Synthesis and properties of second-generation 2-5A-antisense chimeras with enhanced resistance to exonucleases

In order to stabilize 2-5A-antisense chimeras to exonucleases, we have synthesized chimeric oligonucleotides in which the last phosphodiester bond at the 3'-terminus of the antisense domain was inverted from the usual 3',5'-linkage to a 3',3'-linkage. The preparation of such analogues was accomplished through standard phosphoramidite chemistry with the use of a controlled pore glass solid support with a nucleoside attached through its 5'-hydroxyl, thereby permitting elongation at the 3'-hydroxyl. The structures of such terminally inverted linkage chimeras of the general formula pA4-[pBu]2-(pdNn3'-3'dN) were corroborated by a combination of snake venom phosphodiesterase digestion in the presence or absence of bacterial alkaline phosphatase. Most characteristically, the presence of the 3'-terminal-inverted phosphodiester linkage produced an unnatural dinucleotide of general composition dN3'p3'dM. These structures could be confirmed by independent synthesis and fast atom bombardment mass spectroscopy (FAB). 2-5A-Antisense chimeras of this structural class, pA4-[pBu]2-(pdNn'3-3'dN), were 5-6-fold more stable than their unmodified congeners, pA4-[pBu]2-(pdN)n, to degradation by a representative phosphodiesterase from snake venom. In 10% human serum, the new 2-5A-antisense chimeras, pA4-[pBu]2-(pdNn3'-3'dN), possessed a half-life that was 28-fold longer than that of the unmodified chimeras. These results provide entry to a second generation of 2-5A-antisense chimeras.

Allelic imbalance at the beta-catenin gene (CTNNB1 at 3p22-21.3) in various human tumor types

beta-catenin is a multifunctional protein: it plays a central role in the cell-cell adhesive junctions, and participates in transduction of the morphogenic Wingless/Wnt-signal. Upon detailed analysis of the human beta-catenin gene, an intragenic polymorphic microsatellite marker could be identified. This marker shows 62% heterozygosity and was used in a study of eleven different tumor types. A high level of beta-catenin allelic imbalance was observed for small cell lung carcinoma, squamous cell lung carcinoma and cervix carcinoma. Other microsatellite markers on 3p24-21 could demonstrate frequent but not invariable codeletion of flanking chromosomal loci. This intragenic polymorphic marker will allow selection of tumor types and tumor samples possibly bearing recessive mutations in the remaining allele of the beta-catenin gene.

UAS(MAG1), a yeast cis-acting element that regulates the expression of MAG1, is located within the protein coding region of DDI1

MAG1 and DDI1 are two divergently transcribed DNA damage-inducible genes from Saccharomyces cerevisiae. Previous studies have shown that MAG1 induction requires an upstream activating site (UAS) located between nucleotides -376 and -330. Here we show that a 24-bp oligonucleotide from within the UAS(MAG1) region forms a sequence-specific DNA-protein complex with partially purified proteins from S. cerevisiae. Point mutations introduced into the 24-bp oligonucleotide inhibited the formation of the DNA-protein complex and decreased the level of induction of MAG1-lacZ. By determining the transcription and translation start points of both MAG1 and DDI1, an interesting, indeed unprecedented feature of genome organization in eukaryotes was revealed: UAS(MAG1) actually lies within the protein-coding region of DDI1. Although tightly linked to each other, and co-induced upon treatment with DNA-damaging agents, DDI1 does not share the UAS(MAG1) required for DNA damage induction of MAG1. Furthermore, MAG1 and DDI1 respond differently in the presence of the protein synthesis inhibitor cycloheximide, suggesting that these two genes are regulated by different mechanisms in the absence of de novo protein synthesis.

A mutation in the MSH5 gene results in alkylation tolerance

DNA methylating agents such as N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) are potent carcinogens; their carcinogenic effect is mainly due to the effect of production of O6-methylguanine (O6 MeG) on DNA. O6 MeG is not only mutagenic but also toxic to the cell because Mer-/Mex- cells unable to remove O6 MeG are very sensitive to killing by MNNG. It has been proposed that repeated futile mismatch correction of O6 MeG-containing bp is responsible for the genotoxicity of the O6 MeG lesion and that loss of mismatch repair activity results in cellular tolerance to O6 MeG, but the hypothesis has not been proved. We used yeast as a model to test this hypothesis and found that chromosome deletion of any known nuclear mitotic mismatch repair genes, including MLH1, MSH2, MSH3, MSH6, and PMS1, did not rescue mgt1delta O6 MeG DNA repair methyltransferase-deficient cells from killing by MNNG. A large number of mgt1delta, MNNG-tolerant revertants were isolated, among which one cell line, XS-14, has been found to carry a mutated allele of the MSH5 gene. The mutation also affected spore survival but did not increase the spontaneous mutation rate. We further demonstrated that a mutated form of the MSH5 gene, msh5-14, not the msh5delta-null mutation, is responsible for the cellular tolerance to MNNG in XS-14 cells. This observation offers an alternative model that may reconcile seemingly contradictory observations of yeast and mammalian cells.

Correlation of selective modifications to a 2',5'-oligoadenylate-3',5'-deoxyribonucleotide antisense chimera with affinity for the target nucleic acid and with ability to activate RNase L

The use of an antisense oligonucleotide to address a specific targeted RNA sequence and subsequent localized activation of the 2-5A-dependent RNase (RNase L) to effect selective RNA degradation is a new approach to the control of gene expression called 2-5A-antisense. The previously reported biological activity of the 2-5A:AS chimeric oligonucleotide [p5'(A2'p)3A-antiPKR1], directed against nucleotides 55-73 of the coding sequence of the PKR mRNA, has been used as a point of reference to examine the effect of introducing mismatches into the chimeric oligonucleotide, altering the chain length of the antisense domain of the chimeras, removal of the 5'-monophosphate moiety, shortening the 2',5'-oligoadenylate domain, and substitution of 3',5'-linked 2'-deoxyadenosine nucleotides for the 2-5A domain. The general formula for the novel chimeric oligonucleotides is p5'(A2'p)3A2'p(CH2)4p(CH2)4p(5'N3'p)mN, where N is any nucleoside and m is any integer. When the biological activity of these new chimeric oligonucleotides was compared to that of the parent chimera, 2-5A-aPKR, for their ability to effect target PKR RNA cleavage in a cell-free and in an intact cell assay, it was determined that there was a close correlation between the activity of 2-5A-antisense chimeras and their affinity (Tm) for a targeted nucleic acid. In addition, there was also a close correlation between activity of the 2-5A-antisense chimeras and their ability to activate the 2-5A-dependent RNase L.

