[Rapid detection of alpha-thalassemia of Southeast Asian deletion by polymerase chain reaction and its application to prenatal diagnosis]

OBJECTIVE

To establish a rapid and simple polymerase chain reaction (PCR) method for detecting alpha-thalassemia of Southeast Asia deletion, and apply it to the prenatal diagnosis for high risk fetuses.

METHODS

Two pairs of primers were designed: one pair bridging the breakpoints to identify the specific deletion, the other located in the common deletion region of --(SEA), -alpha(3.7) and -alpha(4.2) gene to detect the normal chromosomes. In this system, the two amplifications ran in the same PCR tube under identical condition.

RESULTS

A 740 bp fragment was amplified in chromosomes with --(SEA) determinant and a 1,052 bp fragment in normal chromosomes. For prenatal diagnosis, 3 of 8 at-risk cases were diagnosed as normal, 3 as heterozygotes, and 2 as homozygotes of --(SEA) deletion.

CONCLUSION

This detection method is rapid and accurate and can be used as a routine method for carrier detection and prenatal diagnosis.

Route of administration determines induction of T-cell-independent humoral responses to adeno-associated virus vectors

Vectors based on adeno-associated viruses (AAV) type 2 show promise for treating chronic diseases because transgene expression appears to be stable. This study evaluated the impact of humoral immunity to the capsid proteins on vector uptake by hepatocytes following an intravascular approach. Route of vector administration in mice had a qualitative effect on antivector B cell responses. Administration of vector into the tail vein resulted in T-cell-dependent (TD) B cell responses that were completely inhibited with depleting CD4 antibody. Delivery of vector into the portal circulation via the spleen yielded B cell response that were partially T cell independent (TI) rendering strategies based on T cell inhibition ineffective in allowing vector readministration. The TI B cell response was short lived in comparison to the TD response. Rhesus monkeys produced a B cell memory response to intraportal vector which appeared to be T cell dependent based on Ig isotypes. Gene therapy strategies that require AAV vector readministration should consider vector biodistribution and its impact on B cell activation.

RNase-L-dependent destabilization of interferon-induced mRNAs. A role for the 2-5A system in attenuation of the interferon response

The 2-5A system is an interferon-regulated RNA degradation pathway with antiviral, growth-inhibitory, and pro-apoptotic activities. RNase-L mediates the antiviral activity through the degradation of viral RNAs, and the anticellular effects of the 2-5A system are thought to be similarly mediated through the degradation of cellular transcripts. However, specific RNase-L-regulated cellular RNAs have not been identified. To isolate candidate RNase-L substrates, differential display was used to identify mRNAs that exhibited increased expression in RNase-L-deficient N1E-115 cells as compared with RNase-L-transfected cells. A novel interferon-stimulated gene encoding a 43-kDa ubiquitin-specific protease, designated ISG43, was identified in this screen. ISG43 expression is induced by interferon and negatively regulated by RNase-L. ISG43 induction is a primary response to interferon treatment and requires a functional JAK/STAT signaling pathway. The kinetics of ISG43 induction were identical in wild type and RNase-L knock-out fibroblasts; however, the decline in ISG43 mRNA following interferon treatment was markedly attenuated in RNase-L knock-out fibroblasts. The delayed shut-off kinetics of ISG43 mRNA corresponded to an increase in its half-life in RNase-L-deficient cells. ISG15 mRNA also displayed RNase-L-dependent regulation. These findings identify a novel role for the 2-5A system in the attenuation of the interferon response.

UBC13, a DNA-damage-inducible gene, is a member of the error-free postreplication repair pathway in Saccharomyces cerevisiae

The Ubc13 protein was recently identified for its unique role in ubiquitin (Ub) chain assembly at the Ub Lys-63 residue instead of the conventional Lys-48 residue. This activity requires Ubc13 to form a complex with Mms2 and indeed ubc13 and mms2 mutations have been shown elsewhere to be epistatic with respect to UV sensitivity. The MMS2 gene is known to be a member of the error-free DNA postreplication repair (PRR) pathway. By contrast, the Ub Lys-63 residue has been previously implicated in the error-prone PRR pathway, since yeast cells carrying the ubiK63R mutation are defective in UV-induced mutagenesis. In the present study, we attempted to define the role of UBC13 within the PRR pathway. We found that the ubc13 mutation is epistatic to mms2 and rad6, confirming that UBC13 belongs to the PRR-pathway. We also found that ubc13 is synergistic to the error-prone PRR pathway mutation rev3, indicating that UBC13 is in a pathway alternative to REV3 mutagenesis. The ubc13 mutant displays up to a 30-fold increase in the spontaneous mutation rate, and this increase is largely REV3 dependent. In addition, UV-induced mutagenesis is fully functional in the ubc13 mutant. These results together demonstrate that UBC13 is a member of the error-free PRR pathway. The involvement of UBC13 in cellular tolerance to DNA-damage is further implicated by our finding that the UBC13 transcript level is increased up to 6-fold in response to DNA-damage.

Humoral immunity to adeno-associated virus type 2 vectors following administration to murine and nonhuman primate muscle

Adeno-associated virus (AAV) is being developed as a vector capable of conferring long-term gene expression, which is useful in the treatment of chronic diseases. In most therapeutic applications, it is necessary to readminister the vector. This study characterizes the humoral immune response to AAV capsid proteins following intramuscular injection and its impact on vector readministration. Studies of mice and rhesus monkeys demonstrated the formation of neutralizing antibodies to AAV capsid proteins that persisted for over 1 year and then diminished, but this did not prevent the efficacy of vector readministration. More-detailed studies strongly suggested that the B-cell response was T cell dependent. This was further evaluated with a blocking antibody to human CD4, primatized for clinical trials, in a biologically compatible mouse in which the endogenous murine CD4 gene was functionally replaced with the human counterpart. Transient pharmacologic inhibition of CD4 T cells with CD4 antibody prevented an antivector response long after the effects of the CD4 antibody diminished; readministration of vector without diminution of gene expression was possible. Our studies suggest that truly durable transgene expression (i.e., prolonged genetic engraftment together with vector readministration) is possible with AAV in skeletal muscle, although it will be necessary to transiently inhibit CD4 T-cell function to avoid the activation of memory B cells.

Bench-scale anaerobic bioconversion of newsprint and office paper

Anaerobic bioconversion of newsprint and waste office paper was performed in bench-scale reactors with three inocula sources: landfill, rumen, and anaerobic digester. Office paper bioconversion was nearly complete within 20 days but continued for about 165 days with methane yield efficiencies ranging from 71-85% of potential chemical oxygen demand (COD) conversion. Average newsprint methane conversion efficiencies ranged from 32-41% of total COD under strictly anaerobic conditions for 300 days. Mass balance calculations revealed that more than 80% of newsprint cellulose was biodegraded. The apparent limiting factor for anaerobic bioconversion of newsprint was the physical association between lignin and cellulose. After proper acclimation, the three inocula tested equally well for methane production under strictly anaerobic conditions. Testing of ground, shredded strips, and whole paper pieces showed no effects of feedstock size on bioconversion rate or extent. Alkali pretreatment with NaOH concentration up to 10% significantly improved newsprint biodegradability. Treatment for longer duration or at elevated temperatures increased the solubilization of lignin, but did not improve bioconversion of newsprint to methane. Neutralizing treated samples with carbon dioxide gave higher methane yields compared to sulfuric or hydrochloric acids, suggesting that digester neutralization could be combined with biogas scrubbing.

