A simple and rapid preparation of M13 sequencing templates for manual and automated dideoxy sequencing

Kristensen, Tom; Voß, H.; Ansorge, W.

doi:10.1093/nar/15.14.5507

Cited by 58 publications

(21 citation statements)

References 13 publications

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“…Well-separated M13 plaques were arrayed into 96-well microtiter plates using an automated colony picker designed by Lawrence Berkeley Laboratory. After incubation at 37°C for 7-8 hr, singlestranded DNA for each subclone was isolated using either Qiagen 96-well format M13 kits (per manufacturer's specifications) or a previously described PEG precipitation protocol (Kristensen et al 1987). Fluorescent dye-primer sequence reactions were prepared using a Catalyst 800 Molecular Biology labstation, a PE9600 Thermocycler, and ABD Taq thermosequenase cycle sequencing kits (Perkin-Elmer Applied Biosystems).…”

Section: Library Preparation and Sequencingmentioning

confidence: 99%

Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12

et al. 1998

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We investigated the organization, architecture, and evolution of the largest cluster (∼4 Mb) of Krüppel-associated box zinc finger (KRAB-ZNF) genes located in cytogenetic band interval 19p12. A highly integrated physical map (∼700 kb) of overlapping cosmid and BAC clones was developed between genetic STS markers D19S454 and D19S269. Using ZNF91 exon-specific probes to interrogate a detailed EcoRI restriction map of the region, ZNF genes were found to be distributed in a head-to-tail fashion throughout the region with an average density of one ZNF duplicon every 150-180 kb of genomic distance. Sequence analysis of 208,967 bp of this region indicated the presence of two putative ZNF genes: one consisting of a novel member of this gene family (ZNF208) expressed ubiquitously in all tissues examined and the other representing a nonprocessed pseudogene (ZNF209), located 450 kb proximal to ZNF208. Large blocks of (∼25-kb) inverted ␤-satellite repeats with a remarkably symmetrical higher order repeat structure were found to bracket the functional ZNF gene. Hybridization analysis using the ␤-satellite repeat as a probe indicates that ␤-satellite interspersion between ZNF gene cassettes is a general property for 1.5 Mb of the ZNF gene cluster in 19p12. Both molecular clock data as well as a retroposon-mapping molecular fossil approach indicate that this ZNF cluster arose early during primate evolution (∼50 million years ago). We propose an evolutionary model in which heteromorphic pericentromeric repeat structures such as the ␤ satellites have been coopted to accommodate rapid expansion of a large gene family over a short period of evolutionary time.[The sequence data described in this paper have been submitted to GenBank under accession nos. AC003973 and AC004004.] Zinc finger (ZNF) genes represent one of the largest gene families in the human genome with an estimated 500-600 members (Hoovers et al. 1992;Becker et al. 1995;Klug and Schwabe 1995). Although the specific function of the majority of ZNF genes remains largely unknown, as a class they are believed to encode transcriptional regulators that in a few instances have been shown to play critical roles in cellular and developmental differentiation processes (Pieler and Bellefroid 1994). ZNF proteins have been implicated in many diverse eukaryotic developmental processes, such as segment pattern formation in the Drosophila embryo (Rosenberg et al. 1986); cellular proliferation in the cerebellar hindbrain of the mouse (Wilkinson et al. 1989); and hematopoietic differentiation among human myeloid precursor cells (Hromas et al. 1991). DNA binding of the encoded proteins is typically mediated by a ZNF motif that consists either of two cysteines and two histidines (Krüppel family or C 2 /H 2 type) or four cysteines alone (steroid receptor or C 2 / C 2 type). The conserved cysteines and/or histidines form a tetrahedral complex around a zinc metal ion, generating a folded loop or ''finger'' of 30 amino acids that is capable of making contact with DNA (Miller et al. 1985)...

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Section: Library Preparation and Sequencingmentioning

confidence: 99%

Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12

et al. 1998

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“…Sequence templates were prepared as described (Kristensen et al 1987). Clones were sequenced using random and directed sequencing strategies as described (Civitello et ah 1993).…”

Section: Sequencing Of X and Cosmid Clonesmentioning

confidence: 99%

A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13.

Ansari-Lari¹,

Muzny²,

Lü³

et al. 1996

Genome Res.

