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PubMed1999

Structural analysis of adeno-associated virus transduction circular intermediates.

Recombinant adeno-associated virus (rAAV) has recently been demonstrated to form circular intermediates following transduction in muscle tissue and cell lines. Although restriction enzyme and Southern blot analysis has revealed a consistent monomer and multimer head-to-tail conformation, detailed structural sequence analysis has been lacking due to the high secondary structure of the ITR arrays. To gain further insight into potential mechanisms by which AAV circular genomes are formed from linear single-stranded viral DNA, we have performed chemical sequencing of ITR arrays within seven circular intermediates independently isolated from primary fibroblasts and Hela cells. Results from these studies demonstrated several types of circular intermediates with mosaic ITR elements flanked by two D sequences. The most predominant form consisted of a structure similar to that of previously generated AAV double-D plasmids, with one complete ITR flanked by two D-region elements. However, intermediately deleted ITR arrays with more than one complete ITR were also seen. Based on this structural information, we have proposed a model for formation of AAV circular intermediates by recombination/ligation between ITR ends of panhandle single-stranded AAV genomes.

Base Sequence↗
PubMed2001

The wild-type conformation of the Mos-1 inverted terminal repeats is suboptimal for transposition in bacteria.

The two inverted terminal repeats (ITRs) flanking the Mos-1 mariner element differ in sequence at four positions. Gel retardation experiments indicated that each of these differences has a significant impact on the quality of the interaction between the ITR and the Mos-1 transposase. We showed that the transposase binds to the 3' ITR better than to the 5' ITR. The results of transposition assays performed in Escherichia coli indicated that these differences have an influence on the rate of transposition and the stability of the transposition products. Finally, we find that the wild-type configuration of the Mos-1 element, with one 5' ITR and one 3' ITR, is less efficient for transposition in bacteria than that of an element having two 3' ITRs.

Base Sequence↗
PubMed2006

Treatment recommendations for the various subgroups of neurocytomas.

Neurocytomas gained importance since 1995, which is reflected by the increasing number of reports on this entity. This study was performed to determine the best available treatment for typical and atypical neurocytomas (MIB-1 labeling index >3%, atypical histology) in various age groups ( 18 years). The data of all neurocytoma patients reported since 1982, when this entity were reviewed for age, gender, extent of resection, MIB-1 labeling index, histology, radiotherapy, and outcome of therapy. Patients were treated with complete resection alone (CTR), CTR plus radiotherapy (CTR + RT), incomplete resection alone (ITR), or ITR plus radiotherapy (ITR + RT). If the reported data were incomplete, the authors were contacted for additional data. Follow up had to be at least 12 months. Data were complete in 438 patients (73 children, 365 adults). Three hundred and fifty-one patients had typical, 87 atypical lesions. Typical lesions were associated with better local control and survival than atypical lesions (P < 0.001). CTR was superior to ITR (P < 0.001). After CTR, outcome was not significantly improved by RT. After ITR, RT improved survival in typical lesions (P = 0.03) and atypical lesions (P = 0.05), not in children (P = 0.16). Local control was improved in all groups (P < 0.001, children P = 0.01). Doses >54 Gy appeared beneficial after ITR of atypical lesions. In children, 50 Gy were comparable.CTR does not require post-operative RT. Following ITR, RT improves outcome. Of 50-54 Gy appear sufficient for typical lesions, 50 Gy for children. Atypical lesions require 56-60 Gy.

Adolescent↗
PubMed1991

Redundant elements in the adenovirus type 5 inverted terminal repeat promote bidirectional transcription in vitro and are important for virus growth in vivo.

The adenovirus inverted terminal repeat (ITR) contains a number of cis-acting elements that are involved in the initiation of viral DNA replication, as well as multiple binding motifs for the cellular transcription factors SP1 and ATF. In this study, we utilized a Hela cell transcription extract to demonstrate that the adenovirus type 5 ITR promotes bidirectional transcription in vitro. Primer extension analyses demonstrated that the ITR directed transcription at initiation sites both within the terminal repeat and at fixed distances outside of the ITR. The ITR also strongly stimulated transcription at the early region 1A (E1A) initiation site when it was situated immediately upstream of the E1A TATA box region. Deletion and point mutational analyses demonstrated that two distinct cis-acting elements were involved in these ITR-dependent transcriptional activities in vitro. Cellular transcription factors SP1 and ATF were previously shown to bind to these two regions. Analysis of viral mutants in vivo demonstrated that the NFIII/OCT-1 binding site and a conserved ATF motif were important for efficient viral growth. Regulatory elements in the ITR flanking region were found to functionally substitute for these sites.

