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We introduce a novel experimental strategy for DNA mutation detection named the Mismatch Identification DNA Analysis System (MIDAS) [1, 2], which has an associated isothermal probe amplification step to increase target DNA detection sensitivity to attomole levels. MIDAS exploits DNA glycosylases to remove the sugar moiety on one strand (the probe strand) at a DNA base pair mismatch. The resulting apyrimidinic/ apurinic (AP) site is cleaved by AP endonucleases/lyases either associated with the DNA glycosylase or externally added to the reaction mixture. MIDAS utilizes 32p- or FITC-labeled oligonucleotides as mutation probes. Generally between 20-50 nucleotides in length, the probe hybridizes to the target sequence at the reaction temperature. Mismatch repair enzymes (MREs) then cut the probe at the point of mismatch. Once the probe is cleaved, the fragments become thermally unstable and fall off the target, thereby allowing another full-length probe to hybridize. This oscillating process amplifies the signal (cleaved probe). Cleavage products can be detected by electrophoretic separation followed by autoradiography, or by laser-induced fluorescence-capillary electrophoresis (LIF-CE) of fluorophore-labeled probes in two minutes using a novel CE matrix. In the present experiments, we employed the mesophilic Escherichia coli enzyme deoxyinosine 3'-endonuclease (Endo V), and a novel thermostable T/G DNA glycosylase, TDG mismatch repair enzyme (TDG-MRE). MIDAS differentiated between a clinical sample BRCA 1 wild-type sequence and a BRCA1 185delAG mutation without the need for polymerase chain reaction (PCR). The combination of MIDAS with LIF-CE should make detection of known point mutations, deletions, and insertions a rapid and cost-effective technique well suited for automation.

To study the effects of in vivo DNA methylation, we have developed an inducible system to control the intracellular concentration of S -adenosyl- l -methionine (AdoMet). The product of the bacteriophage T3 AdoMet hydrolase-encoding gene ( amh ), which degrades AdoMet to l -homoserine and 5′-methylthioadenosine, was employed to lower AdoMet concentrations in vivo. The amh gene was placed downstream from the inducible tetA promoter of the Tn10 tetracycline regulon substituting for most of the tetA gene. Unlike in the original isolates [Hughes et al., J. Bacteriol. 169 (1987) 3625-2632], this promoter allows controlled expression. These constructs are stable and can be induced in a dosedependent manner. The system is maximally induced 2–3 h after addition of the inducer, autoclaved chlortetracycline (cTc). DNA methylation in vivo was assessed in this model system by Bam HI cleavage of plasmid DNA isolated from cells cotransformed by two compatible plasmids, one carrying the inducible amh gene, the other M· Bam HI methyltransferase encoding gene. The induction of amh decreased the intracellular pool of AdoMet which M· Bam HII requires as a cofactor. Under these conditions, there is a decrease in DNA methylation. The unmethylated DNA is assayed by Bam HI cleavage. This system will be useful for studying transcription, DNA replication, gene repair and other cellular phenomena affected by methylation.

The equilibrium binding patterns of complementary oligonucleotides to the native and denatured conformers of yeast transfer RNA 3 Leu have been determined. The pattern of binding to the native conformer follows that observed previously with other tRNAs. The results indicate that the anticodon loop and 3′ terminus are free in solution, and that all stems of the cloverleaf appear intact, although the dihydrouracil and “extra arm” stems are sufficiently weak to be subject to competitive binding by the probe oligomers. The T ΨC loop is also inaccessible to oligomer binding, while the dihydrouracil loop shows a low level of binding suggestive of oligomer competition with existing RNA structure. By contrast, in the denatured conformer the dihydrouracil loop and stem show strong oligomer binding characteristics of random RNA segments, whereas the anticodon loop no longer binds complementary oligomers. Binding to other regions remains unchanged, suggesting that the three major cloverleaf stems are intact. These observations are used as a basis for consideration of models for the two conformers.