Targeting RNA decay with 2',5' oligoadenylate-antisense in respiratory syncytial virus-infected cells

Treatment of human cells with 2',5' oligoadenylate covalently linked to antisense (2-5A-antisense) results in the selective cleavage of targeted RNA species by 2-5A-dependent RNase L. Here we show that 2-5A-antisense containing stabilizing modifications at both termini are effective in suppressing the replication of respiratory syncytial virus (RSV) in human tracheal epithelial cells. The affinity of 2-5A-antisense for different regions in the RSV M2 and L mRNAs was predicted from a computer-generated model of the RNA secondary structure. The most potent 2-5A-antisense molecule caused a highly effective, dose-dependent suppression of RSV yields when added to previously infected cells. In contrast, control oligonucleotides, including an inactive dimeric form of 2-5A linked to antisense, 2-5A linked to a randomized sequence of nucleotides, and antisense molecules lacking 2-5A, had minimal effects on virus replication. The specificity of this approach was shown by reverse transcriptase-coupled PCR analysis of RSV M2, P, and N mRNA and of cellular glyceraldehyde-3-phosphate dehydrogenase mRNA. The RSV M2 mRNA amounts were depleted after treating RSV-infected cells with 2-5A-antisense targeted to this mRNA, whereas the amounts of the other RNA species were unchanged. These studies demonstrate that 2',5' oligoadenylate covalently linked to antisense (2-5A-antisense) can effectively suppress RSV replication by directing the cellular RNase L to selectively degrade an essential viral mRNA.

Identification of a promoter-specific transactivation domain in the herpes simplex virus regulatory protein ICP4

ICP4 is expressed during the immediate-early phase of infection by herpes simplex virus (HSV) and activates transcription of viral genes during subsequent phases of productive infection. Several members of the alpha-herpesvirus family encode regulatory proteins that have extensive homology with ICP4 and exhibit a transactivation domain (TAD) at the N terminus. The portions of ICP4 required for nuclear localization, DNA binding, and dimerization have been defined, but a domain that is specifically required for transactivation has not been identified. We have defined a promoter-specific ICP4 TAD by analysis of the activity of GAL4-ICP4 fusion proteins cotransfected into HeLa cells with a luciferase reporter gene linked to a promoter with five GAL4 binding sites. The transactivation activity of GAL4-ICP4 hybrids is located entirely within the first 139 residues of ICP4 and is significantly less potent than the activity of GAL4-TAD hybrids derived from ICP4 homologs. ICP4 residues 97 to 109 are a critical component of this N-terminal TAD. Transient transfection assays performed with nonfusion forms of ICP4 and luciferase genes linked to the HSV glycoprotein D (gD) or thymidine kinase (tk) promoter revealed that ICP4 residues 97 to 109 are required for induction of the gD promoter but are not required for induction of the tk promoter. Comparative experiments with ICP4 homologs revealed that the pseudorabies virus TAD is a potent activator of the gD promoter and a weak activator of the tk promoter. Complementation assays revealed that loss of ICP4 residues 97 to 109 reduced the yield of virus from infected cells nearly 500-fold compared to wild-type ICP4. We conclude that ICP4 residues 97 to 109 are a core component of a promoter-specific transactivation domain that is required for efficient replication of herpes simplex virus.

Robustness of bioequivalence procedures under Box-Cox alternatives

This study investigates the robustness of Schuirmann's two one-sided tests procedure under a set of Box-Cox alternatives. A simulation is conducted to study the level of significance and the power of the procedure. Empirical results show that Schuirmann's procedure is robust under Box-Cox alternatives when the mean of the underlying distribution of the reference formulation is known, which suggests that the assumptions of normality or lognormality are sufficient but may not be necessary. It appears that Schuirmann's procedure cannot maintain the proper level of significance when the mean of the reference formulation is unknown, even under the normality or lognormality assumptions.

Bidirectional regulation of two DNA-damage-inducible genes, MAG1 and DDI1, from Saccharomyces cerevisiae

MAG1 encodes a Saccharomyces cerevisiae 3-methyladenine DNA glycosylase that initiates a base-excision-repair pathway and protects yeast cells from killing by methylating agents such as methyl methanesulphonate (MMS). In the promoter region of the MAG1 gene, there is an 8 bp GC-rich direct repeat (DR). Here we report that the DR sequence functions as an upstream activating site (UAS) that upregulates the expression of MAG1 as well as another DNA-damage-inducible gene, DDI1, which is transcribed divergently from MAG1. Deletions, or point mutations, within this repeat completely abolished DNA-damage induction and resulted in a reduced basal-level expression for both MAG1 and DDI1 genes. Furthermore, yeast cells carrying the MAG1 gene with the DR deletion displayed an increased sensitivity to MMS compared with wildtype cells. The DR sequence alone can activate transcription of a CYC1 minimal promoter and confer a partial DNA-damage responsiveness. Electrophoretic mobility-shift assays indicate that the DR function is not due to interaction with the yeast RPA. Like MAG1, the DDI1 gene is also controlled by an upstream repressing site (URS) located 5' to the direct repeat. Based on this and previous studies, a model is proposed whereby the constitutive expression of MAG1 and DDI1 is controlled by two functionally opposite regulatory elements, UAS and URS, probably through an antagonistic mechanism, whereas the damage-induced expression appears to be regulated by mechanisms of derepression at the URS as well as activation at the UAS.