Adenoviruses, Human↗
PubMed2005

Conservation of Palindromic and Mirror Motifs within Inverted Terminal Repeats of mariner-like Elements.

The transposase of the mariner-like elements (MLEs) specifically binds as a dimer to the inverted terminal repeat of the transposon that encodes it. Two binding-motifs located within the inverted terminal sequences (ITR) are therefore recognized, as previously indicated, by biochemical data obtained with the Mos1 and Himar1 transposases. Here, we define the motifs that are involved in the binding of a MLE transposase to its ITR by analyzing the nucleic acid properties of the 5' and 3' ITR sequences from 45 MLEs, taking into account the fact that the transposase binds to the ITR, using its CRO binding domains and the general characteristics of the cro binding sites so far investigated. Our findings show that in all the MLE ITRs, the outer half was better conserved than the inner half. More interestingly, they allowed us to characterize conserved palindromic and mirror motifs specific to each "MLE species". The presence of the palindromic motifs was correlated to the binding of the transposase dimer, whereas the properties of the mirror motifs were shown to be responsible for the bend in each ITR that helps to stabilize transposase-ITR interactions.

Animals↗
PubMed2006

Interstitial telomeric sequence blocks in constitutive pericentromeric heterochromatin from Pyrgomorpha conica (Orthoptera) are enriched in constitutive alkali-labile sites.

The long interstitial telomeric repeat sequence (ITRS) blocks located in the pericentromeric chromosomal regions of most of Chinese hamster chromosomes behave as hot spots for spontaneous and induced chromosome breakage and recombination. The DBD-FISH (DNA breakage detection-fluorescence in situ hybridization) procedure demonstrated that these ITRS are extremely sensitive to alkaline unwinding, being enriched in constitutive alkali-labile sites (ALS). To determine whether this chromatin modification occurs in other genomes with large ITRS that are not phylogenetically related to mammalian species, the grasshopper Pyrgomorpha conica was analyzed. We chose this species because, with conventional FISH, their chromosomes yield extremely small telomeric signals when probed with the (TTAGG)n polynucleotide, but large ITRS blocks as part of their pericentromeric constitutive heterochromatin. A high density of constitutive ALS was evidenced in the ITRS when intact meiotic cells or somatic cells were subjected to the DBD-FISH technique and probed with the specific telomeric DNA. DBD-FISH with simultaneous hybridization using telomeric and whole genome DNA probes showed that the ITRS tend to colocalize with areas of stronger signal from the whole genome probe. Nevertheless, the signal from the whole genome was more widespread than that from the ITRS, thus providing evidence that a high frequency of constitutive ALS was present in more than one DNA sequence type. Furthermore, stretched DNA fibers processed with DBD-FISH, revealed a distribution of telomeric sequences alternating interspersed with other possible highly repetitive DNA sequences. The abundance of ALS varied from one meiotic stage to another. Interestingly, most of the breakage and meiotic recombination in males takes place close to the constitutive heterochromatin, particularly enriched in ALS. These results provide further evidence of a particular, and possible universal, chromatin structure enriched in constitutive ALS at constitutive heterochromatic regions.

Animals↗
PubMed2005

Genome trimming: a unique strategy for replication control employed by Borna disease virus.

Genome and antigenome synthesis of negative-strand RNA viruses is initiated at promoters located in inverted terminal repeats (ITR). The ITR of Borna disease virus (BDV), a persisting neurotropic virus with a nuclear replication phase, are exceptional in that they appear to be noncomplete. Our analysis showed that the vast majority of genomic and antigenomic RNA molecules of BDV lack four 5'-terminal nucleotides required for perfect complementarity with the 3' ITR. By using a previously undescribed reverse genetics system, we investigated whether the structure of the ITR would affect virus propagation. BDV rescued from cDNA encoding complete ITR (rBDVc) showed wild-type virulence, whereas virus rescued from cDNA encoding a viral genome with noncomplete ITR (rBDVnc) was strongly attenuated. Both recombinant viruses expressed similar RNA and protein levels in persistently infected cells. However, rBDVnc particles were less infectious, indicating that complete ITR are required for high viral replicase but not transcriptase activity. Interestingly, genomic RNA from purified rBDVc particles lacked 5'-terminal nucleotides like authentic BDV, strongly suggesting programmed genome truncation. By specifically trimming its genome at the 5' terminus, BDV seems to limit viral genome amplification, which may favor noncytolytic viral persistence.

