The making of strand-specific M13 probes

Isolation of a genomic clone for bovine pancreatic trypsin inhibitor by using a unique-sequence synthetic DNA probe

Unique-sequence synthetic DNA probes, based on the known amino acid sequence of bovine pancreatic trypsin inhibitor, were constructed from oligodeoxynucleotides. In genomic Southern blot experiments, these probes were shown to hybridize specifically to discrete restriction fragments. A synthetic probe also was used to isolate a cloned BPTI gene from a bovine genomic library. DNA sequence analysis of this clone indicated that the BPTI coding region was neither preceded by a start codon nor immediately followed by a termination codon. This suggests that the mature form of BPTI may be produced through proteolytic processing from a larger polypeptide precursor.

Characterization and nucleotide sequence of the gene for the common alpha subunit of the bovine pituitary glycoprotein hormones

The gene coding for the common alpha subunit of the bovine pituitary glycoprotein hormones was isolated from a bovine genomic library. The gene spans roughly 16.5 kbp, contains three intervening sequences, and codes for a message of approximately 730 nucleotides. The complete coding region of the gene was sequenced as well as 315 nucleotides of 5' flanking sequence and the entire intron C. Only a single base difference was found when the sequence of the gene was compared with that of the cDNA. Genomic blotting experiments suggest the presence of a single alpha subunit gene. Comparison of the bovine and human alpha subunit genes indicated that the high level of homology observed in the coding regions has been maintained throughout the 5' and 3' untranslated regions, and at least 90 nucleotides of the 5'flanking regions. Additionally, there is an 18 base pair sequence present in both the 5' flanking and 5' untranslated regions of the gene that is homologous to a region of the chick ovalbumin gene. This ovalbumin sequence has been suggested as a binding site for the progesterone receptor-complex.

Expression of human alpha-tubulin genes: interspecies conservation of 3' untranslated regions

To examine the sequence complexity and differential expression of human alpha-tubulin genes, we constructed cDNA libraries from two unrelated tissue types (epidermis and fetal brain). The complete sequence of a positively hybridizing alpha-tubulin clone from each library is described. Each is shown to represent an abundantly expressed gene from fetal brain and keratinocytes, respectively. Although the coding regions are extensively homologous (97%), the 3' untranslated regions are totally dissimilar. This property has been used to dissect the human alpha-tubulin multigene family into members bearing sequence relatedness in this region. Surprisingly, each of these noncoding regions shares very high (65 to 80%) interspecies homology with the 3' untranslated region of one of the two rat alpha-tubulin genes of known sequence. These unexpected homologies imply the existence of selective pressure on the 3' untranslated regions of some cytoskeletal genes which maintains sequence fidelity during the course of evolution, perhaps as a consequence of an as yet unidentified functional requirement.

The hisR locus of Salmonella: nucleotide sequence and expression

In S. typhimurium, the hisR locus is defined by mutations causing reduced levels of the histidine transfer RNA. As a preliminary step in the analysis of the hisR mutants, a 972 bp DNA fragment containing the histidine tRNA gene from wild-type Salmonella was cloned and completely sequenced. This analysis revealed the existence of a tRNA gene cluster which, in addition to the tRNAHis gene, includes the genes for tRNALeu1, tRNAPro1 and a tentative tRNAArgCGG. All four tRNA genes are present as single copies and are separated by spacer sequences ranging from 20 to 53 bp in length. The gene cluster is efficiently transcribed in vitro by E. coli RNA polymerase and yields a transcript, approximately 480 nucleotides long, which contains all four tRNA sequences. This tetrameric precursor can be processed to 4S RNA in vitro with a wild-type Salmonella extract, but not with an extract prepared from a hisU (RNase P) mutant. Using portions of the tRNA gene cluster as specific hybridization probes, various processing intermediates were shown to accumulate in vivo in the hisU mutant. Most of these RNAs are monomeric precursors only a few nucleotides longer than the respective mature tRNA species.