Insertional mutagenesis of AAV2 capsid and the production of recombinant virus

The structural genes of adeno-associated virus serotype 2 (AAV2) have been altered by linker insertional mutagenesis in order to define critical components of virion assembly and infectivity. An in-frame restriction site linker was inserted across the capsid coding domain of a recombinant plasmid. After complementation in vivo, recombinant AAV2 viruses were generated and assayed for capsid production, packaging, transduction, heparin agarose binding, and morphology. Three classes of capsid mutants where identified. Class I mutants expressed structural proteins but were defective in virion assembly. Class II mutants generated intact virions that protected the viral genome from DNase, but failed to infect target cells. The majority of these mutants bound the heparin affinity matrix, suggesting that attachment to the AAV primary receptor was not rate limiting. One class II mutant, H2634, assembled virions and bound heparin using only Vp3, indicating that this subunit is responsible for mediating AAV receptor attachment. Finally, class III mutants assembled virions, encapsidated DNA, and infected target cells. Infectivity of these mutants ranged from 5 to 100% of that of the wild-type, demonstrating for the first time the ability to alter capsid proteins without interfering with infectivity. These AAV virions with altered capsid subunits will provide critical templates for manipulating AAV vectors for cell-specific gene delivery in vivo. In summary, the AAV capsid variants described here will facilitate further study of virus assembly, entry, and infection, as well as advance the development of this versatile vector system.

REV3 is required for spontaneous but not methylation damage-induced mutagenesis of Saccharomyces cerevisiae cells lacking O6-methylguanine DNA methyltransferase

O6-methylguanine (O6-MeG) DNA methyltransferase (MTase) removes the methyl group from a DNA lesion and directly restores DNA structure. It has been shown previously that bacterial and yeast cells lacking such MTase activity are not only sensitive to killing and mutagenesis by DNA methylating agents, but also exhibit an increased spontaneous mutation rate. In order to understand molecular mechanisms of endogenous DNA alkylation damage and its effects on mutagenesis, we determined the spontaneous mutational spectra of the SUP4-o gene in various Saccharomyces cerevisiae strains. To our surprise, the mgt1 mutant deficient in DNA repair MTase activity exhibited a significant increase in G:C-->C:G transversions instead of the expected G:C-->A:T transition. Its mutational distribution strongly resembles that of the rad52 mutant defective in DNA recombinational repair. The rad52 mutational spectrum has been shown to be dependent on a mutagenesis pathway mediated by REV3. We demonstrate here that the mgt1 mutational spectrum is also REV3-dependent and that the rev3 deletion offsets the increase of the spontaneous mutation rate seen in the mgt1 strains. These results indicate that the eukaryotic mutagenesis pathway is directly involved in cellular processing of endogenous DNA alkylation damage possibly by the translesion bypass of lesions at the cost of G:C-->C:G transversion mutations. However, the rev3 deletion does not affect methylation damage-induced killing and mutagenesis of the mgt1 mutant, suggesting that endogenous alkyl lesions may be different from O6-MeG.

Methionine reduces spontaneous and alkylation-induced mutagenesis in Saccharomyces cerevisiae cells deficient in O6-methylguanine-DNA methyltransferase

The exposure of DNA to reactive intracellular metabolites is thought to be a major cause of spontaneous mutagenesis. DNA alkylation is implicated in the above process by the fact that bacterial and yeast cells lacking DNA alkylation-specific repair genes exhibit elevated spontaneous mutation rates. The origin of the intracellular alkylating molecules is not clear; however, S-adenosylmethionine (SAM) has been proposed as one source because it has a reactive methyl group known to methylate proteins and DNA. We supplemented yeast cultures with excess methionine and examined the effects of increased endogenous SAM concentration on spontaneous and alkylation-induced mutagenesis in the absence of various DNA repair pathways. Our results show that either the excess methionine, or the increased SAM produced as a result of this treatment, is able to protect yeast cells from mutagenesis, and that this effect is alkylation-damage-specific. The protective effect was observed only in the mgt1 mutant deficient in the O(6)-methylguanine-DNA repair methyltransferase, but not in the wild type or other DNA repair-deficient strains, indicating that the protection is specific for O-methyl lesions. Thus, our results may lend support to the recently reported chemopreventive effect of SAM in rodents and further suggest that the observed tumor prevention by SAM may be, in part, due to its suppression of spontaneous mutagenesis in mammals. Given that a strong correlation has been established between O(6)-methylguanine and carcinogenicity, this study may offer a novel approach to preventing carcinogenesis.

Charge-to-alanine mutagenesis of the adeno-associated virus type 2 Rep78/68 proteins yields temperature-sensitive and magnesium-dependent variants

The adeno-associated virus type 2 (AAV) replication (Rep) proteins Rep78 and 68 (Rep78/68) exhibit a number of biochemical activities required for AAV replication, including specific binding to a 22-bp region of the terminal repeat, site-specific endonuclease activity, and helicase activity. Individual and clusters of charged amino acids were converted to alanines in an effort to generate a collection of conditionally defective Rep78/68 proteins. Rep78 variants were expressed in human 293 cells and analyzed for their ability to mediate replication of recombinant AAV vectors at various temperatures. The biochemical activities of Rep variants were further characterized in vitro by using Rep68 His-tagged proteins purified from bacteria. The results of these analyses identified a temperature-sensitive (ts) Rep protein (D40,42,44A-78) that exhibited a delayed replication phenotype at 32 degrees C, which exceeded wild-type activity by 48 h. Replication activity was reduced by more than threefold at 37 degrees C and was undetectable at 39 degrees C. Stability of the Rep78 protein paralleled replication levels at each temperature, further supporting a ts phenotype. Replication differences resulted in a 3-log-unit difference in virus yields between the permissive and nonpermissive temperatures (2.2 x 10(6) and 3 x 10(3), respectively), demonstrating that this is a relatively tight mutant. In addition to the ts Rep mutant, we identified a nonconditional mutant with a reduced ability to support viral replication in vivo. Additional characterization of this mutant demonstrated an Mg(2+)-dependent phenotype that was specific to Rep endonuclease activity and did not affect helicase activity. The two mutants described here are unique, in that Rep ts mutants have not previously been described and the D412A Rep mutant represents the first mutant in which the helicase and endonuclease functions can be distinguished biochemically. Further understanding of these mutants should facilitate our understanding of AAV replication and integration, as well as provide novel strategies for production of viral vectors.