Base Sequence↗
PubMed2000

Investigation of dissolution enhancement of itraconazole by solid dispersion in superdisintegrants.

Solid dispersions of itraconazole (ITR) in lactose, microcrystalline cellulose (MCC), and three superdisintegrants (Primogel, Kollidon CL, and Ac-Di-Sol) and their formulation into tablets were investigated with an objective of enhancing the dissolution rate of ITR from tablet formulations. X-ray diffraction (XRD) and differential scanning calorimetry (DSC) were used to characterize the dispersions. A marked enhancement in the dissolution rate of ITR was observed with all the excipients. The order for the excipients to enhance the dissolution rate was Ac-Di-Sol > Kollidon CL > Primogel > MCC > lactose. Solid dispersions in superdisintegrants gave much higher rates of dissolution than the dispersions in other excipients. Ac-Di-Sol gave the most improvement (28-fold) in the dissolution rate of ITR at a 1:1 drug:excipient ratio. Solid dispersions in superdisintegrants could be formulated into tablets. These tablets, apart from fulfilling all official and other specifications, exhibited higher rates of dissolution and dissolution efficiency (DE) values. XRD indicated the presence of ITR in amorphous form in the dispersions. DSC indicated a weak interaction between ITR and the excipients. Micronization and conversion of the drug into the amorphous form and the fast disintegrating and dispersing action of the superdisintegrants contribute to the enhancement of the dissolution rate of ITR from its solid dispersions in superdisintegrants and their corresponding tablet formulations.

Antifungal Agents↗
PubMed1998

Zinc pretreatment inhibits isotretinoin teratogenicity and induces embryonic metallothionein in CD-1 mice.

Isotretinoin (ITR), a teratogen in many species, is associated with increased oxidative stress. Metallothionein (MT) is an important tissue antioxidant whose concentrations are induced by zinc. To study the role of supplemental Zn as an inducer of embryonic MT, we injected pregnant CD-1 mice subcutaneously with saline vehicle, or 20 or 40 mg/kg Zn on gestational day (GD) 6.5. After 48 h, embryonic MT concentrations increased in a dose-related manner (r = 0.64, P < 0.05) with Zn treatment. The possible protective role of Zn pretreatment against ITR teratogenicity was investigated in vivo and in vitro. CD-1 mice were pretreated with saline or Zn (20 and 40 mg/kg) on GD 8.5 and 9.5. ITR was administered to both groups of mice via three intragastric intubations of 100 mg ITR/kg at 4 h intervals on GD 10.5. On GD 18.5, Zn pre-treated mice demonstrated decreased ITR-mediated growth retardation, cleft palates and postpartum mortality. A reduction in embryonic MT concentrations was observed in mice exposed to ITR. Mouse embryos cultured on GD 8.5 with an addition of 15 micromol/L Zn for 48 h had a sixfold greater MT concentration (688 microg/g protein) than controls. The Zn pretreatment of cultured embryos prevented malformations and lessened growth retardation caused by 24 h exposure to 17 micromol/L ITR. These results suggest that Zn-mediated induction of MT in mouse embryos could protect against ITR teratogenicity.

Abnormalities, Drug-Induced↗
PubMed1997

A novel terminal resolution-like site in the adeno-associated virus type 2 genome.

The adeno-associated virus 2 (AAV) contains a single-stranded DNA genome of which the terminal 145 nucleotides are palindromic and form T-shaped hairpin structures. These inverted terminal repeats (ITRs) play an important role in AAV DNA replication and resolution, since each of the ITRs contains a terminal resolution site (trs) that is the target site for the AAV rep gene products (Rep). However, the Rep proteins also interact with the AAV DNA sequences that lie outside the ITRs, and the ITRs also play a crucial role in excision of the proviral genome from latently infected cells or from recombinant AAV plasmids. To distinguish between Rep-mediated excision of the viral genome during rescue from recombinant AAV plasmids and the Rep-mediated resolution of the ITRs during AAV DNA replication, we constructed recombinant AAV genomes that lacked either the left or the right ITR sequence and one of the Rep-binding sites (RBSs). No rescue and replication of the AAV genome occurred from these plasmids following transfection into adenovirus type 2-infected human KB cells, as expected. However, excision and abundant replication of the vector sequences was clearly detected from the plasmid that lacked the AAV left ITR, suggesting the existence of an additional putative excision site in the left end of the AAV genome. This site was precisely mapped to one of the AAV promoters at map unit 5 (AAV p5) that also contains an RBS. Furthermore, deletion of this RBS abolished the rescue and replication of the vector sequences. These studies suggest that the Rep-mediated cleavage at the RBS during viral DNA replication may, in part, account for the generation of the AAV defective interfering particles.