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The genomic sequence of the human CD4 gene and its neighboring region, located at chromosome 12pl3, was generated using the large-scale shotgun sequencing strategy. A total of 117 kb of genomic sequence and -I1 kb of cDNA sequence were obtained. Six genes, including CD4, triosephosphate isomerase, B3 subunit of G proteins (GNB3), and ubiquitin isopeptidase T (ISOT), with known functions, and two new genes with unknown functions were identified. Using a battery of strategies, the exon/intron boundaries, splice variants, and tissue expression patterns of the genes were determined. Various computer software was utilized for analyses of the DNA and amino acid sequences. The results of the analyses and sequence-based strategies for gene identification are discussed.

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“…and a fluorescent label [32]. The DNA templates for sequencing were isolated via glass-fibre membranes [33]. Regions with compressions in the sequencing gel were sequenced with dITP or deaza-dGTP instead of dGTP.…”

Section: Subcloning Of'cdna and Sequencingmentioning

confidence: 99%

Human phosvitin/casein kinase type II. Molecular cloning and sequencing of full‐length cDNA encoding subunit beta

Jakobi

Voß²,

Pyerin

1989

European Journal of Biochemistry

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Phosvitin/casein kinase type 11 is an ubiquitous, highly conserved enzyme consisting of subunits CI, a' and /I.Subunit / 3, presumably serving regulatory functions, was prepared from human placenta and the amino acid sequence of a protease digestion peptide was determined. The deduced nucleotide sequence was employed for the synthesis of a mixture of 20mers as a hybridization probe to screen a AgtlO HeLa cell cDNA library for clones encoding subunit p. A full-length clone consisting of 1013 bp was isolated and the sequence of both strands determined. The deduced amino acid sequence of the largest open reading frame encodes 21 5 amino acid residues predicting a maximum M , of 24925. The nucleotide sequence of the human /3 subunit shows a similarity of 75% to that of Drosophila melanogaster and the deduced amino acid sequence a similarity of 88% and 97% to that of D. melunoguster and bovine lung, respectively. No further protein sequence currently known exhibits any notable similarity. Using a 537-bp restriction fragment of the cDNA clone representing 80% of the coding region, a 1-kb subunit-/I transcript was detected by Northern hybridization in total RNA prepared from human epithelial cells and placenta as well as from bovine heart suggesting a single transcript of the /I-subunit gene and also demonstrating high similarity also between the human and bovine nucleotide sequences. The same restriction fragment was used as the probe to indicate in Southern hybridizations that the corresponding genomic DNA contains at least one intron of roughly 2.5 kb in length and presumably is a single copy gene.The phosvitin/casein kinase type 11 (CK 11), so named for its ability to phosphorylate acidic model substrates such as phosvitin or casein, is an enzyme with a remarkably broad list of potential substrates and hence of possible cellular functions. CK I1 phosphorylates a number of nuclear and cytoplasmic proteins intimately involved in transcription and translation of genetic information and phosphorylates metabolic key enzymes (reviewed [I -31). It also phosphorylates structural proteins (e.g. [4, 51) and proteins involved in signal transduction (e.g. [6 -81). In addition, substrates have been localized at the outer surface of mammalian cells and in extracellular fluids. Consistently, an ecto-phosvitin/casein kinase type 11 activity which becomes released under certain conditions has been detected [9 -131. As one would expect of an enzyme playing such versatile and crucial physiological roles, CK 11 occurs ubiquitously. It has been isolated from a variety of vertebrates and invertebrates (reviewed [l -31) and detected in plants [14] Distinguishing biochemical features of CK I1 are the capability to effectively utilize both ATP and GTP as substrate, the phosphorylation of proteins at serine or threonine residues positioned adjacent N-terminally to clusters of acidic residues, [20]. In their hands, subunit p was obviously able to bind to DNA and to act as an endonuclease, and, moreover, to interfere with RNA polymerase I r...

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A simple and rapid preparation of M13 sequencing templates for manual and automated dideoxy sequencing

Cited by 58 publications

References 13 publications

Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12

Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12

A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13.

Human phosvitin/casein kinase type II. Molecular cloning and sequencing of full‐length cDNA encoding subunit beta

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