Sequence of human haptoglobin cDNA: evidence that the alpha and beta subunits are coded by the same mRNA

We have isolated and sequenced a cDNA clone coding for human haptoglobin. Our sequence shows that haptoglobin is very likely synthesized as a single polypeptide chain which is then cleaved at an Arg residue to generate its two characteristic alpha and beta subunit. Southern blot analysis suggests that there are at least two copies of the haptoglobin gene per haploid genome.

The Notch locus of Drosophila melanogaster

The Notch locus appears to correspond to a 37 kb transcription unit. Homologous poly(A)+ RNA is about 11.7 kb. Nine RNA coding regions have been detected and localized within the transcription unit by S1 nuclease analyses. These range in size from 130 to 7250 bp. Sequences within the 3' coding region are variably used. Twenty-four Notch locus "point" mutations have been examined. Seven are associated with DNA insertions. Four insertions are associated with dominant mutations and are located within or very near RNA coding sequences of the 37 kb transcription unit. Three insertions are associated with recessive mutations and fall within intervening sequences. The positions of all insertions agree with the genetic map. It is estimated that, in the Notch region, one map unit corresponds to approximately 275 kb. On this basis, most of the 17 mutations that were not associated with DNA insertions can be placed within coding sequences of the 37 kb transcription unit.

Identification of two human beta-tubulin isotypes

The sequence of a human beta-tubulin cDNA clone (D beta-1) is described; our data revealed 95.6% homology compared with the sequence of a human beta-tubulin processed pseudogene derived by reverse transcription of a processed mRNA (Wilde et al., Nature [London] 297:83-84, 1982). However, the amino acid sequence encoded by this cDNA showed less homology with pig and chicken beta-tubulin sequences than the latter did to each other, with major divergence within the 15 carboxy-terminal amino acids. On the other hand, an independently isolated, functionally expressed genomic human beta-tubulin sequence (5 beta) possessed a very high degree of homology with chicken and pig beta-tubulins in this region. Thus, human cells appear to contain two distinct beta-tubulin isotypes. Both the intact beta-tubulin cDNA clone and a subclone containing only the 3' untranslated region detected two mRNA species in HeLa cells; these mRNAs were 1.8 and 2.6 kilobases long and were present in about equal amounts. Two independently subcloned probes constructed from the 3' untranslated region of the 5 beta genomic sequence also detected a 2.6-kilobase beta-tubulin mRNA. However, the 3'-untranslated-region probes from the cDNA clone and the genomic sequence did not cross-hybridize. Thus, at least two human beta-tubulin genes, each specifying a distinct isotype, are expressed in HeLa cells, and the 2.6-kilobase mRNA band is a composite of at least two comigrating beta-tubulin mRNAs.

Coronavirus JHM: nucleotide sequence of the mRNA that encodes nucleocapsid protein

A DNA copy of the mRNA that encodes the nucleocapsid protein of Mouse Hepatitis Virus JHM has been cloned into pAT153. The DNA copy specifically inhibited the synthesis in vitro of the nucleocapsid protein. The cDNA was subcloned into M13 vectors and the entire sequence, 1767 bases including a 15 base terminal poly (A) tract, has been determined by chain-terminator sequencing. The sequence contained an open-reading frame that could encode a basic protein of mol.wt. 49700. From the predicted sequence it was apparent that the nucleocapsid protein has 5 basic regions, two of which are located near the middle of the sequence, a serine-rich region was also located, a feature which may be of functional importance as the nucleocapsid protein is phosphorylated at serine residues. The carboxy terminus of the nucleocapsid protein was found to be acidic. The 5' non-coding sequence contained a triple repeat of the pentamer AATCT, a structural feature which may play a significant role during the production of subgenomic viral mRNAs.