A novel 165-base-pair terminal repeat sequence is the sole cis requirement for the adeno-associated virus life cycle

Adeno-associated virus (AAV) replication is dependent on two copies of a 145-bp inverted terminal repeat (ITR) that flank the AAV genome. This is the primary cis-acting element required for productive infection and the generation of recombinant AAV (rAAV) vectors. We have engineered a plasmid (pDD-2) containing only 165 bp of AAV sequence: two copies of the D element, a unique sequence adjacent to the AAV nicking site, flanking a single ITR. When assayed in vivo, this modified hairpin was sufficient for the replication of the plasmid vector when Rep and adenovirus (Ad) helper functions were supplied in trans. pDD-2 replication intermediates were characteristic of the AAV replication scheme in which linear monomer, dimer, and other higher-molecular-weight replicative intermediates are generated. Compared to infectious AAV clones for replication, the modified hairpin vector replicated more efficiently independent of size. Further analysis demonstrated conversion of the input circular plasmid to a linear substrate with AAV terminal repeat elements at either end as an initial step for replication. This conversion was independent of both Rep and Ad helper genes, suggesting the role of host factors in the production of these molecules. The generation of these substrates suggested resolution of the modified terminal repeat through a Holliday-like structure rather than replication as a mechanism for rescue. Production of replicative intermediates via this plasmid substrate were competent not only for AAV DNA replication but also for encapsidation, infection, integration, and subsequent rescue from the chromosome when superinfected with Ad and wild-type AAV. These studies demonstrate that this novel 165-bp ITR substrate is sufficient in cis for the AAV life cycle and should provide a valuable reagent for further dissecting the cis sequences involved in AAV replication, packaging, and integration. In addition, this novel plasmid vector can be used as a substrate for both rAAV vector production and synthetic plasmid vector delivery.

The repair of DNA methylation damage in Saccharomyces cerevisiae

The major genotoxicity of methyl methanesulfonate (MMS) is due to the production of a lethal 3-methyladenine (3MeA) lesion. An alkylation-specific base-excision repair pathway in yeast is initiated by a Mag1 3MeA DNA glycosylase that removes the damaged base, followed by an Apn1 apurinic/ apyrimidinic endonuclease that cleaves the DNA strand at the abasic site for subsequent repair. MMS is also regarded as a radiomimetic agent, since a number of DNA radiation-repair mutants are also sensitive to MMS. To understand how these radiation-repair genes are involved in DNA methylation repair, we performed an epistatic analysis by combining yeast mag1 and apn1 mutations with mutations involved in each of the RAD3, RAD6 and RAD52 groups. We found that cells carrying rad6, rad18, rad50 and rad52 single mutations are far more sensitive to killing by MMS than the mag1 mutant, that double mutants were much more sensitive than either of the corresponding single mutants, and that the effects of the double mutants were either additive or synergistic, suggesting that post-replication and recombination-repair pathways recognize either the same lesions as MAG1 and APN1, or else some differ- ent lesions produced by MMS treatment. Lesions handled by recombination and post replication repair are not simply 3MeA, since over-expression of the MAG1 gene does not offset the loss of these pathways. Based on the above analyses, we discuss possible mechanisms for the repair of methylation damage by various pathways.

[Studies of the characteristic features of Ki-1 positive non-Hodgkin's lymphoma]

The clinical histopathological and immunophenotypic features in 5 patients with Ki-1 positive non-Hodgkin's lymphoma (NHL) were studied. When first seen, 4 patients presented enlargement of superficial lymph nodes, with skin lesions in 2 patients. Two patients in stage IV with fever, hepato-splenomegaly and bone marrow invasion, died. Histologically, the tumor cells showed diffused or patchy hyperplasia. The cells were relatively large in size, rich in bosophilic or slightly eosinophilic cytoplasm with irregularly-shaped nuclei, prominent nucleoli, and distinct anaplasia and pleomorphism. Some of the cells looked very much like the Reed-Sternberg cells. Multinucleated giant cells were seen. Immunophenotypically, all the cells were CD30 (Ki-1) and CD25 (IL-2 receptor) positive but CD15 (Leu M1) negative. Thus, the 5 patient T Ki-1 positive NHL were all of T cell type.

High efficiency, long-term clinical expression of cottontail rabbit papillomavirus (CRPV) DNA in rabbit skin following particle-mediated DNA transfer

The ability of skin to support long lasting expression of genes delivered with a particle-mediated system was evaluated in rabbits inoculated with cottontail rabbit papillomavirus (CRPV) DNA. The optimal delivery force for maximal gene expression in rabbit skin was determined in transient beta-galactosidase assays. Forty-five sites in four rabbits were then inoculated at 350-400 p.s.i. with CRPV DNA. All sites (100%) formed papillomas with multiple papillomas at most sites. These results support the feasibility of using a particle-mediated delivery system for gene therapy and suggest that some papillomavirus features, such an origin of replication, may be well suited for use in vectors to target long term expression to skin.

[Analysis of DNA methylation pattern of c-myc oncogene in hepatocellular carcinoma]

OBJECTIVES

To assess whether hypomethylation of c-myc gene occours in HCC and to determine its clinical significance.

METHODS

The methylation pattern at 3' end of c-myc gene was analyzed by Southern blot using methylation sensitive restrcition endonuclease enzymes Hpa I and Msp I in six normal liver tissues and 18 HCCs.

RESULTS

At least 5 CCGG sites were methylated at 3' end of c-myc gene in 6 normal liver tissues. However, the normal hypermethylation pattern was absent in 11 hepatocellular carcinoms (HCC) which showed different degree of hypomethylation even if among subclonal cells of same tumour tissues. The hypomethylation was observed more often in markedly advanced HCC with metastasis and poorly differentiated histological grade.

CONCLUSION

Scattered CpG at 3' end of c-myc gene was methylated in normal liver tissues. Methyl groups were deleted in different extent in HCC, which can lead to abnormal expression of c-myc gene. The hypomethylation of c-myc can reflect the malignlant extent of HCC and may serve as a useful prognostic indicator in clinical practice.