A single polypeptide of leucyl-tRNA synthetase (LRS) has been purified from budding bakers' yeast by a modification of the procedure published earlier. On denaturing polyacrylamide gel electrophoresis LRS was one band corresponding to molecular weight of 120,000 +/- 5,000 daltons. Variable amounts of LRS with a similar molecular weight but which dissociated into equal subunits of 58,000 were also isolated. The affinities (KM) for substrates for this form of the enzyme were similar to those previously reported for the dimeric form of the enzyme.

Pyran covalently linked to cyanogen bromide-activated Sepharose has been shown to be an effective affinity matrix for several viral DNA polymerases. Differential salt elution of viral compared with cellular polymerases, as well as substrate elution, suggests the affinity nature for the matrix. Unlike some other affinity systems described, pyran-Sepharose is totally resistant to nuclease digestion and is stable at 4 degrees for several months. DNA polymerases isolated from several viruses by detergent treatment were recovered in good yield. Analysis of iodinated proteins by sodium dodecyl sulfate-gel electrophoresis revealed that the DNA polymerase of avian myeloblastosis virus found in crude preparations of the virus could be purified nearly to homogeneity by a single passage through the column. These results suggest that pyran-Sepharose is an effective affinity column that is potentially adaptable as part of a general purification procedure for viral DNA polymerases.

We describe a cloning-expression vector system for selecting DNA fragments containing open reading frames (ORFs) and expressing them as beta-galactosidase (beta Gal) hybrid fusion proteins. The plasmid vector, pWS50, utilizes the very strong and easily regulated bacteriophage lambda promoter pL, and the efficient translation initiation signals of the N-terminal segment of the lambda cII gene. Fused distally to and out of translational phase with cII is the E. coli lacZ gene, lacking its own transcriptional and translational initiating signals. A unique restriction enzyme site (NruI) is located between the upstream regulatory sequences and the lacZ gene, which provides a cloning site for the insertion of blunt ended DNA fragments. In addition, there are two other unique restriction sites (NheI and BamHI) located in this region which can also be used as closing sites. If a DNA fragment does not contain any translation termination codons (i.e., an ORF), and is inserted correctly into the vector, the translational reading frame between cII and lacZ can be restored. Colonies containing these recombinants can be easily screened as LacZ+ on lactose indicator media. The beta-galactosidase fusion proteins produced from the LacZ+ recombinants are identified on sodium dodecyl sulfate polyacrylamide gels by their large size and high level of production. To test the ORF cloning-expression system, a segment of the human T-cell lymphotrophic virus type I envelope gene was cloned and expressed at high levels. The envelope-beta Gal fusion protein was recognized by antibodies in serum from a patient with adult T-cell leukemia.

Fractionation of several type II specific restriction endonucleases was achieved by separation on two novel biospecific matrices. The matrices are pyran, a copolymer of divinyl ether of maleic anhydride, and Cibacron Blue F3GA, a blue dye commonly used for the calibration of molecular sieves. Both compounds are insolubilized by coupling to sepharose through a cyanogen bromide linkage and in their soluble form inhibit the restriction endonucleases which we have tested. These affinity matrices can be used to obtain restriction endonucleases from crude extracts after removal of nucleic acids. They have also proven to have a high capacity when used as subsequent steps in enzyme purification. Their additional advantage is the rapid development time and reusability of columns packed with the two matrices.Images

We wish to report the initial characterization of a recombinant clone containing the BamHI methylase gene. Genomic chromosomal DNA purified from Bacillus amyloliquefaciens was partially cleaved with HindIII, fractionated by size, and cloned into pSP64. Plasmid DNA from this library was challenged with BamHI endonuclease and transformed into Escherichia coli HB101. A recombinant plasmid pBamM6.5 and a subclone pBamM2.5 were shown to contain the BamHI methylase gene based on three independent observations. Both plasmids were found to be resistant to BamHI endonuclease cleavage, and chromosomal DNA isolated from E.coli HB101 cells harboring either of the plasmids pBamM6.5 or pBamM2.5 was resistant to cleavage by BamHI endonuclease. In addition, DNA isolated from lambda phage passaged through E.coli HB101 containing either plasmid was also resistant to BamHI cleavage. Expression of the BamHI methylase gene is dependent on orientation in pSP64. In these clones preliminary evidence indicates that methylase gene expression may be under the direction of the plasmid encoded LacZ promoter.