Structure of the hepatitis B virus genome

The extent and position of the single-stranded gap in DNA molecules from Dane particles isolated from two donors of the adw serotype were determined by molecular hybridization and electron microscopic methods. The results showed that in each preparation more than 99% of the circular molecules are of uniform length and contain both single- and double-stranded regions. They confirmed that one end of the short strand is fixed with respect to the single EcoRI site within the molecule and to the nick in the long strand, but they also showed that although the position of the other end is variable, there is a preferred minimum length of about 650 to 700 nucleotides for the single-stranded region.

Sequence analysis of zein cDNAs obtained by an efficient mRNA cloning method

A cDNA library was generated from mRNA isolated from the developing endosperm of W22 maize inbred. cDNA clones for zein, the maize storage protein family, were isolated and analyzed by DNA sequencing. The DNA sequences of four clones containing cDNA copies of mRNAs belonging to one zein subfamily were determined. The data support the following conclusions: a) genes encoding the larger of the two zein species contain eleven instead of nine repeat units within the coding sequence of the gene; b) transcription can be terminated at either of the two polyadenlation signals and c) transcription starts 31 basepairs downstream from the first T in the TATA box. To facilitate this analysis a new method for the construction of cDNA libraries was developed. The mRNA was annealed to linearized and oligo-dT tailed pUC9 plasmid DNA, which then primed synthesis of the first strand of the cDNA. Oligo-dG tails were added to the cDNA-plasmid molecules, which were then centrifuged through an alkaline sucrose gradient. The gradient step removed small molecules and separated the two cDNAs which were formerly attached to the same double stranded plasmid molecule. An excess of oligo-dC tailed denatured pUC9 DNA was added and the DNA was renatured under conditions that favor the circularization of monomers by the oligo-dC and oligo-dG tails. The oligo-dC tail served as primer for the synthesis of the second strand of the cDNA. The library was screened by colony hybridization using 32P-labelled cDNA and DNA from genomic zein clones as probes. We obtained 20,000 clones hybridizing total cDNA starting with 1 microgram of plasmid DNA and 1 microgram of mRNA.

A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity

A technique for conveniently radiolabeling DNA restriction endonuclease fragments to high specific activity is described. DNA fragments are purified from agarose gels directly by ethanol precipitation and are then denatured and labeled with the large fragment of DNA polymerase I, using random oligonucleotides as primers. Over 70% of the precursor triphosphate is routinely incorporated into complementary DNA, and specific activities of over 10(9) dpm/microgram of DNA can be obtained using relatively small amounts of precursor. These "oligolabeled" DNA fragments serve as efficient probes in filter hybridization experiments.

Translocation, breakage and truncated transcripts of c-myc oncogene in murine plasmacytomas

Comparative nucleotide sequence analysis of a rearranged c-myc gene in a murine plasmacytoma and c-myc cDNA from normal spleen reveals that chromosomal translocation in the plasmacytoma breaks the c-myc gene within the first exon or intron. In the plasmacytoma truncated c-myc RNAs initiate from newly exposed promoter sites. Nevertheless, the myc polypeptide produced in the plasmacytoma is probably the same as that from the intact c-myc gene because the exon lost by breakage and translocation is non-coding. The second and third exons of the mouse c-myc gene are substantially conserved in the v-myc gene of the avian retrovirus, MC29.

Evolutionary history of a multigene family: an expressed human beta-tubulin gene and three processed pseudogenes

A 3' untranslated region subclone from a human beta-tubulin cDNA clone has been used to dissect the human beta-tubulin multigene family. Four different beta-tubulin sequences were obtained. One consists of an expressed gene that yields two mRNA species of 1.8 kb and 2.6 kb as a consequence of alternative polyadenylation sites. The three remaining beta-tubulin sequences are all intronless pseudogenes, each containing a 3' poly(A) tract downstream from the poly(A) signal, and each flanked by a different short direct repeat. Two of these sequences were derived by integration into the host germ line of cDNA copies of the 1.8 kb mRNA; the third was derived from the 2.6 kb mRNA. Comparison of the functional and nonfunctional sequences suggests that the integration events took place 4, 10, and 13 million years ago. We anticipate that, in multigene families where germ-line expression occurs, a significant portion of sequences will be accounted for by pseudogenes generated via an RNA intermediate.