Chromosome Mapping↗
PubMed2026

Systematic mapping of insertion-tolerant regions enables capsid engineering of an infectious RNA phage.

RNA phages are attractive platforms for the design of programmable bioparticles, but their development has been constrained by limited knowledge of genomic sites that can tolerate sequence insertion. Here, we combined MuA transposase-mediated in vitro insertion mutagenesis with our established reverse genetics systems to systematically identify insertion-tolerant regions (ITRs) in the RNA phages MS2 and PP7. Screening of 4,555 MS2 and 2,228 PP7 random insertion clones identified 29 and 26 non-redundant ITRs, respectively. We further analyzed and compared these ITRs in the context of RNA genome organization and virion architecture. Both phages contained ITRs within the maturation protein, whereas only PP7 tolerated insertions within the coat protein (CP). On the basis of structural location and plaque-forming capacity, an ITR situated between Gly74 and Glu75 (GGC^GAG) in the PP7 CP was selected for further study. Infectious phage particles generated from complementary DNA clones retained the 15-bp insertion at both the RNA and protein levels. Engineered PP7 phages carrying an Arg-Gly-Asp motif inserted into the CP at this ITR displayed enhanced in vivo clearance in a Drosophila model, despite having in vitro stability comparable to that of the wild type. These findings provide the first example of CP engineering in an infectious RNA phage and establish a framework for engineering RNA phages for biological and biotechnological applications.IMPORTANCEA major obstacle to developing RNA phages as synthetic biology platforms is the lack of design principles for genomic insertion. Here, we address this limitation by establishing a mutagenesis-and-recovery workflow that systematically identifies insertion-tolerant regions (ITRs) in the RNA phages MS2 and PP7. The resulting maps reveal distinct structural constraints in the two phages and enable rational engineering of a peptide-display site in the PP7 capsid. Using this approach, we generated an engineered infectious phage with a modified capsid, thereby providing the first demonstration of capsid engineering in an infectious RNA phage, to our knowledge. This study lays the groundwork for the rational design of live RNA phage virions as tractable and engineerable scaffolds for future biological and biotechnological applications.

Animals↗
PubMed1998

Targeted integration of adeno-associated virus-derived plasmids in transfected human cells.

Adeno-associated virus (AAV) integrates its genomic DNA into a defined region of human chromosome 19 (AAVS1). The specificity of integration is dependent on the presence of the inverted terminal repeats (ITR) and on expression of the rep gene. To develop vectors capable of targeting the insertion of a selected DNA sequence into a specific location of human chromosome, we determined whether the rep gene can mediate site-specific integration when cloned outside of an ITR-flanked transgene cassette. HeLa and Huh-7 cells were transfected with a plasmid containing the rep gene, as well as the green fluorescent protein (GFP) and neomycin (neo) resistance gene inserted between the ITRs of AAV. Southern blot analysis of individual clones detected Rep-mediated site-specific integration of the ITR-flanked DNA in 25% and 12% of the HeLa and Huh-7 clones, respectively. The localization of the GFP-Neo sequence on chromosome 19 also was confirmed by fluorescent in situ hybridization analysis of the transfected HeLa clones. Sequence analysis of the ITR-AAVS1 junction of one of the transfected Huh-7 clones indicated that the insertion of the ITR DNA fragment had occurred at nucleotide 1003. These results have implications for the development of AAV-derived vectors capable of directing the site-specific integration of a gene of interest.

Base Sequence↗
PubMed1986

Analysis of Tn3 sequences required for transposition and immunity.

Tn3 is a 5-kb transposon (Tn) with 38-bp inverted terminal repeats (ITR). The two 38-bp terminal sequences are required in cis for Tn3 transposition. In this study, the role of the ITR in Tn3 transposition has been further dissected by the use of various mini-Tn3 Tn's. The transposition frequency of these mini-Tn's demonstrate that Tn3 contains no sequence other than the ITR sequences that are necessary for the first step in transposition; the two terminal repeats must be oriented as ITR for transposition to occur; the outside 34 bp of the ITR are required for transposition; and reducing the distance between the terminal sequences does not affect transposition frequency. Moreover, mutant copies of the ITR sequences that cannot function in transposition do not confer transposition immunity.

