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Biomedical subjects

J Pan

Publications and source records attributed to J Pan.

At least 307 records · Page 17Linked to original sources
PubMed1985

Structure and polymorphism of class I MHC antigen mRNA.

We have used cDNA cloning and primer extension techniques to determine the complete nucleotide sequence of HLA-B7 mRNA. The 5'-untranslated sequence of the mRNA is rather short and the putative promoter has weak homology to the conventional "TATA" sequences. The 5' end and the polyadenylation site define the transcription unit of the B7 gene to be about 3.5 kb long. Comparison of the translated nucleotide sequence of this cDNA with the amino acid sequence of the heavy chain of the B7 antigen showed two amino acid differences. In addition, comparison with the sequences of the coding and untranslated regions of several HLA and H-2 genes showed that the class I histocompatibility molecules consist of four variable segments separated by three regions of homology. Analysis of the DNA polymorphisms revealed that in the variable segments the majority of the nucleotide substitutions are nonsilent, while in the homology regions the majority of substitutions are silent. Further analysis of the nature of the amino acid substitutions revealed the predominance of nonconservative replacements/changes in both the variable segments and the homology regions except the transmembrane part of the molecule. Selection at both the protein and the codon levels contributes to the pattern of mutations found in class I histocompatibility molecules.

Amino Acid Sequence↗
PubMed1981

Primary structure of the phage P22 repressor and its gene c2.

The amino acid sequence of the Salmonella phage P2 repressor and the DNA sequence of its gene c2 have been determined. Sequential Edman degradations on intact P22 repressor and repressor peptides generated by proteolytic and chemical cleavages have been overlapped to give approximately 97% of the complete protein sequence. Additionally, the nucleotide sequence of the P22 c2 repressor gene has been determined by DNA sequencing techniques. The DNA sequence and partial protein sequence are collinear and together define the complete amino acid sequence of P22 repressor. The repressor is a single-chain 216 amino acid polypeptide. Basic residues in the sequence tend to be clustered, and residues 9-20 are highly basic, containing five arginyl and three lysyl residues. The carboxyl-terminal 133 amino acids of the c2 repressor are homologous to the carboxyl-terminal sequence of the coliphage lambda cI repressor. The amino-terminal sequences of these two repressors show little similarity.

Amino Acid Sequence↗
PubMed1981

Transcriptional analysis of interspersed repetitive polymerase III transcription units in human DNA.

The template for RNA polymerase III in vitro transcription found on the human DNA clone pJP53 was shown in the previous paper to enclose a member of the Alu famiy of interspersed repetitive DNA sequences. We have mapped this transcript onto its template in greater detail by comparison of the template DNA sequence to the base composition of the Tl ribonuclease digestion products of the in vitro transcript. We find that the 5' end of the transcript lies in close proximity to the 5' end of the conserved Alu family sequence as analyzed in the preceding paper. The 3' end of the transcript appears to terminate in a U-rich region beyond the region of Alu family sequence conservation. Analysis of cellular RNA by Northern blotting and hybridization with a DNA probe derived from another Alu family transcription template demonstrates abundant representation of sequences homologous to the reiterated DNA. Cytoplasmic, nonpolyadenylated RNA from human and murine cells contains a monodisperse, 300 nucleotide species, recently determined by Weiner (4) to be the 7S RNA. In contrast, the Alu-homologous transcripts are heterodisperse in mRNA and hnRNA, with the highest specific representation of Alu family sequences being found in oligo(dT)-retained hnRNA.

Animals↗
PubMed1981

Structural analysis of interspersed repetitive polymerase III transcription units in human DNA.

The nucleotide sequences of two cloned fragments of human DNA which function as templates for RNA polymerase III in vitro confirm their identities as members of the Alu family of human interspersed repetitive DNA sequences (1,2). The interspersed and repetitive nature of these sequences in the genome was demonstrated by hybridization of nick-translated DNA from one of these clones to total genomic DNA and to DNA of individual random clones from a lambda Ch4A-based human genomic library. Short, direct terminal repeats of non-conserved sequence flank the 300 nucleotide Alu family conserved sequence. Within the Alu family sequence is found a 40-nucleotide region which is directly repeated 135 nucleotides downstream. This 40 nucleotide sequence is found once in the murine B1 interspersed repetitive sequence family (8). This and other evidence indicates that the human Alu family resembles a partial duplication of the murine B1 sequence.