Genetic interactions between error-prone and error-free postreplication repair pathways in Saccharomyces cerevisiae

Evidence obtained from recent studies supports the existence of an error-free postreplication repair (PRR) and a mutagenesis pathway within the Saccharomyces cerevisiae RAD6 DNA repair group. The MMS2 gene is the only known yeast gene involved in error-free PRR that, when mutated, significantly increases the spontaneous mutation rate. In this study, the mutational spectrum of the mms2 mutator was determined and compared to the wild type strain. In addition, mutagenenic effects and genetic interactions of the mms2 mutator and rev3 anti-mutator were examined with respect to forward mutations, frameshift reversions as well as amber and ochre suppressions. It was concluded from these results that the mms2 mutator phenotype is largely dependent on the functional REV3 gene. The synergistic effects of mms2 and rev3 mutations towards killing by a variety of DNA-damaging agents ruled out the possibility that MMS2 simply acts to suppress REV3 activity and favored the hypothesis that MMS2 and REV3 form two alternative subpathways within the RAD6 DNA repair pathway. Taken together, we propose that two pathways represented by MMS2 and REV3 deal with a similar range of endogenous and environmental DNA damage but with different biological consequences, namely, error-free repair and mutagenesis, respectively.

A piston model for transmembrane signaling of the aspartate receptor

To characterize the mechanism by which receptors propagate conformational changes across membranes, nitroxide spin labels were attached at strategic positions in the bacterial aspartate receptor. By collecting the electron paramagnetic resonance spectra of these labeled receptors in the presence and absence of the ligand aspartate, ligand binding was shown to generate an approximately 1 angstrom intrasubunit piston-type movement of one transmembrane helix downward relative to the other transmembrane helix. The receptor-associated phosphorylation cascade proteins CheA and CheW did not alter the ligand-induced movement. Because the piston movement is very small, the ability of receptors to produce large outcomes in response to stimuli is caused by the ability of the receptor-coupled enzymes to detect small changes in the conformation of the receptor.

Incorporation of an (125)I-labeled hexa-iodinated diglyceride analog into low-density lipoprotein and high specific uptake by cells of cervical carcinoma cell lines

The feasibility of using low-density lipoprotein (LDL) to deliver cytotoxic drugs to tumor cells has been explored since the 1980s, when cells of a number of cancer cell lines were found to have higher LDL receptor activity than normal cells. Such differential uptake between tumor and normal cells may provide a unique opportunity to use LDL as a tumor-specific carrier of radiopharmaceuticals for the clinical management of cancer. In this study, an (125)I-labeled hexa-iodinated diglyceride analog, 1, 3-dihydroxypropan-2-one 1,3-diiopanoate (DPIP), was synthesized and incorporated into LDL using a fusion technique. It was found that approximately 500 [(125)I] DPIP molecules were incorporated into each LDL particle. Cells of three human cervical tumor cell lines, HeLa, SiHa and C-33A, were used to examine the cellular uptake of the [(125)I]DPIP-LDL conjugate. It was shown that the [(125)I]DPIP-LDL conjugate was specifically bound to and taken up by cervical tumor cells through an LDL receptor-mediated endocytosis pathway. The results suggest that LDL may be a selective carrier for delivering hydrophobic radiopharmaceuticals to cancer cells and particularly for the diagnosis of cervical tumors.

Transduction of well-differentiated airway epithelium by recombinant adeno-associated virus is limited by vector entry

The limitations of adeno-associated virus (AAV)-mediated vectors for lung-directed gene transfer were investigated by using differentiated human respiratory epithelium in air-liquid interface cultures. Transduction efficiency was high in undifferentiated cells and was enhanced in well-differentiated cells after basolateral application of the vector or after apical application following disruption of tight junctions or pretreatment of the cultures with glycosidases. These results indicate that transduction of airway epithelia by AAV vectors is limited by entry and reinforce the importance of a physical barrier on the airway surface.

Formation of the yeast Mre11-Rad50-Xrs2 complex is correlated with DNA repair and telomere maintenance

The yeast Mre11 is a multi-functional protein and is known to form a protein complex with Rad50 and Xrs2. In order to elucidate the relationship between Mre11 complex formation and its mitotic functions, and to determine domain(s) required for Mre11 protein interactions, we performed yeast two-hybrid and functional analyses with respect to Mre11 DNA repair and telomere maintenance. Evidence presented in this study indicates that the N-terminal region of Mre11 constitutes the core homo-dimerization and hetero-dimerization domain and is sufficient for Mre11 DNA repair and maintaining the wild-type telomere length. In contrast, a stretch of 134 amino acids from the extreme C-terminus, although essential for achieving a full level of self-association, is not required for the aforementioned Mre11 mitotic functions. Interestingly, deletion of these same 134 amino acids enhanced the interaction of Mre11 with Rad50 and Xrs2, which is consistent with the notion that this region is specific for meiotic functions. While Mre11 self-association alone is insufficient to provide the above mitotic activities, our results are consistent with a strong correlation between Mre11-Rad50-Xrs2 complex formation, mitotic DNA repair and telomere maintenance. This correlation was further strengthened by analyzing two mre11 phosphoesterase motif mutants ( mre11-2 and rad58S ), which are defective in DNA repair, telomere maintenance and protein interactions, and a rad50S mutant, which is normal in both complex formation and mitotic functions. Together, these results support and extend a current model regarding Mre11 structure and functions in mitosis and meiosis.

Gene therapy vectors based on adeno-associated virus type 1

The complete sequence of adeno-associated virus type 1 (AAV-1) was defined. Its genome of 4,718 nucleotides demonstrates high homology with those of other AAV serotypes, including AAV-6, which appears to have arisen from homologous recombination between AAV-1 and AAV-2. Analysis of sera from nonhuman and human primates for neutralizing antibodies (NAB) against AAV-1 and AAV-2 revealed the following. (i) NAB to AAV-1 are more common than NAB to AAV-2 in nonhuman primates, while the reverse is true in humans; and (ii) sera from 36% of nonhuman primates neutralized AAV-1 but not AAV-2, while sera from 8% of humans neutralized AAV-2 but not AAV-1. An infectious clone of AAV-1 was isolated from a replicated monomer form, and vectors were created with AAV-2 inverted terminal repeats and AAV-1 Rep and Cap functions. Both AAV-1- and AAV-2-based vectors transduced murine liver and muscle in vivo; AAV-1 was more efficient for muscle, while AAV-2 transduced liver more efficiently. Strong NAB responses were detected for each vector administered to murine skeletal muscle; these responses prevented readministration of the same serotype but did not substantially cross-neutralize the other serotype. Similar results were observed in the context of liver-directed gene transfer, except for a significant, but incomplete, neutralization of AAV-1 from a previous treatment with AAV-2. Vectors based on AAV-1 may be preferred in some applications of human gene therapy.