Base Composition↗
PubMed2005

Effect of Wortmannin on the repair profiles of DNA double-strand breaks in the whole genome and in interstitial telomeric sequences of Chinese hamster cells.

The DNA breakage detection-fluorescence in situ hybridization (DBD-FISH) procedure was applied to analyze the effect of Wortmannin (WM) in the rejoining kinetics of ionizing radiation-induced DNA double-strand breaks (DSBs) in the whole genome and in the long interstitial telomeric repeat sequence (ITRS) blocks from Chinese hamster cell lines. The results indicate that the ITRS blocks from wild-type Chinese hamster cell lines, CHO9 and V79B, exhibit a slower initial rejoining rate of ionizing radiation-induced DSBs than the genome overall. Neither Rad51C nor the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) activities, involved in homologous recombination (HR) and in non-homologous end-joining (NHEJ) pathways of DSB repair respectively, influenced the rejoining kinetics within ITRS in contrast to DNA sequences in the whole genome. Nevertheless, DSB removal rate within ITRS was decreased in the absence of Ku86 activity, though at a lower affectation level than in the whole genome, thus homogenizing both rejoining kinetics rates. WM treatment slowed down the DSB rejoining kinetics rate in ITRS, this effect being more pronounced in the whole genome, resulting in a similar pattern to that of the Ku86 deficient cells. In fact, no WM effect was detected in the Ku86 deficient Chinese hamster cells, so probably WM does not add further impairment in DSB rejoining than that resulted as a consequence of absence of Ku activity. The same slowing effect was also observed after treatment of Rad51C and DNA-PKcs defective hamster cells by WM, suggesting that: (1) there is no potentiation of the HR when the NHEJ is impaired by WM, either in the whole genome or in the ITRS, and (2) that this impairment may probably involve more targets than DNA-PKcs. These results suggest that there is an intragenomic heterogeneity in DSB repair, as well as in the effect of WM on this process.

Androstadienes↗
PubMed2004

Differences in repair profiles of interstitial telomeric sites between normal and DNA double-strand break repair deficient Chinese hamster cells.

Interstitial Telomeric Repeat Sequence (ITRS) blocks are recognized as hot spots for spontaneous and ionizing radiation-induced chromosome breakage and recombination. Background and ionizing radiation-induced DNA breaks in large blocks of ITRS from Chinese hamster cell lines were analyzed using the DNA Breakage Detection-Fluorescence In Situ Hybridization (DBD-FISH) procedure. Our results indicate an extremely alkali-sensitivity of ITRS. Furthermore, it appears that ITRS blocks exhibit a particular chromatin structure, being enriched in short unpaired DNA segments. These segments could be liable to severe topological stress in highly compacted areas of the genome resulting in their spontaneous fragility and thus explaining their alkali-sensitivity. The induction and repair kinetics of DNA single-strand breaks (ssb) and DNA double-strand breaks (dsb) induced by ionizing radiation were assessed by DBD-FISH on neutral comets using Chinese hamster cells deficient in either DNA-PKcs or Rad51C. Our results indicate that the initial rejoining rate of dsb within ITRS is slower than that in the whole genome, in wild-type cells, demonstrating an intragenomic heterogeneity in dsb repair. Interestingly, in the absence of DNA-PKcs activity, the rejoining rate of dsb within ITRS is not modified, unlike in the whole genome. This was also found in the case of Rad51C mutant cells. Our results suggest the possibility that different DNA sequences or chromatin organizations may be targeted by specific dsb repair pathways. Furthermore, it appears that additional unknown dsb repair pathways may be operational in mammalian cells.

Animals↗
PubMedDate not supplied

Qualitative and quantitative features of axons projecting from caudal to rostral inferior temporal cortex of squirrel monkeys.