The expression of prokaryotic tRNA genes in frog oocytes

A tRNA gene cluster in Salmonella typhimurium includes the genes for tRNAArg, tRNAHis, tRNA1Leu and tRNAPro. DNA clones were constructed with different portions of this tRNA gene cluster. These clones were microinjected into the nuclei of Xenopus laevis oocytes and assayed for expression. Two of the bacterial tRNA genes (tRNAArg and tRNAPro) are transcribed at high rates and the primary transcripts are processed into mature tRNAs. Transcription and processing are largely independent of whether the two genes are injected individually or as part of a tRNA gene cluster. A third tRNA gene (tRNA1Leu) is expressed less efficiently. Synthesis of this tRNA is totally abolished by a deletion removing 22 bp in the first half of the tRNA1Leu coding sequence. The expression of the fourth tRNA gene (tRNAHis) is very inefficient and dependent upon the gene organization within the injected DNA. No significant tRNA synthesis is detected upon injection of a clone containing only the tRNAHis gene. Evidence is presented suggesting that the impaired expression of the tRNAHis gene is not caused by inefficient transcription, but rather by defective processing of the primary transcript. The prokaryotic tRNAs synthesized in the oocytes show a modification pattern that is specific of eukaryotic tRNAs. Overall, our results are consistent with the hypothesis that the intragenic signals for eukaryotic tRNA gene transcription have appeared early in evolution for reasons other than gene expression.

Sequence diversity among related genes for recognition of specific targets in DNA molecules

Escherichia coli strains K12 and B, and a new strain designated D, each encode a characteristic restriction and modification enzyme. These enzymes (EcoK, EcoB and presumably EcoD) comprise three subunits of which one, that encoded by the so-called specificity gene (hsdS), is responsible for recognition of the DNA sequence specific to that system. The other two subunits, encoded by hsdR and hsdM, are interchangeable between systems, and the available molecular evidence suggests that the hsdR and hsdM genes are highly conserved. The DNA sequence of a segment of the hsd region that includes the hsdS gene has been determined for each of the three strains. The hsdS gene varies in length from 1335 to 1425 base-pairs and the only regions showing obvious homology, one of about 100 base-pairs and a second of about 250 base-pairs, are highly conserved. The remainder of each hsd S gene shares little, or no, homology with either of the other related specificity genes. Thus, the specificity subunits, though components of a family of closely related enzymes with very similar functions, have remarkably dissimilar primary structure.

Identification of two human beta-tubulin isotypes

The sequence of a human beta-tubulin cDNA clone (D beta-1) is described; our data revealed 95.6% homology compared with the sequence of a human beta-tubulin processed pseudogene derived by reverse transcription of a processed mRNA (Wilde et al., Nature [London] 297:83-84, 1982). However, the amino acid sequence encoded by this cDNA showed less homology with pig and chicken beta-tubulin sequences than the latter did to each other, with major divergence within the 15 carboxy-terminal amino acids. On the other hand, an independently isolated, functionally expressed genomic human beta-tubulin sequence (5 beta) possessed a very high degree of homology with chicken and pig beta-tubulins in this region. Thus, human cells appear to contain two distinct beta-tubulin isotypes. Both the intact beta-tubulin cDNA clone and a subclone containing only the 3' untranslated region detected two mRNA species in HeLa cells; these mRNAs were 1.8 and 2.6 kilobases long and were present in about equal amounts. Two independently subcloned probes constructed from the 3' untranslated region of the 5 beta genomic sequence also detected a 2.6-kilobase beta-tubulin mRNA. However, the 3'-untranslated-region probes from the cDNA clone and the genomic sequence did not cross-hybridize. Thus, at least two human beta-tubulin genes, each specifying a distinct isotype, are expressed in HeLa cells, and the 2.6-kilobase mRNA band is a composite of at least two comigrating beta-tubulin mRNAs.