Microemulsion of seal oil markedly enhances the transfer of a hydrophobic radiopharmaceutical into acetylated low density lipoprotein

Four different microemulsions differing in their core lipid component (triolein, canola oil, squalene, or seal oil) and containing 1,3-dihydroxypropan-2-one 1,3-diiopanoate (DPIP), a potential radioimaging probe, were prepared by means of ultrasonication. The DPIP microemulsions were incubated with acetylated human low density lipoprotein (AcLDL) and the amount of DPIP transferred into AcLDL was examined. The amount of DPIP in the microemulsions expressed as DPIP/oil (w/w) was dependent on the core lipid component of the microemulsion in the order of seal oil (0.19+/-0.04, mean +/- standard deviation) > squalene (0.15+/-0.02) > canola oil (0.12+/-0.02) > triolein (0.07+/-0.004). With the exception of canola oil, all microemulsions were effective in enhancing the transfer of DPIP into AcLDL in comparison with commonly used methods, i.e., direct diffusion and detergent solubilization. DPIP in seal oil resulted in the highest amount of DPIP transferred into AcLDL [309.16+/-34.82 vs. 203.19+/-64.51 using squalene and 151.31+/-28.54 using triolein (DPIP molecules per AcLDL particle)]. For the first time, oil from harp seals, was studied as a major core lipid component of formulating pharmaceutical microemulsions. DPIP in seal oil resulted in the highest transfer of DPIP into AcLDL which is likely due to the highest DPIP concentration found in this microemulsion as well as the high fluidity of seal oil.

2-5A-DNA conjugate inhibition of respiratory syncytial virus replication: effects of oligonucleotide structure modifications and RNA target site selection

To define more fully the conditions for 2-5A-antisense inhibition of respiratory syncytial virus (RSV), relationships between 2-5A antisense oligonucleotide structure and the choice of RNA target sites to inhibition of RSV replication have been explored. The lead 2-5A-antisense chimera for this study was the previously reported NIH8281 that targets the RSV M2 RNA. We have confirmed and extended the earlier study by showing that NIH8281 inhibited RSV strain A2 replication in a variety of antiviral assays, including virus yield reduction assays performed in monkey (EC90 = 0.02 microM) and human cells (EC90 = microM). This 2-5A-antisense chimera also inhibited other A strains, B strains and bovine RSV in cytopathic effect inhibition and Neutral Red Assays (EC50 values = 0.1-1.6 microM). The 2'-O-methylation modification of NIH8281 to increase affinity for the complementary RNA and provide nuclease resistance, the introduction of phosphothioate groups in the antisense backbone to enhance resistance to exo- and endonucleases, and the addition of cholesterol to the 3'-terminus of the antisense oligonucleotide to increase cellular uptake, all resulted in loss of activity. Of the antisense chimeras targeting other RSV mRNAs (NS1, NS2, P, M. G, F, and L), only those complementary to L mRNA were inhibitory. These results suggest that lower abundance mRNAs may be the best targets for 2-5A-antisense; moreover, the active 2-5A antisense chimeras in this study may serve as useful guides for the development of compounds with improved stability, uptake and anti-RSV activity.

Anisotropic Templating Effect in the Formation of Two-Dimensional Anionic Cadmium-Thiocyanate Coordination Solids [(12C4)(2)Cd][Cd(2)(SCN)(6)] and [(12C4)(2)Cd][Cd(3)(SCN)(8)] with Checkerboard and Herringbone Patterns, Respectively

This paper reports the syntheses, characterization, and structures of two new two-dimensional cadmium-thiocyanate coordination solids [(12C4)(2)Cd][Cd(2)(SCN)(6)] (1) and [(12C4)(2)Cd][Cd(3)(SCN)(8)] (2), where 12C4 denotes 12-crown-4, C(8)H(16)O(4). 1 crystallizes in a monoclinic unit cell, space group C2/c with lattice parameters a = 16.297(3) Å, b = 26.267(3) Å, c = 16.296(2) Å, beta = 90.20(1) degrees, and Z = 8. 2 crystallizes in a monoclinic unit cell, space group P2(1)/n with lattice parameters a = 11.604(7) Å, b = 11.366(7) Å, c = 15.736(4) Å, beta = 92.84(3) degrees, and Z = 2. The structure of 1 exhibits a two-dimensional tetragonal motif consisting of Cd(2) units arranged in a checkerboard pattern with the dimeric [Cd(2)(SCN)(6)](2)(-) complex as the building block. The crystal structure of 2 can be described as a two-dimensional hexagonal array of linear trimeric Cd(3) units arranged in a herringbone pattern with the [Cd(3)(SCN)(8)](2)(-) complex as the building block. In both 1 and 2, the [(12C4)(2)Cd](2+) dications are housed in cavities within and between the anionic cadmium-thiocyanate layers but with different orientations ("upright" in 1 and "sideways" in 2) with respect to the cadmium-thiocyanate layers, giving rise to an anisotropic templating effect.

Radiolabeled cholesteryl iopanoate/acetylated low density lipoprotein as a potential probe for visualization of early atherosclerotic lesions in rabbits

PURPOSE

Atherosclerosis is the underlying factor leading to such cardiovascular diseases (CVD) as stroke, aneurysm, and myocardial infarction. The early detection of atherosclerotic plaques is considered to be crucial for successful prevention and/or therapeutic and dietary intervention of CVD. Current diagnostic practice, on the other hand, can only detect the problem at an advanced stage. The purpose of this study was to examine the potential of using a radiolabeled cholesterol ester analog/acetylated low density lipoprotein (AcLDL) conjugate as a diagnostic agent for the early and non-invasive detection of atherosclerosis and for the monitoring of the effects of drug therapy.

METHODS

Cholesteryl iopanoate (CI), a cholesterylester analog, was synthesized, radiolabeled, and incorporated into AcLDL. Early atherosclerotic lesions were induced in New Zealand White rabbits. 125[-CI/AcLDL was injected intravenously at 2 microCi/kg. Blood samples were taken at different time intervals after injection and clearance of the injected drug from blood was studied. The rabbits were sacrificed after 72 hours and the distribution of radioactivity in various organs was investigated. Aortae of both atherosclerotic lesion and control rabbits were removed for Sudan IV staining and autoradiography in order to confirm the formation of the atherosclerotic lesion and localization of radioactivity.

RESULTS

The injected drug was found to be cleared from blood following a two compartment model. Radioactivity in the atherosclerotic aorta was found to be about 8 times higher than that in normal aorta, suggesting that the proposed diagnostic probe was selectively taken up by the atherosclerotic lesion. The autoradiography and staining confirmed that the localization of the proposed probe was superimposed with the atherosclerotic lesion site.