Extracts from Agrobacterium tumefaciens strain ID135 contain three enzymes that have been characterized and partially purified. The first enzyme, a DNA topoisomerase, appeared to relax only negatively twisted DNA. The second enzyme, Atu I, a type II restriction endonuclease, generated the identical DNA digestion pattern as EcoRII when several DNAs were used. The third enzyme, endonuclease A, showed a preference for superhelical DNAs as substrates. When plasmid pCK135DNA, obtained from the virulent strain IDI135 of A. tumefaciens, or plant DNA was exposed to the three enzymes, changes in DNA patterns were observed due to either conformational changes or digestion of the DNAs. These enzymes may function in vivo in the processing and incorporation of bacterial DNA in plant cells.

We have inserted a genomic clone of the human EJ bladder oncogene into a murine retrovirus shuttle vector. Cotransfection of this shuttle vector DNA containing the activated ras oncogene with molecularly cloned Moloney murine leukemia virus into NIH/3T3 cells was able to rescue a replicating and transforming retrovirus. The viral DNA from infected cells was excised by fusion to mouse COP-5 cells and recloned into Escherichia coli as plasmid DNA. Analysis of the recloned plasmids by size, restriction enzyme mapping, and DNA sequence indicated that approximately 5% of the recloned plasmids contained the intronless EJ ras oncogene.

The DNA topoisomerase from Agrobacterium tumefaciens has been purified to apparent homogeneity. The enzyme is a single polypeptide of about 100,000 in molecular weight. No apparent separation of the nicking and sealing activities could be obtained in attempts to separate the two activities by a variety of methods, including limited protease digestion, thermal denaturation, and differential inhibition. Monoclonal antibodies obtained from hybridomas likewise did not preferentially inhibit one of the two activities. These results suggest that the two catalytic functions are carried by the same essential residues of the active enzyme site.

Leucyl-tRNA synthetase from bakers' yeast was purified to homogeneity and characterized. The native enzyme has a molecular weight of 120,000 and contains two identical subunits that upon dissociation display very low aminoacylation activity. From the molecular weight and the sedimentation coefficient of the native enzyme (s20,w0 = 6.05 x 10-13) a value of 5.18 x 10-7 was calculated for d20,w0, which leads to a Stokes radius of 40.7 A. For a spherical molecule this radius corresponds to a volume of 282,000 A3. The kinetic parameters for the enzyme with its substrates are typical for this class of enzymes.

tRNA Leu -Synthetase from baker's yeast has been crystallized from ammonium sulfate solution. The crystals are of orthorhombic symmetry, falling into space group [unk] or [unk] with a = 75.5 Å, b = 110.7 Å, and c = 124.0 Å. This unit cell contains four molecules of the native (dimeric) enzyme, with eight asymmetric units, each corresponding to the enzyme subunit. Diffraction patterns obtained for the three major projections contain reflections to spacings of less than 3.5 Å, indicating that this crystal form is amenable to structure analysis to atomic resolution.

Avian myeloblastosis virus is defective in reproductive capacity, requiring a helper virus to provide the viral proteins essential for synthesis of new infectious virus. This virus arose by recombination of the nondefective helper virus and host cellular sequences present within the normal avian genome. These latter sequences are essential for leukemogenic activity. The complete nucleotide sequence of this region is reported. Within the acquired cellular sequences there is an open reading frame of 795 nucleotides starting with the initiation codon ATG (adenine, thymine, guanine) and terminating with the triplet TAG. This open reading frame could code for the putative transforming protein of 265 amino acids with a molecular weight of approximately 30,000.

Type II restriction endonucleases Bam HI and Eco RI were covalently coupled to Sepharose. These insolubilized enzymes generated fragment patterns for several viral DNAs identical to those produced by the respective free enzymes. Conditions for optimal activity were similar for both bound and unbound forms of the enzymes. Insolubilization improved thermal stability of Bam HI and Eco RI. The bound enzyme can be recovered from reaction mixtures and reused several times. Upon storage at 4 degrees C, coupled endonucleases remained stable for several months.

