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PubMedDate not supplied

Sequence and analysis of bovine enteritic coronavirus (F15) genome. I. Sequence of the gene coding for the nucleocapsid protein; analysis of the predicted protein.

Sequences encoding the N protein of the bovine enteritic coronavirus-F15 strain (BECV-F15) have been cloned in PBR322 plasmid using cDNA produced by priming with oligo-dT on purified viral genomic RNA. Some 265 insert-containing clones were studied. Hybridization of these inserts with poly(A)+ RNA extracted from infected cells led to the conclusion that they were located at the 3'-end of the genome. After subcloning in M13 phage DNA, clones were sequenced by the Sanger technique. A 1,710-nucleotide sequence corresponding to the gene coding for the viral N-protein was established. It shows 2 overlapping open reading frames (ORF). The 3'-non-coding end of the gene has an 8-nucleotide sequence in common with the homologous genome areas of MHV, TGE and IBV viruses. This sequence may represent the polymerase RNA binding site. An upstream sequence surrounding the first AUG of the smaller ORF corresponds to a potentially functional initiation codon. The sequence of the primary translation product deduced from the DNA sequence predicts a polypeptide of 207 amino acids (22.9 Kd) with a high leucine (19.8%) content, possessing a hydrophobic N-terminal end. The larger ORF has a coding capacity of 448 amino acids (49.4 Kd), corresponding to the N-protein molecular weight. The deduced protein possesses 43 serine residues (9.6% of the total amino acid content) which may be phosphorylated and involved in N-protein/RNA binding. N-protein also has 5 regions with a high basic amino acid content. One of them is also serine-rich and has a strong homology site with MHV, TGE and IBV viruses. In the first part of the N-terminal, a 12-amino-acid sequence (PRWYFYYLGTGP) is highly conserved for BECV-F15, JHM, TGE and IBV viruses. BCV Mebus strain and BECV-F15 have only minor differences in their N-protein sequence.

Amino Acid Sequence↗
PubMedDate not supplied

Site-specific fluorescent labeling of DNA using Staudinger ligation.

We report the site-specific fluorescent labeling of DNA using Staudinger ligation with high efficiency and high selectivity. An oligonucleotide modified at its 5' end by an azido group was selectively reacted with 5-[(N-(3'-diphenylphosphinyl-4'-methoxycarbonyl)phenylcarbonyl)aminoacetamido]fluorescein (Fam) under aqueous conditions to produce a Fam-labeled oligonucleotide with a high yield (approximately 90%). The fluorescent oligonucleotide was characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Because of the relatively high yield of the Staudinger ligation, simple purification of the product by size-exclusion chromatography and desalting is sufficient for the resulting fluorescent oligonucleotide to be used as a primer in a Sanger dideoxy sequencing reaction to produce fluorescent DNA extension fragments, which are analyzed by a fluorescent electrophoresis DNA sequencer. The results indicate that the Staudinger ligation can be used successfully and site-specifically to prepare fluorescent oligonucleotides to produce DNA sequencing products, which are detected with single base resolution in a capillary electrophoresis DNA sequencer using laser-induced fluorescence detection.

Binding Sites↗
PubMed1996

Sequence analysis of the DNA binding domain of the estrogen receptor gene in ER (+)/PR (-) breast cancer.

Estrogen stimulates the proliferation of breast cancer cells and regulates the expression of other proteins, including the progesterone receptor (PR), via interaction with a unique estrogen receptor (ER), a ligand-inducible transcription factor that binds to regulatory DNA sequences associated with target genes. The best indirect evidence of an intact ER gene signaling system in a tumor is the demonstration of both ER and PR cytosol protein. The molecular basis of the ER (+)/PR (-) phenotype is unknown and may reflect either defective PR gene expression or alterations in the ER-specifically, inability of the ligand-receptor complex to effectively bind to regulatory sequences in DNA. To test the latter possibility, we evaluated 10 ER (+)/PR (-) resected human breast cancers for small deletions and point mutations in the DNA binding domain of the ER gene. Exons 2 and 3 and their flanking intron sequences were selectively amplified using the polymerase chain reaction and then directly sequenced using the Sanger dideoxynucleotide method. A normal gene sequence was found in all cases studied. We conclude that sequence aberrations in the DNA binding domain of the ER are not a common cause of absent PR expression in ER (+)/PR (-) breast carcinomas.