CONCLUSIONS

The results suggested that incorporation of CI into AcLDL resulted in the selective localization of CI at the atherosclerotic plaque areas. CI/AcLDL labeled with appropriate radioisotope has the potential to be used as a probe for visualization of early atherosclerotic lesion using scintigraphy technology.

Isolation of hMRE11B: failure to complement yeast mre11 defects due to species-specific protein interactions

The Saccharomyces cerevisiae MRE11 gene plays an important role in meiotic recombination, mitotic DNA repair and telomere maintenance. We present the isolation of hMRE11B cDNA from a human HeLa cell cDNA library as an MRE11 homolog. Compared to the previously identified hMRE11, hMRE11B contains an additional 84bp sequence that results in a 28 amino-acid insertion close to the C-terminus. The expression pattern of hMRE11B in different tissues shows the presence of two mRNA species of approx. 2.6 and 7.5kb. Overexpression of hMRE11B does not complement the alkylation sensitivity of the mre11 null and temperature-sensitive mutant strains. In this study, we examine factors that may explain this lack of complementation. First, both Northern and Western analyses rule out the lack of hMRE11B transcription and/or translation in yeast. Second, we demonstrate that hMre11B, like the yeast Mre11 protein, dimerizes in vivo in a yeast two-hybrid system. This dimerization requires the C-terminal one-third of hMre11B protein, which includes the 28 amino acids absent in hMre11. However, hMre11B does not interact with Mre11, Rad50 and Xrs2. Hence, the lack of protein-protein interaction between hMre11B and the yeast Mre11, Rad50, and Xrs2 may explain the inability of hMRE11B to complement the yeast mre11 mutants. We rule out the hypothesis that the lack of interaction and, in turn of complementation, is due to the absence of sequence homology at the C-terminal domain of hMre11B compared to the yeast Mre11. Instead, we propose that the C-terminus of hMre11B participates in protein-protein interaction and functions in a species-specific manner.

Adeno-associated virus as a vector for liver-directed gene therapy

Factors relevant to the successful application of adeno-associated virus (AAV) vectors for liver-directed gene therapy were evaluated. Vectors with different promoters driving expression of human alpha-1-antitrypsin (alpha-1AT) were injected into the portal circulation of immunodeficient mice. alpha-1AT expression was stable but dependent on the promoter. Southern analysis of liver DNA revealed approximately 0.1 to 2.0 provirus copies/diploid genome in presumed head-to-tail concatamers. In situ hybridization and immunohistochemical analysis revealed expression in approximately 5% of hepatocytes clustered in the pericentral region. These results support the use of AAV as a vector for diseases treatable by targeting of hepatocytes.

2',5'-Oligoadenylate-antisense chimeras cause RNase L to selectively degrade bcr/abl mRNA in chronic myelogenous leukemia cells

We report an RNA targeting strategy, which selectively degrades bcr/abl mRNA in chronic myelogenous leukemia (CML) cells. A 2', 5'-tetraadenylate activator (2-5A) of RNase L was chemically linked to oligonucleotide antisense directed against either the fusion site or against the translation start sequence in bcr/abl mRNA. Selective degradation of the targeted RNA sequences was demonstrated in assays with purified RNase L and decreases of p210(bcr/abl) kinase activity levels were obtained in the CML cell line, K562. Furthermore, the 2-5A-antisense chimeras suppressed growth of K562, while having substantially reduced effects on the promyelocytic leukemia cell line, HL60. Findings were extended to primary CML cells isolated from bone marrow of patients. The 2-5A-antisense treatments both suppressed proliferation of the leukemia cells and selectively depleted levels of bcr/abl mRNA without affecting levels of beta-actin mRNA, determined by reverse transcriptase-polymerase chain reaction (RT-PCR). The specificity of this approach was further shown with control oligonucleotides, such as chimeras containing an inactive dimeric form of 2-5A, antisense lacking 2-5A, or chimeras with altered sequences including several mismatched nucleotides. The control oligonucleotides had either reduced or no effect on CML cell growth and bcr/abl mRNA levels. These findings show that CML cell growth can be selectively suppressed by targeting bcr/abl mRNA with 2-5A-antisense for decay by RNase L and suggest that these compounds should be further explored for their potential as ex vivo purging agents of autologous hematopoietic stem cell transplants from CML patients.

Differential regulation of two closely clustered yeast genes, MAG1 and DDI1, by cell-cycle checkpoints

Eukaryotic DNA-damage checkpoint genes have been shown to not only arrest cells at certain stages, but are also involved in the transcriptional response to DNA damage. However, while the signal transduction for cell-cycle checkpoint is well characterized, it is not clear whether the same signal transduction pathway is responsible for the regulation of all DNA damage-inducible genes. In order to understand how different checkpoint genes are involved in gene regulation, the effects of various checkpoint mutations on the expression of a unique yeast MAG1 - DDI1 dual promoter were examined in this study. MAG1 and DDI1 are transcribed from a common promoter region and co-induced by a variety of DNA damaging agents. However, gene-specific cis -acting elements were also identified, and the two genes are indeed differentially expressed under certain conditions. We found that DDI1 induction was not affected in any of the checkpoint mutants. In contrast, MAG1 induction was completely abolished in the pol2 and rad53 mutants. However, in the mec1-1 or any of the G1/S and G2/M checkpoint mutants, including rad9, rad17 and rad24, DNA damage-induced MAG1 expression was not significantly affected, and a rad9 rad17 double mutation only slightly reduced MAG1 induction. Based on this and previous studies, we present two models for the role of checkpoint genes in transcriptional regulation in response to DNA damage.

Molecular cloning and genetic characterization of the Saccharomyces cerevisiae NGS1/MRE11 gene

The Saccharomyces cerevisiae ngs1-1 mutant was previously identified by its enhanced sensitivity to simple DNA-alkylating agents such as methyl methanesulfonate but not to UV. Molecular cloning and sequencing of NGS1 as a putative DNA-alkylation repair gene revealed that it isidentical to MRE11, a gene that is involved in DNA recombinational repair. In order to investigate functional domains of the Mre11 protein, nucleotide-sequence alterations of a number of mre11 mutant alleles, including ngs1-1, mre11-1 (ts), mre11-2, mre11-3 and mre11-58, were determined. Most of these mutations map to the N-terminus ofMre11, emphasizing the importance of this highly conserved domain. The ngs1-1 and mre11-3 mutants carry nonsense mutations resulting in truncated proteins. Missense mutations were found in mre11-1 (ts), mre11-2 and mre11-58, of which mre11-2 and mre11-58 mapped to the conserved phosphoesterase domains, indicating the involvement of these motifs in the formation and/or processing of DNA double-strand breaks. Finally, mitotic-recombination assays show that the mre11 delta mutation enhances inter-chromosomal recombination but decreases the intra-chromosomal deletion frequency. In addition, MRE11 appears to play different roles during spontaneous and alkylation-induced homologous mitotic recombination.