The 2 micron plasmid of laboratory yeast strains is a type-1/type-2 hybrid

Industrial yeast strains carry one of two homeologous 2 microns plasmids designated as type-1 or type-2. The 2 microns plasmid, Scp1, found in common laboratory strains of Saccharomyces cerevisiae is considered a type-2 plasmid, since the ori, STB, RAF and REP1 loci and intergenic sequences of the right-unique region of Scp1 are homologous to the corresponding loci in industrial strain type-2 plasmids. However, within both its 599 bp inverted repeats Scp1 has 142-bp sequences homologous to the bakers' yeast type-1 plasmid. DNA sequence analyses and oligonucleotide hybridizations indicate that the 142-bp insertion in Scp1 was probably due to homeologous recombination between type-1 and type-2 plasmids. These results suggest that some of the plasmid and chromosomal sequence polymorphisms seen in laboratory yeast strains result from homeologous recombination in their ancestral breeding stock.

Essential region for self-replication of Coryneform bacteria plasmid pXZ10145

A pTSK series of recombinant plasmids were constructed by cloning DNA fragments of pXZ10145 or its deleted deriviate pATN65 into plasmid vector pACYC177 of E. coli. Experiment results of Coryneform bacteria transformation with these pTSK plasmids allowed us to localize the essential region for self-replication on plasmid pXZ10145. The minimal replication region of the pXZ10145 was located on a 1.2kb Nael-Nrul DNA fragment in which only one open reading frame was found. This ORF was believed to be encoded a trans-acting replication factor. The replication origin (oriV) was locate on a 0.3kb NaeI-SalI fragment which was within the ORF region.

Modulation of interferon (IFN)-inducible gene expression by retinoic acid. Up-regulation of STAT1 protein in IFN-unresponsive cells

Interferons (IFN) and retinoids failed to inhibit the growth of a number of breast tumor cell lines. However, a combination of these two biological response modifiers significantly suppressed the cell growth at pharmacologically achievable doses. The molecular basis for such enhancement was investigated in MCF-7, a breast tumor cell line resistant to growth inhibition by IFN-beta. Pretreatment of cells with retinoic acid (RA) for 16 h followed by IFN-beta, but not the converse, induced cytotoxic effects in the cells. Continuous presence of RA was not necessary, although it enhanced the degree of cell death when present. Further analyses revealed that IFN-beta failed to activate IFN-stimulated gene transcription. However, IFN-beta strongly up-regulated the gene expression in RA-pretreated cells. Both IFN-beta- and IFN-gamma-inducible gene expression were enhanced via a modulation of the transcriptional factor IFN-stimulated gene factors-3 and GAF binding to respective cognate regulatory elements. STAT1 was undetectable in these cells prior to RA treatment. RA increased the levels of this crucial regulator, thereby restoring IFN responses. Thus, RA augmentation of STAT1 may be an early step in the cooperative anti-tumor effects of IFN and RA.

Mutagenicity and toxicity of the DNA alkylation carcinogens 1,2-dimethylhydrazine and azoxymethane in Escherichia coli and Salmonella typhimurium

DNA alkylating agents such as 1,2-dimethylhydrazine (SDMH) and azoxymethane (AOM) are potent carcinogens and are widely used to induce colon tumors in experimental animals. However, standard bacterial mutagenesis assays have failed to detect the mutagenic effects of these chemicals. Using derivatives of a set of Escherichia coli test strains developed by Cupples and Miller (Proc. Natl. Acad. Sci. USA, 86, 5345, 1989), we hve demonstrated that under two conditions, SDMH and AOM induced point mutations by several-fold in a dose-dependent manner: (i) of six possible base substitutions, they only induced GC-->AT transitions; and (ii) the cells must be deficient in O6-methylguanine (O6MeG) DNA methyltransferase (MTase) activity. SDMH and AOM up to 200 microg/ml were unable to induce His+ revertants in a Salmonella Ames test strain TA1535 (GC-->AT); however, in the absence of mammalian S9 extract, His+ revertants increased up to 55-fold upon treatment of an isogenic Salmonella strain deficient in MTase activity. These results indicate that SDMH and AOM are indeed bacterial mutagens and that lesions induced by them are the target of DNA repair MTases, which probably include mutagenic and carcinogenic lesions such as O6MeG. Furthermore, variable responses of bacterial species to SDMH- and AOM-induced mutagenicity suggests a difference either in the metabolism of potential mutagens or in the repair of specific lesions. Since O6MeG is not only a mutagenic lesion but also a lethal lesion if left unrepaired, we compared the mutagenicity and toxicity of SDMH and AOM with an SN-type methylating carcinogen. N-methyl-N'-nitro-N-nitrosoguanidine, and conclude that SDMH and AOM are weak bacterial mutagens.

Particle-mediated delivery of recombinant expression vectors to rabbit skin induces high-titered polyclonal antisera (and circumvents purification of a protein immunogen)

Polyclonal antibodies were generated in rabbits by delivery to skin of gold particles coated with mammalian expression vectors encoding a cytoplasmic (beta-galactosidase) or a nuclear (L1 capsid of cottontail rabbit papillomavirus) protein. One primary and one booster immunization of 30 micrograms DNA per rabbit yielded specific antisera with titers from 1:24 000 to 1:120 000 in each of eight rabbits, as detected by ELISA and Western blot analysis. Genetic immunization requires relatively small amounts of DNA, eliminates the need to purify the protein immunogen, and does not require irritating adjuvants.

[Changes of peripheral blood stem cells of patients with malignant hematopoietic tumor after chemotherapy]

To investigate the most appropriate condition for collecting stem cells during peripheral blood stem cells transplantation (PBSCT), we used colony forming unit-granulocyte, macrophage (CFU-GM) as index to observe the change of PBSC after chemotherapy in 12 patients with malignant hematopoietic tumor. The results showed that it was more suitable to collect PBSC when the number of leucocytes was 2 x 10(9)/L, neutrophils 0.8 x 10(9)/L and platelets 110 x 10(9)/L after chemotherapy for 2 weeks. After chemotherapy, the number of leucocytes were suppressed evidently. On the contrary, a lot of CFU-GM appeared during the recovery phase of peripheral hemogram. At the nadir of peripheral hemogram, the number of leucocytes correlated negatively with the number of CFU-GM (P < 0.05). The longer the time of chemotherapy, the less the CFU-GM that in the same patients. After chemotherapy the CD34+ cells which appeared early might not form CFU-GM, but the CD34+ cells at the recovery phase of peripheral hemogram had the same trend of change with CFU-GM.