Animals↗
PubMed1978

The genome of simian virus 40.

The nucleotide sequence of SV40 DNA was determined, and the sequence was correlated with known genes of the virus and with the structure of viral messenger RNA's. There is a limited overlap of the coding regions for structural proteins and a complex pattern of leader sequences at the 5' end of late messenger RNA. The sequence of the early region is consistent with recent proposals that the large early polypeptide of SV40 is encoded in noncontinguous segments of DNA.

Base Sequence↗
PubMed1977

Studies of low molecular weight RNA from cells infected with adenovirus 2. I. The sequences at the 3' end of VA-RNA I.

VA-RNA I is a low molecular weight RNA produced in large amounts in cells infected with adenoviruses. The 3' terminus of this RNA may represent a transcription termination site. We have demonstrated that this RNA occurs in infected cells in several forms which differ in the number of uridylic acid residues at the 3' ends. The nucleotide sequence of a DNA fragment overlapping the 3' end of VA-RNA I has been determined. The DNA could encode up to 4 uridylic acid residues at the 3' end of the RNA. The DNA sequence shows some similarity to known transcription termination sequences in prokaryotic systems.

Adenoviridae↗
PubMed1977

Studies of low molecular weight RNA from cells infected with adenovirus 2. II. Heterogeneity at the 5' end of VA-RNA I.

The 5'-terminal sequences of VA-RNA I produced in cells infected with adenovirus 2 were analyzed. The RNA contained a mixture of mono-, di-, and triphosphate ends. The largest part of the RNA has 5'-terminal mono-, di-, or triphosphoguanylic acid, but a portion of the RNA has a 5'-terminal mono-, di-, or triphosphoadenylic acid. An RNA with 5'-terminal adenylic acid was purified and gave the same oligonucleotide map as the major form of VA-RNA I, except for the 5'-terminal products. We therefore conclude that transcription of VA-RNA I can initiate at two different nearby sites.

Adenine Nucleotides↗
PubMed1977

Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. IV. Localization of the SV40 DNA complementary to the 5' ends of viral mRNA.

Cytoplasmic mRNA isolated from cells infected with SV40 was isolated by passage over oligo(dT)-cellulose columns. This RNA was annealed to SV40 DNA fragments produced by cleavage with EcoRII endonuclease. The RNA resistant to RNase digestion was analyzed by digestion with ribonucleases and oligonucleotide mapping. The results were compared with oligonucleotides from in vitro transcripts of the fragments and with whole genome SV40 cRNA which had been fractionated by hybridization to the fragments. The 5' ends of "early" and the large "late" SV40 mRNA, transcribed from opposite DNA strands, overlap for a region of 60 to 100 nucleotides. The region of overlap includes a portion of the segment of DNA containing the origin of DNA replication.

Base Sequence↗
PubMed1977

Structure of a large segment of the genome of simian virus 40 that does not encode known proteins.

The nucleotide sequence of the region of DNA of simian virus 40 extending from 0.595 to 0.790 map unit has been derived. The sequence includes the DNA complementary to the 5' end of early mRNA and to the 5' end of some of the forms of late RNA. Because there are termination codons in all three phases in early and late RNA, there is a sequence of almost 800 nucleotides of simian virus 40 DNA that probably does not code for known viral proteins. The sequence spans the 5' end of the early mRNA at 0.67 map unit and overlaps a species of late RNA whose 5' end is at 0.65 map unit and whose 3' end is at 0.77 map unit. This RNA is retained on oligo(dT)-cellulose columns in high salt concentrations. Analysis of the sequence of late strand RNA suggests that this RNA is not covalently linked to the mRNA that encodes structural proteins. There is another species of late RNA of simian virus 40 whose 5' end is at 0.775 map unit. The nucleotide sequence of this region of simian virus 40 DNA contains several examples of repeated sequences, most of which are located in DNA that does not encode known peptides. These may be analogous to the reiterated sequences that have been described in animal cell DNA.

Base Sequence↗
PubMed1977

Nucleotide sequence of the gene for the major structural protein of SV40 virus.

We have determined the sequence of the portion of Simian Virus 40 (SV40) that codes for the major structural protein of the virus. The gene contains 361 codons. Synonym codons for an amino acid are not used randomly. The dinucleotide CG occurs only once and there is 2 to 1 preference for uridylic acid in the third position of codons.

Base Sequence↗