High-titer adeno-associated viral vectors from a Rep/Cap cell line and hybrid shuttle virus

Adeno-associated virus (AAV) is a potential vector for in vivo gene therapy. A critical analysis of its utility has been hampered by methods of production that are inefficient, difficult to scale up, and that often generate substantial quantities of replication-competent AAV. We describe a novel method for producing AAV that addresses these problems. A cell line, called B50, was created by stably transfecting into HeLa cells a rep/cap-containing plasmid utilizing endogenous AAV promoters. Production of AAV occurs in a two-step process. B50 is infected with an adenovirus defective in E2b, to induce Rep and Cap expression and provide helper functions, followed by a hybrid virus in which the AAV vector is cloned in the E1 region of a replication-defective adenovirus. This results in a 100-fold amplification and rescue of the AAV genome, leading to a high yield of recombinant AAV that is free of replication-competent AAV. Intramuscular injection of vector encoding erythropoietin into skeletal muscle of mice resulted in supraphysiologic levels of hormone in serum that was sustained and caused polycythemia. This method of AAV production should be useful in scaling up for studies in large animals, including humans.

[Study on the joint effects of acrylonitrile and alcohol in rats]

In order to learn the joint effects of acrylonitrile and alcohol, acrylonitrile(40 micrograms/g), alcohol (1000 micrograms/g) and the mixed liquid of the both (40, 1000 micrograms/g) were given to rats by gavage for 8 weeks. The results revealed the joint effects of acrylonitrile and alcohol. Hypofunction and structural lesion of hepatocyte were found in the rats. The numbers of white blood cells decreased remarkably in these two groups.

Up-regulation of CIR1/CROC1 expression upon cell immortalization and in tumor-derived human cell lines

Acquisition of the immortal phenotype by tumor cells represents an essential and potentially rate-limiting step in tumorigenesis. To identify changes in gene expression that are associated with the early stages of cell immortalization, we compared genetically matched pairs of pre-immortal and immortal human cell clones by mRNA differential display. Two transcripts, denoted CIR1 and CIR2, were identified which were up-regulated in immortal cells. Sequence analysis revealed CIR1 to be identical to the recently cloned CROC1/UEV-1 gene, whereas CIR2 corresponds to an as yet uncharacterized 1.2 kb mRNA. A 5-6-fold elevation in CIR1/CROC1 expression and a 2-3-fold elevation in CIR2 expression were observed in SV40-transformed human embryonic kidney cells immediately following proliferative crisis, suggesting a potential role for these genes in immortalization. Expression of CIR1/CROC1 was found to be elevated also in a variety of immortal human tumor-derived cell lines, as compared to their normal tissue counterparts. These results are compatible with induction of CIR1/CROC1 being an early event in the acquisition of immortality and with a role for this gene in the immortal phenotype of tumor cells.

The products of the yeast MMS2 and two human homologs (hMMS2 and CROC-1) define a structurally and functionally conserved Ubc-like protein family

Eukaryotic genes encoding ubiquitin-congugating enzyme (Ubc)-like proteins have been isolated from both human and yeast cells. The CROC-1 gene was isolated by its ability to transactivate c- fos expression in cell culture through a tandem repeat enhancer sequence. The yeast MMS2 gene was cloned by its ability to complement the methyl methanesulfonate sensitivity of the mms2-1 mutant and was later shown to be involved in DNA post-replication repair. We report here the identification of a human MMS2 ( hMMS2 ) cDNA encoding a novel human Ubc-like protein. hMMS2 and CROC-1 share >90% amino acid sequence identity, but their DNA probes hybridize to distinct transcripts. hMMS2 and CROC-1 also share approximately 50% identity and 75% similarity with the entire length of yeast Mms2. Unlike CROC-1 , whose transcript appears to be elevated in all tumor cell lines examined, the hMMS2 transcript is only elevated in some tumor cell lines. Collectively, these results indicate that eukaryotic cells may contain a highly conserved family of Ubc-like proteins that play roles in diverse cellular processes, ranging from DNA repair to signal transduction and cell differentiation. The hMMS2 and CROC-1 genes are able to functionally complement the yeast mms2 defects with regard to sensitivity to DNA damaging agents and spontaneous mutagenesis. Conversely, both MMS2 and hMMS2 were able to transactivate a c- fos - CAT reporter gene in Rat-1 cells in a transient co-transfection assay. We propose that either these proteins function in a common cellular process, such as DNA repair, or they exert their diverse biological roles through a similar biochemical interaction relative to ubiquitination.

The synaptic SNARE complex is a parallel four-stranded helical bundle

The heterotrimeric synaptic soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, consisting of the synaptic vesicle-associated membrane protein 2 (VAMP2) and presynaptic plasma membrane proteins SNAP-25 (synaptosome-associated protein of 25,000 Mr) and syntaxin 1A, is a critical component of the exocytotic machinery. We have used spin labeling electron paramagnetic resonance spectroscopy to investigate the structural organization of this complex, particularly the two predicted helical domains contributed by SNAP-25. Our results indicate that the N- and C-terminal domains of SNAP-25 are parallel to each other and to the C-terminal domain of syntaxin 1A. Based on these findings, we propose a parallel four-stranded coiled coil model for the structure of the synaptic SNARE complex.

Identification of a repressor of the differentiation of WEHI-3B D- leukemia cells

The WEHI-3B D+ leukemia is a near-diploid differentiation-competent cell line that undergoes myeloid differentiation in response to retinoic acid. WEHI-3B D- cells, derived from WEHI-3B D+ cells, are near tetraploid and not responsive to the differentiation-inducing properties of the retinoid. To gain information on mechanisms that regulate the maturation of these two cell lines, several multiploid cell lines have been established through fusion of WEHI-3B D+ and WEHI-3B D- cells. Studies with the multiploid cell lines have shown that (a) the cellular growth rate decreases with increased DNA ploidy; (b) near-tetraploid D+/+ cells, obtained by fusing WEHI-3B D+ with WEHI-3B D+ cells, remain differentiation-competent, demonstrating that no direct relationship exists between differentiation competency and DNA ploidy; and (c) near-hexaploid D +/- and D -/+ cells, formed by fusion of WEHI-3B D+ with WEHI-3B D- cells, do not respond to differentiation inducers, suggesting the inhibition of the differentiation machinery of WEHI-3B D+ cells by components from maturation-incompetent WEHI-3B D- cells. The scl transcription factor gene is expressed in WEHI-3B D- cells and is absent in WEHI-3B D+ cells. Overexpression of scl by transfection of scl cDNA in WEHI-3B D+ cells markedly decreased the capacity of retinoic acid to induce differentiation, suggesting that scl functions as a repressor of differentiation in WEHI-3B cell lines.