Breast Neoplasms↗
PubMed2026

The Neanderthal-Derived 3p21 Haplotype at LZTFL1 in Modern-Day Moroccans Is Associated With COVID-19 Severity and Further Suggests the Presence of Neanderthals in North Africa.

There is considerable variability in the clinical presentation of COVID-19 among patients infected with SARS-CoV-2. Genome-wide association studies (GWASs) have identified the 12q24.13 and 3p21.31 regions, derived from Neanderthal DNA, as the human genetic loci most strongly associated with COVID-19 severity. We examined in this study the 3p locus in the Moroccan population by analysing allele and haplotype frequencies at the LZTFL1 gene and their associations with COVID-19 outcomes. Three SNPs at LZTFL1, tagging the Neanderthal-derived COVID-19 risk haplotype, were sequenced by Sanger's method in 102 ambulatory participants and 105 hospitalized patients and have been compared to 118 controls negative for SARS-CoV-2 infection using logistic regression analysis. Results showed that the prevalence of the lead variant rs11385942 in this locus was 8.9%, whereas the variants rs35044562 and rs13078854, which tag the Neanderthal haplotype, were present in only 6.3%. Our study showed that only the rs35044562-T and rs13078854-A alleles were associated with a 2.5-fold increased risk of severe COVID-19 (p = 0.028). These two alleles, in LD with the rs11385942-AA one, form the haplotype inherited from the Neanderthal, the only haplotype associated with COVID-19 severity in the Moroccan population (p = 0.030), whereas sub-Saharan African and the rare local haplotype also containing the rs11385942 variant do not influence the COVID-19 outcomes 19 (p > 0.05). Furthermore, our study showed that the Neanderthal haplotype at 3p21 locus exists in the inhabitants of Morocco at a frequency close to that of Europeans and suggests a close connection between North Africa and Eurasia.

Adult↗
PubMed2002

[Encoding genes and genotypes of gamma-lactamases produced by a multiple resistant Klebsiella pneumoniae]

OBJECTIVE: To determine the sequence of gene for encoding beta-lactamase produced by Klebsiella pneumoniae E3 isolated from Jiaxing Area in Zhejiang Province. METHODS The Klebsiella pneumoniae strain E3 was identified as an ESBLs-producing bacterium by inhibitor-potentiated broth dilution test. The gene encoding gamma-lactamase of the strain was amplified by PCR. The purified PCR product was cloned and sequenced by Sanger's dideoxy chain termination composition method. RESULTS The Klebsiella pneumoniae strain E3 produced both TEM and SHV gamma lactamases. The SHV encoding gene had 812 nucleotide residues responsible for encoding SHV-11 gamma-lactamase and the TEM encoding gene had 973 nucleotide residues responsible for encoding TEM-1 gamma-lactamase. CONCLUSION The Klebsiella pneumoniae strain E3 isolated from a patient in Jiaxing Area in Zhejiang Province is able to produce both TEM-1 and SHV-11 gamma-lactamases.

Journal Article↗
PubMed2006

[Novel SCN5A gene mutations associated with Brugada syndrome: V95I, A1649V and delF1617].