Low-temperature femtosecond-resolution transient absorption spectroscopy of large-scale symmetry mutants of bacterial reaction centers

Reaction centers isolated from three large-scale symmetry mutants sym0, sym2-1, and sym5-2 described in the previous article of this issue [Taguchi, A. K. W., Eastman, J. E., Gallo, D. M., Jr., Sheagley, E.. Xiao, W., & Woodbury, N. W. (1996) Biochemistry 35, 3175-3186] have been investigated by low-temperature ground state and ferntosecond-resolution transient absorption spectroscopy. All three of these large-scale symmetry mutants undergo electron transfer at 20 K. The mutants sym0 and sym5-2 have yields and dominant rates of charge separation comparable to wild type. However. the sym2-mutant shows a roughly 35%, quantum yield at this temperature, and the major kinetic component of the initial electron transfer is slower than wild type by nearly a factor of 100. The sym0 mutant showed substantial changes in the monomer bacteriochiorophyll ground state and transient spectra, and both sym0 sym2-1 showed changes in the bacteriopheophyll ground state and transient spectra. In particular, sym2-1 shows a small absorbance decrease in the region of the Qx band of the B side bacteriopheophytin which could be attributed to 10%-20% electron transfer along the B pathway.

Asymmetry requirements in the photosynthetic reaction center of Rhodobacter capsulatus

Nine large-scale symmetry reaction center mutants were constructed in Rhodobacter capsulatus by replacing segments of the M subunit gene with the homologous region of the L subunit gene. Between them, the mutations resulted in symmetrization of essentially the entire region from the carboxy terminal portion of the C helix through most of the E helix. The amino acids in this region define about 80% of the environment of the reaction center cofactors. These studies show that roughly 80% of the amino acids that come in close contact with the cofactors involved in initial electron transfer can be made symmetric in a piecewise manner without loss of the ability to grow photoheterotrophically. However, the amino acid regions near the quinones and iron atom are much more sensitive to symmetrization and most of the large-scale changes in this region resulted in the loss of photosynthetic viability, probably due to loss of stable reaction centers from the photosynthetic membrane. More detailed analysis of the isolated photosynthetic membranes from these mutants showed that in all cases but one, there was some amount of charge separation occurring in the mutant reaction centers. This bank of mutants serves as a useful starting point for more detailed studies of the differential molecular interactions which occur between the two reaction center subunits and their associated cofactors.

Neurobiological mechanisms of the meridian and the propagation of needle feeling along the meridian pathway

The present experiments attempt to find the meridian phenomenon and how the needle feeling propagates along the given meridian channels. The neurobiological mechanisms of the meridian were studied with neuroelectrical recording from the motor neurons and CB-HRP retrograde histochemistry technique in both rats and cats. The results demonstrated that most, but not all, of alpha motor neurons supplying a muscle group of a given meridian were selectively activated by afferent inputs originating not only from homonymous or heterogeneous, but synergistic muscle, but also from the skin nerve overlying the muscle group of the homonymous meridian. However, the afferent inputs from the heterogeneous meridian have very weak or no effect. On the other hand, the labeled motor neurons supplying a given meridian muscles from a discrete longitudinal column with a definite bound in the lateral ventral horn. There are oriented dendro-dendristes projections between the labeled motor neurons. The characteristics of both selective responses of the motor neurons to afferent inputs and their neuro-anatomical arrangements in spinal cord offer neurobiological evidence for the meridian phenomenon.

Synthesis and characterization of composite nucleic acids containing 2', 5'-oligoriboadenylate linked to antisense DNA

Composite nucleic acids, known as 2-5A antisense chimeras, cause the 2-5A-dependent ribonuclease (RNase L) to catalyze the specific cleavage of RNA in cell free systems and in intact cells. Such 2-5A antisense chimeras are 5'-monophosphorylated, 2,'5'-linked oligoadenylates covalently attached to antisense 3',5'-oligodeoxyribonucleotides by means of a linker containing two residues of 1,4-butanediol phosphate. Here we report a fully automated synthesis of 2-5A antisense chimeras on a solid support using phosphoramidite methodology with specific coupling time modifications and their subsequent purification by reverse-phase ion-pair and anion exchange HPLC. Purified 2-5A antisense chimeras were characterized by [1H]NMR and [31P]NMR, MALDIMS, and capillary gel electrophoresis. The synthetic 2',5'-linked oligoadenylate showed no phosphodiester isomerization to 3',5' during or after synthesis. In addition, we have developed facile methodologies to characterize the chimeras using digestion with various hydrolytic enzymes including snake venom phosphodiesterase I and nuclease P1. Finally, Maxam-Gilbert chemical sequencing protocols have been developed to confirm the entire sequence of these chimeric oligonucleotides.

DNA mismatch repair mutants do not increase N-methyl-N'-nitro-N-nitrosoguanidine tolerance in O6-methylguanine DNA methyltransferase-deficient yeast cells

Treatment of cells with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) produces, among other lesions, mutagenic and carcinogenic lesions such as O6-methylguanine (O6MeG) and O4-methylthymine in DNA. An O6MeG DNA methyl-transferase (MTase) specifically and efficiently repairs such lesions. MTase-deficient bacterial, yeast and mammalian cells exhibit increased sensitivity not only to MNNG-induced mutagenesis, but also to MNNG-induced killing, suggesting that O6MeG-type lesions are also lethal to the cells. The lethal effect caused by O6MeG is not clear. Results from several recent experiments indicate that some MNNG-tolerant cell lines exhibit a loss of DNA mismatch binding/repair activity, suggesting that functional mismatch repair is probably responsible for the cellular sensitivity to DNA methylating agents. We tested this abortive O6MeG-T mismatch repair hypothesis in a well-defined lower eukaryote, Saccharomyces cerevisiae. We found that while mgt1-deleted MTase-deficient yeast strains are hypersensitive to MNNG-induced killing, combination of this mutation with any of the mlh1, msh2 or pms1 mutations did not render cells more tolerant to killing. msh3 mutation also did not rescue MNNG-induced genotoxicity. Furthermore, through the isolation and characterization of MNNG-tolerant cell lines from the MTase-deficient mutants we demonstrated that a DNA mismatch repair defect is neither sufficient nor required for this process. Since both DNA repair MTases and mismatch repair proteins are highly conserved between yeast and mammalian cells, our results could suggest alternative mechanisms in the cellular tolerance to O6MeG-induced killing.