Publisher Summary This chapter discusses the preparation and properties of immobilized sequence specific endonucleases. The type II restriction endonucleases have become valuable reagents for research in molecular biology. This is primarily due to their unique property of cleaving DNAs at a limited number of specific sites. These enzymes have been employed for use in physical DNA mapping, plasmid construction, and gene cloning. Most of these enzymes recognize and cleave DNA at specific sequences, which are usually in the form of a palindrome. There is evidence implying that these endonucleases are membrane bound, therefore, one approach to study them is to determine what effect in-solubilization (that is, mimicking membrane binding) has on their activity. The immobilized enzymes can be packed in the form of a column or rapidly pelleted from solutions by centrifugation. These procedures allow quick removal of restriction endonucleases from reaction mixtures. Such recovered enzymes are reusable several times over, permitting cleavage of large amounts of DNA with relatively few units of enzyme. Furthermore, the chapter describes the catalytic and functional characterization of covalently bound restriction endonucleases.

Publisher Summary This chapter describes the in vitro and enzymatic synthesis and structural organization of avian myeloblastosis virus (AMV) linear duplex DNA. Avian retroviruses contain a unique genome composed of a diploid single-stranded RNA. AMV RNA consists of two 35S subunits which code for at least three viral gene products. These include gag, pol, and env, which code for viral structural proteins, a polymerase, and glycoproteins of the viral envelope, respectively. The identification and location of the leuk gene responsible for leukemogenic transformation remain unknown. In an experiment described in the chapter, full-length cDNA transcripts of intact RNA were isolated after an alkaline sucrose gradient centrifugation. The complete copy is 11% double stranded after nuclease S 1 digestion. A hairpin structure at the 3′ end of the cDNA self-primes synthesis of the second strand. The product of this two-step reaction catalyzed by reverse transcriptase is a linear duplex of 5.2 × 10 6 daltons. The chapter discusses the mechanism of hairpin formation by reverse transcriptase and its possible involvement in proviral synthesis in vivo .

A DNA polymerase purified from a particulate fraction of human milk has biochemical and biophysical properties similar to those of viral reverse transcriptases. This enzyme is immunologically distinct from cellular DNA polymerases obtained from a variety of human sources.

Sheared chromatin prepared from chicken embryo fibroblasts and fibroblasts transformed by exogenous Rous sarcoma virus (Schmidt--Ruppin strain D) was separated by rate sedimentation on glycerol gradients into two components: fast-migrating (heavy chromatin fraction) and slow-migrating (light chromatin fraction). DNAs extracted from these fractions were assayed for proviral sequences by molecular hybridization using DNA complementary to the viral sequences. In uninfected cells, the endogenous complementary sequences were found to be equally distributed between heavy and light fractions. However, the newly integrated exogenous proviral sequences were found mostly in the light chromatin fraction in the transformed cells. Additionally, the light fraction was more sensitive to DNase I digestion and contains more material melting at low temperatures when compared with the heavy fraction. The results show that (i) distribution of endogenous proviral sequences is independent of chromatin conformation, and (ii) most of the newly acquired exogenous sequences are integrated within the host's chromatin fraction that exhibits properties of euchromatin. Because chromatin fragmentation and fractionation is accomplished without digestion with degrading enzymes, the chromatin fractions enriched in exogenous sequences remain intact and thus are suitable for further studies.

Two virus-specific RNA species of 7.5 and 7.0 kilobases have been identified in avian myeloblastosis virus (AMV) by denaturing gel electrophoresis and blot hybridization analysis, and they were found to be in a 10:1 ratio. The individual RNAs direccted the cell-free synthesis of the 76,000-dalton "gag" protein and the 180,000-dalton "gal-pol" protein, thereby demonstrating 5' sequence homology of approximately 4.9 kilobases between the two species. Synthesis of these two precursor proteins by the AMV genome indicates structural differences between AMV and other avian acute leukemia viruses. The two viral RNAs were transcribed into complete cDNA copies with AMV DNA polymerase. Linear proviruses were found to be 90--100% resistant to S1 nuclease. Analysis of single-stranded transcripts demonstrated two distinct species of 2.6 and 2.3 x 10(6) daltons, and analysis of duplexes formed from the single-stranded transcripts demonstrated species of 5.2 and 4.0 x 10(6) daltons.