[Sequence analysis of the serotype specific gene fragment of VP4 from three rotavirus field strains]

Rotaviruses are the major pathogens that cause life threatening diarrhea in young children and animals. The 4th gene, encodes the nonglycosylated major neutralizing protein VP4 which can be cleaved into VP8 and VP5. The regions of the fourth genes coding for the VP8 protein, downstream cleavage site and the NH2 terminus of VP5 from three Beijing human rotavirus field strains (T65 [P1A], R50[P1B], N16[P2]) were cloned and sequenced. Comparative analysis of the deduced amino acid sequences of these 887 bp fragments from three strains indicates a high degree of homology (92%-96.6%) between field and reference strains within the same serotype and a high degree of divergence (70.5%-71%) among different serotypes. Notably, the most divergence of amino acid sequence is located in a region delimited by aa 84-172 of VP8 protein. In addition, the possibility of trypsin cleavage sites in virulence is discussed.

Design, synthesis, and structure-activity relationships of the first highly potent, selective, and bioavailable adenosine 5'-monophosphate deaminase inhibitors

Structure-activity studies have been performed to optimize the potency of this novel series of AMPDA inhibitors. Conformational rigidification of the N-3 sidechain resulted in substantial effect on the potency. Addition of the hydrophobic groups provided further benefit. The most potent compound identified, 4g (Ki = 3 nM), bears little structural resemblance to AMP and exhibits a remarkable improvement (10(3) and 10(5)) in binding affinity relative to the original lead and AMP, respectively. The application of prodrug strategy achieved a large improvement (benzyl ester 5d) in oral bioavailability, resulting in compounds that should be useful in evaluating the role of AMPDA in normo- and pathophysiological states.

MMS2, encoding a ubiquitin-conjugating-enzyme-like protein, is a member of the yeast error-free postreplication repair pathway

Among the three Saccharomyces cerevisiae DNA repair epistasis groups, the RAD6 group is the most complicated and least characterized, primarily because it consists of two separate repair pathways: an error-free postreplication repair pathway, and a mutagenesis pathway. The rad6 and rad18 mutants are defective in both pathways, and the rev3 mutant affects only the mutagenesis pathway, but a yeast gene that is involved only in error-free postreplication repair has not been reported. We cloned the MMS2 gene from a yeast genomic library by functional complementation of the mms2-1 mutant [Prakash, L. & Prakash, S. (1977) Genetics 86, 33-55]. MMS2 encodes a 137-amino acid, 15.2-kDa protein with significant sequence homology to a conserved family of ubiquitin-conjugating (Ubc) proteins. However, Mms2 does not appear to possess Ubc activity. Genetic analyses indicate that the mms2 mutation is hypostatic to rad6 and rad18 but is synergistic with the rev3 mutation, and the mms2 mutant is proficient in UV-induced mutagenesis. These phenotypes are reminiscent of a pol30-46 mutant known to be impaired in postreplication repair. The mms2 mutant also displayed a REV3-dependent mutator phenotype, strongly suggesting that the MMS2 gene functions in the error-free postreplication repair pathway, parallel to the REV3 mutagenesis pathway. Furthermore, with respect to UV sensitivity, mms2 was found to be hypostatic to the rad6Delta1-9 mutation, which results in the absence of the first nine amino acids of Rad6. On the basis of these collective results, we propose that the mms2 null mutation and two other allele-specific mutations, rad6Delta1-9 and pol30-46, define the error-free mode of DNA postreplication repair, and that these mutations may enhance both spontaneous and DNA damage-induced mutagenesis.

Identification, chromosomal mapping and tissue-specific expression of hREV3 encoding a putative human DNA polymerase zeta

The Saccharomyces cerevisiae REV3 gene encodes the catalytic subunit of a non-essential DNA polymerase zeta, which is required for mutagenesis. The rev3 mutants significantly reduce both spontaneous and DNA damage-induced mutation rates. We have identified human cDNA clones from two different libraries whose deduced amino acid sequences bear remarkable homology to the yeast Rev3, and named this gene hREV3. The hREV3 gene was mapped to chromosome 1p32-33 by fluorescence in situ hybridization. The hREV3 encodes an mRNA of >10 kb, and its expression varies in different tissues and appears to be elevated in some but not all of the tumor cell lines we have examined. In light of recent reports of a putative mouse REV3, these results indicate that mammalian cells may also contain a mutagenic pathway which aids in cell survival at the cost of increased mutation.

Nuclease-resistant composite 2',5'-oligoadenylate-3', 5'-oligonucleotides for the targeted destruction of RNA: 2-5A-iso-antisense

A new modification of 2-5A-antisense, 2-5A-iso-antisense, has been developed based on a reversal of the direction of the polarity of the antisense domain of a 2-5A-antisense composite nucleic acid. This modification was able to anneal with its target RNA as well as the parental 2-5A-antisense chimera. The 2-5A-iso-antisense oligonucleotide displayed enhanced resistance to degradation by 3'-exonuclease enzyme activity such as that represented by snake venom phosphodiesterase and by that found in human serum. 2-5A-Iso-antisense was able to effect the degradation of a synthetic nontargeted substrate, [5'-32P]pC11U2C7, and two targeted RNAs, PKR and BCR mRNAs, in a cell-free system containing purified recombinant human 2-5A-dependent RNase L. These results demonstrated that the novel structural modification represented by 2-5A-iso-antisense provided a stabilized biologically active formulation of the 2-5A-antisense strategy.

Intracutaneous vaccination of rabbits with the E6 gene of cottontail rabbit papillomavirus provides partial protection against virus challenge

DNA vaccination of rabbit skin with the L1 gene of cottontail rabbit papillomavirus (CRPV) has previously been shown to induce prophylactic immunity against CRPV. We now describe the effects of vaccination with the CRPV E6 gene, using the same approach. The experimental vaccine pdCMV-E6 encoded both the truncated and full length forms of CRPV E6 protein. The control vaccine pCMV-beta encoded beta galactosidase. Rabbits were vaccinated with DNA-coated gold particles, using a gene gun. Each rabbit received an initial vaccination with 30 micrograms DNA and 3 weeks later a booster vaccination, also with 30 micrograms DNA. pdCMV-E6-vaccinated rabbits developed E6-specific cellular immunity as determined by proliferation assays using peripheral blood mononuclear cells from animals prior to challenge, but did not develop detectable humoral immunity to E6 proteins, as evaluated by ELISA using two different E6 antigen preparations. Control rabbits developed humoral immunity to beta galactosidase. All rabbits were challenged by infection of nine skin sites with live CRPV virus and monitored for papilloma formation. None of four control rabbits was protected at any of the challenge sites. Of six rabbits vaccinated with pdCMV-E6, two were completely protected and one was virtually completely protected (tiny papillomas at just two of nine challenge sites). These three rabbits also exhibited significant E6-specific in vitro proliferative responses. The four E6 DNA-vaccinated rabbits that were not completely protected exhibited evidence of partial protection: some challenge sites did not form papillomas; papilloma onset was delayed; papilloma burden was less. These results demonstrate that partial prophylaxis against papillomavirus-induced disease can be achieved by intracutaneous vaccination with a recombinant plasmid encoding the papillomavirus.