Catalytic cleavage of an RNA target by 2-5A antisense and RNase L

2-5A antisense (2-5A-AS) molecules are chimeric oligonucleotides that cause 2-5A-dependent RNase (RNase L) to catalyze the selective cleavage of RNA in human cells. These composite nucleic acids consist of a 5'-monophosphorylated, 2',5'-linked oligoadenylate known as 2-5A (an activator of RNase L) covalently attached to antisense 3',5'-oligodeoxyribonucleotides. Here, we characterize the targeted cleavage of the double-stranded RNA-dependent protein kinase (PKR) mRNA by purified, recombinant human RNase L. A 2-5A-AS chimera, which contains complementary sequence to PKR mRNA, and unmodified 2-5A, which causes general RNA decay, were about 20- and 40-fold more active, respectively, than 2-5A-AS chimeras in which the DNA domains are not complementary to sequences in PKR mRNA. Directed cleavage was efficient because each 2-5A-AS chimera targeted many RNA molecules. Moreover, RNase L caused the catalytic cleavage of the RNA target (kcat of approximately 7 s-1). The precise sites of PKR mRNA cleavage caused by 2-5A-AS were mapped, using a primer extension assay, to phosphodiester bonds adjacent to the 3' terminus of the chimera binding site (5' on the RNA target) as well as within the chimera's oligonucleotide binding site itself. The selectivity of this approach is shown to be provided by the antisense arm of the chimera, which places the RNA target in close proximity to the RNase.

Papilloma formation in human foreskin xenografts after inoculation of human papillomavirus type 16 DNA

A mouse model of high-risk human papillomavirus infection was developed in which human papillomavirus (HPV) type 16 DNA was inoculated into human foreskin grafted to the skin of severe combined immunodeficient (scid) mice. Grafted skin contained human epidermis and dermis and, like normal human skin, expressed involucrin in differentiating keratinocytes. HPV type 16 DNA, attached to gold particles, was delivered directly into human epidermal cells and induced exophytic papilloma with histologic features of papillomavirus infection, including koilocytosis and expression of papillomavirus capsid antigen. This model should be useful for determining in vivo the functions of viral genes and for developing strategies to prevent and treat HPV-associated disease. It may also be of value in developing animal models of other human skin diseases.

Expression of the human MGMT O6-methylguanine DNA methyltransferase gene in a yeast alkylation-sensitive mutant: its effects on both exogenous and endogenous DNA alkylation damage

Common Mer- cell lines deficient in O6-methylguanine DNA methyltransferase (MTase) activity probably result from the down-regulation of, rather than mutations in, the MGMT gene. However, the down-regulation of other unrelated genes was also observed in some of these cell lines, making it difficult to determine the precise functions of the MGMT MTase gene. To study the biological function of human MGMT MTase, we seek to utilize a newly created yeast mgt1 mutant deficient in the DNA repair MTase activity. The human MGMT cDNA was cloned into yeast expression vectors so that the MGMT gene is under the control of either an inducible GAL1 promoter or a constitutive ADH1 promoter. Upon galactose induction, the PGAL1-MGMT transformant had about 40-fold MTase activity compared to the wild-type strain. MGMT overexpression protected the yeast mgt1 mutant against alkylation-induced killing and mutation. Limited expression of the MGMT gene in the mgt1 mutant still provides significant alkylation resistance, albeit at a reduced level. The yeast mgt1 mutants increase spontaneous mutation rate, whereas constitutive expression of the MGMT gene lowered the spontaneous mutation rate in the mgt1 mutant to the wild-type level. We suggest that MGMT MTase may play the same role in human cells as the MGT1 MTase in yeast cells. Thus our results demonstrate that the human MGMT gene functionally complements the yeast MTase-deficient mutant in the protection against exogenous and endogenous DNA alkylation damage, which provides a useful tool for the study of in vivo mammalian MTase functions.

UBP5 encodes a putative yeast ubiquitin-specific protease that is related to the human Tre-2 oncogene product

A gene from chromosome V of the yeast Saccharomyces cerevisiae has been cloned and sequenced. The deduced amino acid sequence encoded by this gene is similar to several ubiquitin-specific proteases from yeast, especially at the highly conserved domain. It is thus named UBP5. UBP5 is also closely related to the human Tre-2 and the mouse Unp oncogene products. This study adds a new member to the ubiquitin protease family and suggests that alteration of ubiquitin protease activity may result in cancer in mammals. However, disruption of the UBP5 gene in a haploid strain did not result in a noticeable phenotypic alteration.

Development of 2',5'-Oligonucleotides as Therapeutic Agents

Abstract:

The unique 2',5'-phosphodie.ster bond-linked oligonucleo­ tide known as 2-5A (Pn5'A2'(p5'A2')mp5'A) plays a key role in mediation of the anti-encephalomyocarditis virus action of interferon. 2-5A acts as a potent inhibitor of translation through the activation of a constituent latent endonuclease, the 2-5A-dependent ribonuclease (RNase) , which degrades RNAs. This 2-5A system, as part of a natural defense mechanism against virus infection, provides a paradigm for a new approach to the regulation of gene expression. Realization of this poten­ tial requires an understanding of the 2-5A oligoribonucleotide-associated structural parameters which govern its lifetime in biological systems and its interaction with the 2-5A-dependent ribonuclease responsible for RNA destruction. In this review, we describe the partial realization of such an understanding and the resulting development of a new approach to the specific and targeted cleavage of RNA by directing 2-5A-dependent RNase action to a precise target with an antisense DNA. The synthesis and mechanism of action of these novel composite nucleic acids permits exploration of the potent RNA destruction ability of the 2-5A-dependent RNase coupled with the specificity of antisense oligonucleotides as potential therapeutic agents for a variety of diseases.