The primary structures for tTNATrp (bovine) and primer tRNATrp (avian) show only minor differences in nucleotide sequence. The heterologous tRNATrp (bovine) appears to have properties similar to the tRNATrp (avian) in its ability to bind the alphabeta from of RNA-dependent DNA nucleotidyltransferase of avian myeloblastosis virus. A stable enzyme-tRNA complex has been isolated by gel filtration. In addition, tRNATrp (bovine) can hydridize to the avian viral 35S RNA and act as a primer for transcription of the RNA. tRNATrp (bovine) can be obtained in larger amounts than the avian primer and can be used to study the interactions between the primer and the viral enzyme.

Summary Polyriboadenylic acid was treated with chloroacetaldehyde under conditions known to introduce e-adenosine groups. The degree of modification was monitored by increase in fluorescence intensity. Modified e-poly rA was found to be inhibitory when unprimed 70S AMV RNA was used as a substrate, suggesting direct competition with the poly rA tract of the RNA. Since e-poly rA cannot effectively base pair with nucleic acids normally involved in cellular processes, it has the potential of being useful as an inhibitor of oncogenic viral polymerases.

The effect of glycerol on the specificity of DNA cleavage by the restriction endonuclease BamHI has been examined. In addition to the canonical G decreases from G-A-T-C-C site, BamHI cuts DNA at several sites that we have named noncanonical BamHI.1 sites. The number of BamHI.1 sites in simian virus 40 and pBR322 was determined to be 13 for each DNA. Cutting sites determined by DNA sequence analysis include G decreases from G-A-A-C-C, G decreases from G-C-T-C-C, G decreases from G-G-T-C-C, and G-A-A-T-C-C with the complementary strand sequence assignments of G-G-T-T-C-C, G-G-A-G-C-C, G-G-A-C-C-C, and G-G-A-T-T-C. The relaxation in specificity was related to hydrogen bond acceptor and donor sites in the recognition sequence, in an attempt to generate a model of BamHI recognition of cognate sites in DNA.

A DNA endonuclease, Endo-I, which cleaves superhelical DNAs, has been isolated from avian myeloblastosis virions stripped of their coats by mild detergent treatment. The enzyme has a broad pH optimum around 7.5-8.0 and requires Mg2+ for activity. A second endonuclease, Endo-II, with a requirement for Mn2+, also present in viral cores, copurified with avian myeloblastosis virus alpha beta DNA polymerase (reverse transcriptase, RNA-dependent DNA nucleotidyltransferase) and similarly cleaved superhelical DNAs. Heat denaturation and sodium fluoride and N-ethylmaleimide inhibition studies were carried out to demonstrate a possible relationship between the two endonucleases and the viral DNA polymerase and RNase H activities. It appears that Endo-II may be an intrinsic activity of the polymerase.

The nucleotide sequence of the integrated avian myeloblastosis virus long terminal repeat has been determined. The sequence is 385 base pairs long and is present at both ends of the viral DNA. The cell-virus junctions at each end consist of a 6-base-pair direct repeat of cell DNA next to the inverted repeat of viral DNA. The long terminal repeat also contains promoter-like sequences, an mRNA capping site, and polyadenylation signals. Several features of this long terminal repeat suggest a structural and functional similarity with sequences of transposable and other genetic elements. Comparison of these sequences with long terminal repeats of other avian retroviruses indicates that there is a great variation in the 3' unique sequence (U3), whereas the 5' specific sequences (U5) and the R region are highly conserved.

The hydrogen-bonded protons of the base pairs in the native and denatured conformers of transfer RNA3Leu from bakers' yeast have been investigated by high resolution proton nuclear magnetic resonance at 220 MHz. Widespread changes in the nuclear magnetic resonance spectrum observed on going from the denatured to the native state indicate a change from 18 base pairs in the former conformer to 22 in the latter, corresponding to a gain of 3 to 5 G · C pairs, and a loss of 0 to 2 A · U pairs. These changes are compared with other data on the two conformers, affording further insight into their differences.