On the basis of cortical and subcortical connections and architectonics, inferior temporal (IT) cortex of squirrel monkeys consists of a caudal region, ITC, with dorsal (ITCd) and ventral (ITCv) subdivisions; a rostral region, ITR; and possibly a third region intermediate to ITC and ITR, ITI (Weller & Steele, 1992; Steele & Weller, 1993). The present study qualitatively and quantitatively examined the terminal arborizations of 26 axons in ITR and ITI labeled by injections of biocytin or, in one case, horseradish peroxidase, in ITCv. The majority of axons gave rise to a single terminal arbor, with a small number branching into two overlapping or nearby arbors. Presumptive terminal specializations consisted of rounded, bead-like swellings, most often located en passant. All axons terminated in layer 4 of cortex, and most had additional terminations in layers 3 and 5. The total extent of each axon's terminal arbor was 125-750 microns dorsoventrally (mean = 360.6 microns) and 150-725 microns anteroposteriorly (mean = 328.1 microns; all values uncorrected for shrinkage). In most axons, especially those with larger terminal fields, boutons were not uniformly distributed, but formed 2-4 clumps (mean = 2.2), with a mean width of 149 microns, separated by narrower regions of fewer boutons. Based on a cluster analysis of characteristics of the 26 axons, axons projecting from caudal (ITCv) to rostral (ITR or ITI) IT cortex of squirrel monkeys comprised three groups that we called Type I, Type II, and Type III. Type I axons, the smallest in area extent of terminal arbor, terminated predominantly in dorsal ITR. Type III axons, largest in areal extent, and Type II axons, intermediate in areal extent, terminated in ventral ITR and throughout ITI. The three classes of axons may correspond to different types of visual information entering rostral IT cortex. The clumping of boutons suggests that individual axons terminate in limited patches within their terminal fields.

Animals↗
PubMed2004

IRI-1, a LIN-15B homologue, interacts with inositol-1,4,5-triphosphate receptors and regulates gonadogenesis, defecation, and pharyngeal pumping in Caenorhabditis elegans.

Inositol-1,4,5-triphosphate receptors (IP(3)Rs) are ligand-gated Ca(2+) channels that control Ca(2+) release from intracellular stores. They are central to a wide range of cellular responses. IP(3)Rs in Caenorhabditis elegans are encoded by a single gene, itr-1, and are widely expressed. Signaling through IP(3) and IP(3)Rs is important in ovulation, control of the defecation cycle, modulation of pharyngeal pumping rate, and embryogenesis. To further elucidate the molecular basis of the diversity of IP(3)R function, we used a yeast two-hybrid screen to search for proteins that interact with ITR-1. We identified an interaction between ITR-1 and IRI-1, a previously uncharacterized protein with homology to LIN-15B. Iri-1 is widely expressed, and its expression overlaps significantly with that of itr-1. In agreement with this observation, iri-1 functions in known itr-1-mediated processes, namely, upregulation of pharyngeal pumping in response to food and control of the defecation cycle. Knockdown of iri-1 in an itr-1 loss-of-function mutant potentiates some of these effects and sheds light on the signaling pathways that control pharyngeal pumping rate. Knockdown of iri-1 expression also results in a sterile, evl phenotype, as a consequence of failures in early Z1/Z4 lineage divisions, such that gonadogenesis is severely disrupted.

Amino Acid Sequence↗
PubMed1982

Colinearity of RNAs with the vaccinia virus genome: anomalies with two complementary early and late RNAs result from a small deletion or rearrangement within the inverted terminal repetition.

The colinearity of RNA transcripts with the vaccinia virus genome was investigated. Cytoplasmic RNA from infected cells was annealed to a cloned DNA segment that extended from 9 to 15.6 kilobase pairs from the left end of the genome and contained approximately 800 base pairs of the inverted terminal repetition (ITR). Remaining unhybridized single strands of DNA were digested with nuclease S1, and the lengths of the protected DNA fragments were determined by agarose gel electrophoresis under neutral and alkaline conditions. Uniformly 32P-labeled cloned DNA insert, separated recombinant DNA strands, and smaller restriction fragments, as well as 3' and 5' end-labeled DNA, were employed to map five early RNAs and one late RNA. One of the early RNAs hybridized to sequences within the ITR, and the other four hybridized to sequences proximal to the ITR. The late RNA was initiated proximal to the ITR but extended into it. Interestingly, the 3' portion of this late RNA was complementary to the early RNA transcribed from the opposite strand of the ITR. From a comparison of the lengths of the protected DNA fragments on neutral and alkaline gels, all except the complementary early and late RNAs appeared to be colinear with the genome. Although the anomalous nuclease S1 data obtained with the latter RNAs mimicked splicing, they were shown by DNA-DNA hybridization to result from a small deletion or rearrangement within the ITR. Thus far, no true examples of spliced vaccinia virus RNAs have been found.

Base Sequence↗