Transpogenes: the transposition-like integration of short sequence DNA into the yeast 2 micron plasmid creates the STB locus and plasmid-size polymorphism

The type-2 2 mu plasmid of industrial yeast strains exhibits extensive size polymorphism in the STB (plasmid stability) locus and IR (inverted repeat)-right region. Comparative DNA sequence analyses of STB alleles identified a 38-bp sequence flanked by a 25-bp direct repeat as the underlying structural motif. Variable unequal recombination within the direct repeat accounted for the observed polymorphism of STB alleles. IR-right polymorphism was observed to result from tandem duplication of a 22-bp sequence flanked by a 9-bp direct repeat. The flanking direct repeats marked both loci as originating from the transposition-like integration of short DNA fragments. We call these structures transpogenes and note that these are hybrid structures of host and foreign DNA which can evolve into functional loci.

Papilloma formation by cottontail rabbit papillomavirus requires E1 and E2 regulatory genes in addition to E6 and E7 transforming genes

The present study used the cottontail rabbit papillomavirus DNA-rabbit system to evaluate whether the regulatory genes E1 and E2 and the transforming gene E6 are required for papilloma formation. Frameshift mutations were generated in the individual genes in the context of a full-length cottontail rabbit papillomavirus genome, and the mutant DNAs were intradermally inoculated into domestic rabbits. None of the mutants induced papillomas. Marker rescue experiments confirmed that the defects were due to mutations that we deliberately introduced. Marker rescue also confirmed our previous report that the upstream region of E7 around position 9 was critical for papilloma induction. These results demonstrate that the E1 and E2 regulatory genes as well as the E6 and E7 transforming genes are each required for papilloma formation. Each gene may provide molecular targets for therapeutic intervention.

Blockage of NF-kappa B signaling by selective ablation of an mRNA target by 2-5A antisense chimeras

Activation of 2-5A-dependent ribonuclease by 5'-phosphorylated, 2',5'-linked oligoadenylates, known as 2-5A, is one pathway of interferon action. Unaided uptake into HeLa cells of 2-5A linked to an antisense oligonucleotide resulted in the selective ablation of messenger RNA for the double-stranded RNA (dsRNA)-dependent protein kinase PKR. Similarly, purified, recombinant human 2-5A-dependent ribonuclease was induced to selectively cleave PKR messenger RNA. Cells depleted of PKR activity were unresponsive to activation of nuclear factor-kappa B (NF-kappa B) by the dsRNA poly(I):poly(C), which provides direct evidence that PKR is a transducer for the dsRNA signaling of NF-kappa B.

Femtosecond pump-probe analysis of energy and electron transfer in photosynthetic membranes of Rhodobacter capsulatus

Low-intensity, 295 K, femtosecond pump-probe transient absorption measurements are described that have been performed to investigate energy and electron transfer in photosynthetic membranes from a Rhodobacter capsulatus strain lacking functional light harvesting antenna complex II. Spectral and kinetic similarities between the absorption changes of isolated reaction centers and those of reaction centers in membranes upon 800-nm excitation suggest that the charge separation process in both cases is very similar. An ultrafast energy relaxation process observed near 872 nm when 800-nm excitation is used is interpreted as interexcitonic relaxation within the antenna, though other interpretations, such as vibrational relaxation, are possible. On the basis of global exponential fitting analysis of the time-dependent spectral changes using 800- and 880-nm excitation wavelengths to selectively excite the reaction center and the LHI antenna, respectively, it is found that excitation energy transfer and trapping in Rb. capsulatus is limited by the overall rate of energy transfer between the antenna and the reaction center. This conclusion is supported by the observation that excitation at 800 nm, but not 880 nm, results in absorbance changes indicative of charge separation with a lifetime (3.1 ps) very close to that reported for charge separation in isolated reaction centers (3.5 ps). Thus, most reaction centers that are directly excited undergo charge separation and not backward energy transfer to the LHI antenna complexes. Both a kinetic model analysis and a direct comparison between time-resolved spectra obtained using different excitation wavelengths resulted in an energy-detrapping efficiency of about 15 +/- 10%.

The MAG1* 3-methyladenine DNA glycosylase gene is closely linked to the SPT15 TATA-binding TFIID gene on chromosome V-R in Saccharomyces cerevisiae

The MAG1 gene encodes a 3-methyladenine DNA glycoslyase, which is involved in DNA alkylation repair in Saccharomyces cerevisiae. The mag1 mutant is deficient in 3-methyladenine DNA glycosylase activity and shows enhanced sensitivity to several monofunctional alkylating agents. MAG1 is allelic to MMS5. This gene has been previously located on chromosome V by chromosomal hybridization. We present physical and genetic mapping data here showing that the MAG1 gene is located on chromosome V-R, proximal to and about 10 kilobase pairs away from the SPT15 gene coding for the yeast TATA-binding protein TFIID.

Evidence for Darwinian selection of the 2-micron plasmid STB locus in Saccharomyces cerevisiae

The 2-microns plasmid of industrial and laboratory strains of Saccharomyces cerevisiae exists as two main polymorphic forms designated type I and type II. Polymorphism is restricted to the 3200-bp right unique region where types I and II show approximately 10% nucleotide divergence in trans-acting REP1 and RAF loci and 30% divergence in the cis-acting STB locus. In addition, the cis-acting STB plasmid partition locus of type II plasmids varies in sequence and copy number of a 125-bp repeat. We devised chimeric and 2-microns plasmid stability experiments to evaluate the effect of STB polymorphism on plasmid fitness in amphiploid industrial and haploid laboratory strains. Reciprocal experiments of type-II STB chimeric plasmids in type-I bakers' yeast or a type-I chimeric plasmid in type-II distillers', wine, or haploid strains showed similar partition efficiencies. However, chimeric and 2-microns plasmids carrying a 250-bp STB from a type-II haploid strain had reduced fitness in a type-II industrial wine strain. These results in conjunction with molecular analyses of 2-microns-like and 2-microns plasmids indicates the coevolution of STB with trans-acting plasmid and host-cell factors.