Core and E antigen synthesis in rodent cells transformed with hepatitis B virus DNA is associated with greater than genome length viral messenger RNAs

The viral RNA sequences in a number of rodent cell lines which contain integrated hepatitis B virus DNA were examined. In one of the cell lines, which produces the hepatitis B virus surface, core and e antigens, there are four polyadenylated, cytoplasmic RNA species, estimated to be 4425, 3968, 2435 and 1054 nucleotides in length, which hybridize with hepatitis B virus DNA. All four were shown to be transcripts of the coding strand of the virus genome and the regions contained in each RNA molecule were determined by hybridization with probes from different parts of the genome. The two largest RNAs hybridized with probes from all parts of the genome. The 2.4 x 10(3) nucleotide RNA, which is the same size as the previously identified surface antigen messenger RNA, hybridized with probes covering the surface antigen gene but not with probes corresponding to the core antigen gene. It also hybridized with a probe mapping upstream of a sequence previously suggested to be its promoter. The 10(3) nucleotide RNA was mapped to the X gene region and thus provides evidence that this open translational reading frame does encode a product. This RNA is possibly 3' coterminal with the surface antigen mRNA. The two largest RNAs, which are greater than the length of the hepatitis B virus genome, are present in three independent cell lines which produce core antigen and e antigen in addition to surface antigen, but absent from two cell lines which produce only surface antigen. Therefore, it appears that these RNAs are entirely hepatitis B virus-specified, rather than being co-transcripts with cellular sequences, and also that one of them encodes the core and e antigen produced by these cells.

Using iodinated single-stranded M13 probes to facilitate rapid DNA sequence analysis--nucleotide sequence of a mouse lysine tRNA gene

From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. However, the mouse gene contains a 14 bp region comprising 13 A-T base pairs, 30-44 bp from the 5' end of the coding region. Cognate A-T rich regions are present in human and Drosophila genes. The coding region is flanked by two 11 bp direct repeats, similar to those associated with alu family sequences. The sequence was determined by a "walking" protocol that employs, as a novel feature, iodinated single-stranded M13 probes to identify M13 subclones which contain sequences partially overlapping and contiguous to an initially determined sequence. The probes can also be used to screen lambda phage and in Southern and dot blot experiments.

Cellular myc oncogene is altered by chromosome translocation to an immunoglobulin locus in murine plasmacytomas and is rearranged similarly in human Burkitt lymphomas

Molecular cloning has recently established that the 15;12 chromosome translocations in murine plasmacytomas fuse DNA from chromosome 15 to the immunoglobulin heavy (H) chain locus, usually within the switch recombination region near the alpha constant region gene. We show here that the incoming DNA bears the cellular gene (c-myc) homologous to the oncogene (v-myc) of avian retrovirus MC29. In human Burkitt lymphomas bearing an 8;14 translocation, c-myc was also rearranged, apparently (in at least two cases) to an H chain switch recombination region (mu or alpha), and both products of a reciprocal chromosome exchange were detectable. Both the murine and human c-myc genes contain two exons homologous to v-myc, and additional 5' and 3' murine genomic segments (apparent exons) were defined by hybridization to c-myc mRNAs. In plasmacytomas, chromosome breakpoints fall near or within the 5' exon and apparently disrupt the normal c-myc transcriptional unit, because plasmacytoma c-myc mRNAs differ from the mRNA in lines without c-myc rearrangement. The translocated gene presumably has lost its normal 5' regulatory sequences and may well encode an altered myc polypeptide. We propose that altered expression of the c-myc gene, induced by translocation to an immunoglobulin locus, is a critical oncogenic event for these B lymphoid tumors. Two events may be required, because the plasmacytoma oncogene capable of transforming fibroblasts is not c-myc.