Mms4, a putative transcriptional (co)activator, protects Saccharomyces cerevisiae cells from endogenous and environmental DNA damage

mms4-1 is one of several Saccharomyces cerevisiae mutants that exhibit an increased sensitivity to methyl methanesulfonate (MMS), but not to UV or X-rays. We have isolated the MMS4 gene by functional complementation of the MMS-sensitive phenotype in the mms4-1 strain. The MMS4 gene encodes a 691-amino acid, 78.7-kDa protein. The deduced Mms4 protein does not show significant homology to any of the known proteins in the database. However, several putative functional domains suggest that it may be a nuclear protein capable of interacting with other proteins. Examination of the mms4delta mutant phenotype indicates that the mutation not only sensitizes DNA to methylating and ethylating agents, but also to other DNA damage that blocks DNA replication. However, the mms4delta mutant appears to be more sensitive to chronic treatment than to acute treatment by DNA-damaging agents. Furthermore, the spontaneous mutation rate increases significantly in the mms4delta mutant. Mms4 alone, when fused to a Gal4 DNA-binding domain, is able to activate P(GAL1)-lacZ and P(GAL1)-HIS3 reporter genes in a two-hybrid system; the Mms4 transactivation domain maps to the highly acidic N-terminal region. These results collectively suggest that Mms4 may function as a transcriptional (co)activator and play an important role in DNA repair and/or synthesis.

Synergism between yeast nucleotide and base excision repair pathways in the protection against DNA methylation damage

The treatment of cells with simple DNA methylating agents such as methyl methanesulfonate (MMS) results in genotoxic lesions, including 3-methyladenine which blocks DNA replication. All the organisms studied to date contain an alkylation-specific base excision repair pathway. In the yeast Saccharomyces cerevisiae, the base excision repair pathway is initiated by a Mag1 3-methyladenine DNA glycosylase that removes the damaged base, followed by the Apn1 apurinic/apyrimidinic endonuclease which cleaves the DNA strand at the abasic site for subsequent repair and synthesis. Several nucleotide excision repair pathway mutants display only slightly increased sensitivity to killing by MMS, indicating that nucleotide excision repair per se does not play a major role in the repair of DNA methylation damage. However, mag1 and apn1 mutants that are also defective in nucleotide excision repair are extremely sensitive to MMS-induced killing and the effects are synergistic. These observations suggest that nucleotide excision repair and alkylation-specific base excision repair provide alternative pathways for the repair of DNA methylation damage. In addition to their role in nucleotide excision repair, Rad1 and Rad10 form a complex that is involved in recombination repair. It was found that the apn1 rad1 and apn1 rad10 double mutants have a growth defect and are significantly more sensitive to MMS killing than apn1 rad2 and apn1 rad4 double mutants in a gradient plate assay. Furthermore, the apn1 rad1 double mutant increased both the spontaneous and MMS-induced mutation frequency. Thus, the recombination repair defects of rad1 and rad10 may confer an additional synergistic effect when combined with the apn1 mutation.

Methods for the characterization of phosphatase-stabilized 2-5A-antisense chimeras

We have developed chromatographic and spectrophotometric assays for determining the degree of thiolation in phosphatase-resistant 5'-monothiophosphate-capped 2-5A-antisense chimeras. Concomitantly, we have explored the reactivity of this 5'-monophosphorothioate moiety with reporter reagents such as 5-iodoacetomidofluorescein and 5,5'-dithiobis(2-nitrobenzoic acid). On the basis of these reactions, analyses for 5'-monothiophosphate-functionalized 2-5A-antisense chimeras were made possible. Kinetic experiments demonstrated that oligonucleotide backbone negative charge could retard mixed disulfide formation in the reaction of 5,5'-dithiobis(2-nitrobenzoic acid) with 5'-monothiophosphorylated 2-5A-antisense chimeras.

Defects in base excision repair combined with elevated intracellular dCTP levels dramatically reduce mutation induction in yeast by ethyl methanesulfonate and N-methyl-N'-nitro-N-nitrosoguanidine

Previously, we determined that elimination of deoxycytidylate (dCMP) deaminase (DCD1) in the yeast Saccharomyces cerevisiae increases the intracellular dCTP:dTTP ratio and reduces the induction of G x C --> A x T transitions in the SUP4-o gene by ethyl methanesulfonate (EMS) and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Simultaneously, the G x C --> C x G transversion frequency rises substantially. We attributed the first response to dCTP outcompeting dTTP for incorporation opposite O6-alkylguanine, and the second outcome to the increased dCTP pool causing error-prone repair of apurinic (AP) sites resulting from the removal or lability of N7-alkylguanine. To test the latter hypothesis, we used isogenic dcd1 strains deleted for either of two genes (MAG1: 3-methyladenine glycosylase; APN1: apurinic endonuclease) involved in the repair of N7-alkylguanine. In these backgrounds, EMS or MNNG induction of total SUP4-o mutations, G x C --> A x T transitions and G x C --> C x G transversions were reduced by >98%, >97%, and >80%, respectively. Mutation frequencies in the dcd1 apn1 strain were close to those for spontaneous mutagenesis in the wild-type parent. These findings argue that misincorporation of dCTP during repair of alkylation-induced AP sites is responsible for the increased G x C --> C x G transversion frequency in the dcd1 strain treated with EMS or MNNG. The data also demonstrate that defective repair of AP sites coupled with an elevated dCTP:dTTP ratio eliminates most EMS and MNNG mutagenesis. In addition, the results point to a role for AP sites in the production of some EMS- and MNNG-induced G x C --> A x T transitions as well as other substitutions in the dcd1 strain.

Transient channel-opening in bacteriorhodopsin: an EPR study

Active translocation of ions across membranes requires alternating access of the ion binding site inside the pump to the two membrane surfaces. Proton translocation by bacteriorhodopsin (bR), the light-driven proton pump in Halobacterium salinarium, involves this kind of a change in the accessibility of the centrally located retinal Schiff base. This key event in bR's photocycle ensures that proton release occurs to the extracellular side and proton uptake from the cytoplasmic side. To study the role of protein conformational changes in this reprotonation switch, spin labels were attached to pairs of engineered cysteine residues in the cytoplasmic interhelical loops of bR. Light-induced changes in the distance between a spin label on the EF interhelical loop and a label on either the AB or the CD interhelical loop were observed, and the changes were monitored following photoactivation with time-resolved electron paramagnetic resonance (EPR) spectroscopy. Both distances increase transiently by about 5 A during the photocycle. This opening occurs between proton release and uptake, and may be the conformational switch that changes the accessibility of the retinal Schiff base to the cytoplasmic surface after proton release to the extracellular side.

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.