A common element involved in transcriptional regulation of two DNA alkylation repair genes (MAG and MGT1) of Saccharomyces cerevisiae

The Saccharomyces cerevisiae MAG gene encodes a 3-methyladenine DNA glycosylase that protects cells from killing by alkylating agents. MAG mRNA levels are induced not only by alkylating agents but also by DNA-damaging agents that do not produce alkylated DNA. We constructed a MAG-lacZ gene fusion to help identify the cis-acting promoter elements involved in regulating MAG expression. Deletion analysis defined the presence of one upstream activating sequence and one upstream repressing sequence (URS) and suggested the presence of a second URS. One of the MAG URS elements matches a decamer consensus sequence present in the promoters of 11 other S. cerevisiae DNA repair and metabolism genes, including the MGT1 gene, which encodes an O6-methylguanine DNA repair methyltransferase. Two proteins of 26 and 39 kDa bind specifically to the MAG and MGT1 URS elements. We suggest that the URS-binding proteins may play an important role in the coordinate regulation of these S. cerevisiae DNA repair genes.

Polymorphism of 2-microns plasmids in industrial strains of Saccharomyces cerevisiae

Restriction fragment length polymorphism (RFLP) analyses of industrial Saccharomyces yeast DNA have identified eight 2-microns plasmid variants that fall into two distinct types. Type-I plasmids are of unique form, whereas type-II plasmids exist in seven distinct RFLP forms. Only two different 2-microns variants were observed in 35 bakers' strains analysed. One variant was the unique type-I whereas the second variant represents an ancestral form of the type-II plasmid. Sixteen of nineteen wine yeasts carried a distinctive type-II plasmid with a homologous STB repeat whereas ale and lager yeasts had a wide range of type-II variants. Relative to nuclear and mtDNA, 2-microns polymorphism is less diverse and not diagnostic for a specific strain. This 2-microns DNA polymorphism is a convenient and useful addendum to nuclear and mtDNA RFLP analyses but cannot serve as the sole marker for strain identification. A tentative phylogeny of industrial S. cerevisiae yeasts is suggested with origins in bakers' yeast carrying the ancestral type-II form.

In vivo evidence for endogenous DNA alkylation damage as a source of spontaneous mutation in eukaryotic cells

Three genes that participate in the repair of DNA alkylation damage were recently cloned from Saccharomyces cerevisiae: the MGT1 O6-methylguanine DNA methyltransferase gene, the MAG 3-methyladenine DNA glycosylase gene, and the APN1 apurinic/apyrimidinic (AP) endonuclease gene. Altering the expression levels of these three genes produced significant changes in the S. cerevisiae spontaneous mutation rate. Spontaneous mutation increased in the absence of the MGT1 DNA methyltransferase, presumably because unrepaired, spontaneously produced, O6-alkylguanine lesions mispair during replication. Moreover, changing the ratios of the MAG 3-methyladenine DNA glycosylase and the APN1 AP endonuclease had profound effects on spontaneous mutation rates. In the absence of APN1, the overexpression of MAG increased spontaneous mutation, and the underexpression of MAG decreased spontaneous mutation. We infer that the MAG glycosylase acts upon spontaneously produced 3-alkyladenine and 7-alkylguanine DNA lesions to produce mutagenic abasic sites, and that if the repair of these abasic sites is not initiated by the APN1 AP endonuclease they cause mutations during replication. Our results indicate that eukaryotic cells harbor endogenous metabolites that alkylate nuclear DNA at both oxygens and nitrogens.

Infectious virus replication in papillomas induced by molecularly cloned cottontail rabbit papillomavirus DNA

The ability to obtain infectious papillomavirus virions from molecularly cloned DNA has not been previously reported. We demonstrate here that viral genomes isolated from a recombinant++ DNA clone of cottontail rabbit papillomavirus (CRPV) gave rise to infectious virus when inoculated into cottontail rabbit skin. Replication occurred in papillomas that formed at inoculation sites. Extract of a DNA-induced papilloma was serially passaged to naive rabbits with high efficiency. Complete virus was fractionated on cesium chloride density gradients, and papillomavirus particles were visualized by electron microscopy. CRPV DNA isolated from virions contained DNA sequence polymorphisms that are characteristic of the input CRPV-WA strain of virus, thereby proving that the newly generated virus originated from the molecularly cloned viral genome. These findings indicate that this will be a useful system in which to perform genetic analysis of viral gene functions involved in replication.

Healing response of the epithelium after lateral needle injury of mouse lens

Characteristic changes of the epithelial healing process in germinative and equatorial zones of the ddY mouse lens were studied morphologically. After germinative zone injury, the wound was covered by proliferating epithelial cells which increased and migrated posteriorly as a function of time after injury. Epithelial posterior migration from the lens equator was mild. By contrast, with equatorial injury, the wound was covered by proliferated epithelial cells. Moreover, the equatorial area was characterized by disconfiguration of the lens bow and posterior epithelial migration. The results suggest that the larger capsulectomy in IOL operation, which damages the peripheral part of the lens epithelium, might contribute to secondary cataract.

The putative E5 open reading frame of cottontail rabbit papillomavirus is dispensable for papilloma formation in domestic rabbits

In the cottontail rabbit papillomavirus (CRPV)-rabbit system, recombinant CRPV DNA can induce papillomas. This investigation was undertaken to evaluate whether the E5 open reading frame (ORF) of CRPV is required for papilloma formation. The CRPV genome we utilized, CRPV-WA, was sequenced in the E5 region and was found to contain one deletion, two insertions, and one transition mutation compared with CRPV-KS, the CRPV genome that has been fully sequenced. Despite these differences, an intact E5 ORF is preserved, supporting the notion that this gene may serve a biological function. One frameshift and two in-frame mutations were constructed in the small region of the 5' end of the E5 ORF that follows the E2 stop codon and precedes the L2 ORF. Several hundred rabbit skin sites were inoculated with each DNA preparation with a jet injector to test the ability of three CRPV E5 mutant DNAs to induce papillomas. In vivo results showed that each of the mutants induced papillomas, and biochemical analysis demonstrated that the E5 mutations present in DNA inocula were retained in the papillomas. The frequency of papilloma formation, however, was generally lower with each of the CRPV E5 mutants than with wild-type CRPV DNA, particularly so for the E5 frameshift mutant, suggesting that although the recognized E5 ORF is not required in domestic rabbits for the induction of papillomas by CRPV DNA, it may facilitate their formation.