by reaction of N-[m-(dihydroxyboryl)phenyl)]succinamic acid with 1,3-propanediol to protect the boronate moiety followed by esterification with N-hydroxysuccinimide in the presence of dicyclohexylcarbodiimide.

'Single addition' and 'transnucleotidation' reactions catalyzed by polynucleotide phosphorylase. Effect of enzymatic removal of inorganic phosphate during reaction.

The reaction of the tetranucleotide, pA-A(2)-A, with 2'(3')-0-(alpha-methoxyethyl)uridine 5'-diphosphate, Mg(2+) ions, and M. luteus polynucleotide phosphorylase followed by mild acid treatment to remove the blocking groups results in a 49% yield of the desired single addition product, pA-A(3)-U, together with smaller amounts of pA-A-U, pA-A-A, pA-A(2)-U, pA-A(2)-A, pA-A(3)-A, pA-A(4)-U, and pA-A(4)-A. The side products are thought to arise from the phosphorolysis of the acceptor molecule by the inorganic phosphate formed in the reaction mixture and from subsequent additions to the various oligonucleotide species by the resulting adenosine 5'-diphosphate. A system developed for the removal of inorganic phosphate as it is formed in the synthesis involves the addition to the reaction mixture of calf spleen nucleoside phosphorylase and nicotinamide riboside and, under these conditions, pA-A(3)-U can be prepared in 90% yield with essentially no side products. Under similar conditions, pA-A(3)-A, pA-A(3)-G, and pA-A(3)-C may be prepared from pA-A(2)-A and the appropriate blocked nucleoside diphosphate in yields of 85-94%. The incubation of pA-A(2)-A alone with polynucleotide phosphorylase exhibits the phenomenon of "transnucleotidation" in that the molecule is partially converted to oligonucleotides of smaller and larger chain lengths. In the presence of the phosphate removal system, however, the tetranucleotide is not attacked by the enzyme, and thus, "transnucleotidation" appears to be simply a combination of phosphorolytic and addition reactions catalyzed by trace amounts of inorganic phosphate contaminating the enzyme and/or the substrate.

Synthesis and properties of adenosine oligonucleotide analogues containing methylene groups in place of phosphodiester 5'-oxygens.

The ADP analogue in which the 5'-oxygen has been replaced by a methylene group can be prepared by condensing 5'-deoxy-5'-phosphonomethyladenosine with inorganic phosphate. This analogue readily polymerizes onto the primer A-A in the presence of the enzyme polynucleotide phosphorylase and either Mg2+ or Mn2+. The initial products are of the form A-A(-cA)n-cA (where "-" and "-c" stand for the normal phosphodiester linkage and the linkage in which the 5'-oxygen is replaced with the methylene group, respectively). Treatment of these with alkali yields adenosine 2'(3')-phosphate and the series (A(-cA)n-cA containing only phosphonomethylene linkages. The decamer A(-cA)8-cA interacts with two molecules of U(-U)8-U to form a triple-standard structure that has a stability similar to that exhibited by the analogous complex formed from A(-A)8-A and U(-U)8-U. This property, along with the resistance of these oligomer analogues toward nucleases that cleave phosphodiester linkages between the phosphorus and the 5'-oxygen, should provide a strong rationale for application of phosphonomethylene linkages in schemes for therapeutic drug design that use the antisense strategy.