Complete nucleotide sequence of an EcoRI-1.35-kb repeated element of mouse: homology with the cellular flanking region between two intracisternal A-particle genes.

The complete DNA sequence (1369 bp) of an EcoRI-1.35-kb repeated element (ER-1) of the mouse BamHI family has been determined. Analysis of this sequence revealed that a portion of the 3' end (positions 1277-1369) of ER-1 was found to share 91% homology with the flanking cellular sequence between two adjacent intracisternal A-particle (IAP) genes, IAP-19A and IAP-19B.

Polyoma virus minichromosomes: characterization of the products of in vitro DNA synthesis.

A two-dimensional (neutral-alkali) agarose gel electrophoretic system was used to separate three families of replicative intermediate (RI) polyoma virus DNA molecules (form I, form II, and form III RIs). Two of these families, form II and III RIs, are the result of artifactual nicking of one of the parental strands of supercoiled RIs (form I RIs) during in vitro replication of soluble minichromosomes. Kinetic studies in vitro showed that the nicked RIs serve as templates for limited DNA synthesis. The nicked species are not converted into normal products, however. The nicking reaction, which appears to be specific for the parental strands, is dependent on magnesium ions and occurs concurrently with the in vitro synthesis of DNA.

Preferential use of a H chain V region in antitumor-associated glycoprotein-72 monoclonal antibodies.

The DNA sequence of the mouse H chain V regions from five hybridomas directed against the human tumor Ag tumor-associated glycoprotein-72 (TAG-72) have been determined. This includes a previously determined VH gene sequence from a first-generation anti-TAG-72 mAb, B72.3, and the VH gene sequences from four second-generation anti-TAG-72 mAb, CC49, CC83, CC46, and CC92. A sequence comparison revealed a high degree of shared sequence identity between the five productively rearranged VH genes, suggesting derivation from a common germ line V region gene. In the process of cloning the unrearranged germ line gene, two highly related VH germ line genes were identified and designated VH alpha TAG-1 and VH alpha TAG-2. A comparison of the productively rearranged anti-TAG-72 VH sequences with the two germ line VH genes demonstrated that they were all derived from VH alpha TAG-1. In contrast, the L chain V regions are all derived from separate germ line V region genes. The preferential use of VH alpha TAG-1 in these five mouse hybridomas suggests that VH alpha TAG-1 is a preferred anti-TAG-72 H V chain region germ line gene and that the H chain plays a predominant role in the recognition of this Ag.

Nucleotide sequences of murine intracisternal A-particle gene LTRs have extensive variability within the R region.

Nucleotide sequences of the long terminal repeats (LTRs) of four murine intracisternal A-particle (IAP) genes IAP62, 19, 81 and 14 were determined. Each IAP LTR contains three sequence domains, 5'-U3-R-U5-3', and each is bound by 4 bp imperfect inverted repeats. The transcriptional regulatory sequences, CAAT and TATA, as well as the enhancer core sequence GTGGTAA are conserved and precisely positioned within the U3 region. In the R region, the sequence AATAAA is located twenty base pairs preceding the dinucleotide CA, the polyadenylation site. In IAP19 and IAP81, the 5' and 3' LTRs are flanked by a six nucleotide direct repeat of cellular sequences representing the possible integration sites for these IAP proviruses. Both the size and sequences of different IAP LTRs vary considerably, with the majority of the variation localized within the R regions. The size of R varies from 66 bp in IAP14 to 222 bp in IAP62; in contrast, the U3 and U5 regions are all similar in size. These extra sequences within the R region of large LTRs consist of several unusual directly repeating sequences which account for this variability.

Polyomavirus minichromosomes: associated DNA topoisomerase II and DNA ligase activities.

Polyomavirus minichromosomes were isolated and fractionated as described previously (B. B. Gourlie, M. R. Krauss, A. J. Buckler-White, R. M. Benbow, and V. Pigiet, J. Virol. 38:805-814, 1981). Specific assays for DNA topoisomerase II and DNA ligase activity were carried out on each fraction. The enzymatic activity in each fraction was determined by quantitative electron microscopy and compared with the number of replicative intermediate and total polyomavirus DNA molecules in each fraction. DNA topoisomerase II activity cosedimented with polyomavirus replicative intermediate minichromosomes. DNA ligase activity cosedimented with mature polyomavirus minichromosomes.

Polyoma virus minichromosomes: a soluble in vitro replication system.

Polyoma virus minichromosomes were isolated from infected 3T6 cells by hypotonic extraction of isolated nuclei. The kinetics of in vitro DNA synthesis in the nuclear extract was similar to that observed with intact nuclei. The majority of the products of in vitro DNA synthesis sedimented with replicative intermediate (RI) minichromosomes and migrated as two bands (RI-a and RI-b) on 1.4% agarose gels. The kinetics of deoxynucleotide monophosphate incorporation into these species was consistent with the existence of several rate-limiting steps in in vitro replication by polyoma minichromosomes. Electron microscope analysis showed that the RI-a band consisted almost entirely of RI theta structures ranging from 46 to 87% replicated, with one-half of all theta structures 67 +/- 4% replicated. The RI-b material was more complex, consisting of sigma and alpha structures with tails ranging from 7 to 114% of polyoma genome length and, less frequently, of linked and multiple linked dimeric structures.

Polyoma virus minichromosomes: associated enzyme activities.

Polyoma minichromosomes were isolated and fractionated on glycerol gradients as described by Gourlie et al. (J. Virol. 38:805-814, 1981). Specific assays for DNa polymerases alpha, beta, and gamma, DNA topoisomerase I, and RNase H were carried out on each fraction. The number of units of activity in each fraction was compared with the number of total polyoma and replicative intermediate DNA molecules in each fraction determined by quantitative electron microscopy (M. R. Krauss and R. M. Benbow, J. Virol. 38:815-825, 1981). DNA polymerase alpha cosedimented with polyoma replicative intermediate DNA molecules. DNA polymerase beta and DNA topoisomerase I activities sedimented with mature polyoma minichromosomes. Although the bulk of RNase H activity sedimented in the minichromosome region, the peak of activity was found one fraction behind the peak of mature minichromosomes. Virtually no DNA polymerase gamma activity cosedimented with polyoma minichromosomes.