Molecular cloning and nucleotide sequence of a transforming gene detected by transfection of chicken B-cell lymphoma DNA

A transforming gene detected by transfection of chicken B-cell lymphoma DNA has been isolated by molecular cloning. It is homologous to a conserved family of sequences present in normal chicken and human DNAs but is not related to transforming genes of acutely transforming retroviruses. The nucleotide sequence of the cloned transforming gene suggests that it encodes a protein that is partially homologous to the amino terminus of transferrin and related proteins although only about one tenth the size of transferrin.

Transcriptionally active c-myc oncogene is contained within NIARD, a DNA sequence associated with chromosome translocations in B-cell neoplasia

NIARD (non-immunoglobulin-associated rearranging DNA) is located on mouse chromosome 15 at the break point of a commonly observed translocation event involving chromosomes 15 and 12 in murine plasmacytomas. The human cellular analogue of the v-myc oncogene of avian myelocytomatosis virus, strain MC-29, is known to reside on the distal end of human chromosome 8 and has been observed to translocate to chromosome 14 in Burkitt lymphomas. Using a cDNA clone specific for the transcript of the human c-myc gene (H c-myc), we show that the mouse c-myc (M c-myc) gene is contained within NIARD. NIARD-associated chromosome translocations occurred 1.3-2 kilobases (kb) 5' of the mouse c-myc gene where NIARD recombines with the switch region of the C(alpha) immunoglobulin gene in various murine plasmacytomas. The mouse c-myc encoding region within NIARD spanned <2.4 kb of DNA and expressed a low level of a 2.3-kb polyadenylylated RNA in BALB/c spleen. Increased (10- to 20-fold) levels of rearranged mouse c-myc transcripts (i.e., approximately 1.8-2.1 kb) were observed in plasmacytomas that have NIARD-associated chromosome translocations. Human c-myc and NIARD probes detected DNA rearrangements of human c-myc in four of seven Burkitt lymphomas. DNA sequences adjacent to the human c-myc gene recombined with the C(mu) immunoglobulin gene locus on chromosome 14 in several Burkitt lymphomas. The activation of the c-myc oncogene by chromosome translocation implicates its involvement in B-cell oncogenesis.

Sequence of the murine and human cellular myc oncogenes and two modes of myc transcription resulting from chromosome translocation in B lymphoid tumours

The 15;12 chromosome translocation in murine plasmacytomas and the 8;14 in human Burkitt lymphomas often link the cellular myc oncogene to the locus for constant regions of immunoglobulin heavy chains (CH locus). To clarify how and why c-myc translocation occurs, we have sequenced the mouse and human c-myc genes and correlated c-myc transcription with c-myc rearrangement. Both genes comprise three exons; the second and third encode the myc polypeptide, which is conserved between mammals and birds, particularly in its more basic C-terminal half. Southern blots showed that four of 12 Burkitt lines have c-myc linked near CH switch regions and two near the joining region (JH) locus. Hence, immunoglobulin recombination machinery may participate in translocation, although the common myc breakpoint region around exon 1 does not resemble a switch region. Tumours with breakpoints just 5' to exon 1, or distant from c-myc, had normal c-myc mRNAs of 2.25 and 2.4 kb, which differ at their 5' ends, while tumours with breakpoints within exon 1 or intron 1 had altered c-myc mRNAs (2.1-2.7 kb in Burkitt lines), initiated within intron 1. Both types of mRNAs probably yield the same polypeptide. Since the untranslocated c-myc allele was generally silent, translocation to the CH locus must induce constitutive c-myc expression. The presence of c-myc mRNA in immortal but non-tumorigenic lymphoblastoid cell lines may implicate c-myc in an immortalization step.

Sensitive detection of RNA using strand-specific M13 probes

We have extended the method of Hu and Messing (Gene 17 (1982) 271-277) to prepare highly radioactive M13 probes suitable for use in RNA-DNA hybridization experiments. Single strands of M13 DNA carrying cloned sequences are rendered partially double-stranded by primed synthesis using a synthetic oligonucleotide primer complementary to a region 5' to the cloning site. The newly synthesized radioactive complementary strand is then covalently cross-linked to the M13 phage DNA by UV irradiation in the presence of 4,5,8-trimethylpsoralen (trioxsalen). Since the cross-linked probe is stable to heat denaturation, and the region of cloned sequence is kept single-stranded, these complexes may be used as strand-specific hybridization probes to detect RNA sequences under conditions which would denature DNA-DNA duplexes.

The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers

A series of plasmid vectors containing the multiple cloning site (MCS7) of M13mp7 has been constructed. In one of these vectors a kanamycin-resistance marker has been inserted into the center of the symmetrical MCS7 to yield a restriction-site-mobilizing element (RSM). The drug-resistance marker can be cleaved out of this vector with any of the restriction enzymes that recognize a site of the flanking sequences of the RSM to generate an RSM with either various sticky ends or blunt ends. These fragments can be used for insertion mutagenesis of any target molecule with compatible restriction sites. Insertion mutants are selected by their resistance to kanamycin. When the drug-resistance marker is removed with PstI, a small in-frame insertion can be generated. In addition, two new MCSs having single restriction sites have been formed by altering the symmetrical structure of MCS7. The resulting plasmids pUC8 and pUC9 allow one to clone doubly digested restriction fragments separately with both orientations in respect to the lac promoter. The terminal sequences of any DNA cloned in these plasmids can be characterized using the universal M13 primers.

A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments

The strategy of shotgun cloning with M13 is based on obtaining random fragments used for the rapid accumulation of sequence data. A strategy, however, is sometimes needed for obtaining subcloned sequences preferentially out of a mixture of fragments. Shotgun sequencing experiments have shown that not all DNA fragments are obtained with the same frequency and that the redundant information increases during the last third of a sequencing project. In addition, experiments have shown that particular fragments are obtained more frequently in one orientation, allowing the use of only one of the two DNA strands as a template for M13 shotgun sequencing. Two new M13 vectors, M13mp8 and M13mp9, have been constructed that permit the cloning of the same restriction fragment in both possible orientations. Consequently, each of the two strands becomes a (+) strand in a pair of vectors. The fragments to be cloned are cleaved with two restriction enzymes to produce a fragment with two different ends. The insertion of such a fragment into the vector can occur only in one orientation. Since M13mp8 and M13mp9 have their array of cloning sites in an antiparallel order, either orientation for inserting a double-digest fragment can be selected by the choice of the vector.

The filamentous phage (Ff) as vectors for recombinant DNA--a review

Derivatives of filamentous phage, f1, fd, and M13, useful as cloning vectors are listed, and procedures for their use are reviewed. Methods for growing phage, preparing single- and double-stranded DNA, and cloning are given in the "cook-book" form. These procedures minimize the practical problem often associated with filamentous-phage cloning, i.e., deletion of inserts.

Primary structure of a genomic zein sequence of maize

The nucleotide sequence of a genomic clone (termed Z4 ) of the zein multigene family was compared to the nucleotide sequence of related cDNA clones of zein mRNAs. A tandem duplication of a 96-bp sequence is found in the genomic clone that is not present in the related cDNA clones. When the duplication is disregarded, the nucleotide sequence homology between Z4 and its related cDNAs was approximately 97%. The nucleotide sequence is also compared to other isolated cDNAs. No introns in the coding region of the zein gene are detected. The first nucleotide of a putative TATA box, TATAAATA , was located 88 nucleotides upstream of the first nucleotide of the first ATG codon which initiated the open reading frame. The first nucleotide of a putative CCAAT box, CAAAAT , appeared 45 nucleotides upstream of the first nucleotide of the zein cDNA clones in the 3' non-coding region also appeared in the genomic sequence at the same locations. The amino acid composition of the polypeptide specified by the Z4 nucleotide sequence is similar to the known composition of zein proteins.