OBJECTIVE: Brugada syndrome is an inherited channelopathy that characterized by ST-segment elevation in the right precordial lead (V(1)-V(3)) on the electrocardiogram with or without right bundle branch block and related with high risk of sudden cardiac death and structurally normal hearts. The first and only gene linked to this disease is SCN5A, a gene encodes for alpha subunit of the cardiac sodium channel. The objective of this study is to explore SCN5A gene mutations in Chinese patients with Brugada syndrome. METHODS: Four patients diagnosed as Brugada syndrome and nine patients with suspected Brugada syndrome were chosen for the study. The exons in the functional regions of SCN5A gene were amplified with polymerase chain reaction and the amplified products were sequenced with Sanger method. If a mutation was identified, patient's family members were also screened. RESULTS: Two heterozygous mutations were found in one family diagnosed as Brugada syndrome. One missense mutation was a G-->A transition in the first nucleotide of codon 95 in SCN5A gene exon 3, which was predicted to result in substitution of Valine with Isoleucine (V95I). The other missense mutation was a C-->T transition in the second nucleotide of codon 1649 in SCN5A gene exon 28, which was predicted to result in substitution of Alanine with Valine (A1649V). A heterozygous mutation was identified in one family suspected to have the disease. The mutation was a three nucleotides (TCT) deletion that caused Phenylalanine deletion in codon 1617 in SCN5A gene exon 28. The three mutations were not detected in 100 control chromosomes. CONCLUSIONS: Mutation in SCN5A gene is one of the causes of Brugada syndrome in Chinese. Three novel SCN5A gene mutations were identified in Chinese with Brugada syndrome, which expands the spectrum of SCN5A mutations associated with the disease.

Adolescent↗
PubMed1993

Method for sequencing synthetic oligodeoxynucleotide phosphorothioates.

Sequencing of oligodeoxynucleotide phosphorothioate by a modified Sanger method of sequencing is described. The procedure involves ligation of synthetic oligodeoxynucleotide phosphorothioate to an oligodeoxynucleotide, referred to here as "helper oligonucleotide." The helper oligonucleotide has a region which is complementary to T7 primer. By using DNA polymerase and nucleoside triphosphate mixture, 5'-labeled T7 primer is extended onto ligated oligodeoxynucleotide phosphorothioate, which is then analyzed on gel electrophoresis.

Base Sequence↗
PubMed2002

A general approach to the analysis of errors and failure modes in the base-calling function in automated fluorescent DNA sequencing.

We describe the analysis of errors and failure modes in the base-calling function in automated DNA sequencing, on instruments in which fluorescently-labeled Sanger dideoxy-sequencing ladders are detected via their times of migration past a fixed detector. A general approach entails the joint use of: (i) well-defined control samples such as M13mp18, and (ii) mathematical simulation of sequencing electropherograms, with the deliberate introduction of different types of distortion and noise. An algorithm, the electrophoretic trace simulator (ETS), is used to calculate electrophoresis traces corresponding to the output data stream of an automated fluorescent DNA sequencer. The ETS accepts a user-defined sequence of nucleotide bases (A, C, G, T) as input, and employs user-adjustable functions to compute the following critical parameters of an electropherogram: peak intensity, peak spacing, peak shape as a function of base number; background, noise, and spectral cross-talk correction (for a sequencer using multiple dyes). We use a combination of M13mp18 controls and simulated electropherograms to analyze two problems of considerable practical importance: (i) variation in electrophoretic migration rates between different lanes of a gel, and (ii) variation in signal intensity due to user-dependent loading artifacts. The issue of base-calling errors and failure modes, for electropherograms that contain noise and distortion, is addressed.

Algorithms↗
PubMed1998

Rapid sequencing of the p53 gene with a new automated DNA sequencer.

p53 is the most commonly mutated gene in human cancers. Approximately 90% of the p53 gene mutations are localized between domains encoding exons 5 to 8. Sequencing methods currently available are tedious and time-consuming and are not suitable for routine laboratory testing. In an effort to identify a simple and rapid sequencing method, we analyzed 16 preselected breast tumors and 18 preselected ovarian tumors, using a newly developed automated DNA sequencer. p53 gene mutations had been previously identified in these tumors, using a conventional automated sequencing procedure. Exons 5 to 8 were amplified by PCR, and the PCR products were subsequently subjected to cycle sequencing with the Sanger chain termination method, using Cy5.5-labeled primers. The sequencing mixture was then resolved on a newly developed automated DNA sequencer that can sequence approximately 300 bases of DNA in 30 min. Of these 16 breast tumors, two had mutations in exon 5, four in exon 6, three in exon 7, and three in exon 8. Of the 18 ovarian tumors, two had mutations in exon 5, five in exon 6, two in exon 7, and three in exon 8. In all cases, we identified the same mutations by both the new and the conventional sequencing procedures. Most mutations affected an arginine codon. These data demonstrate that the new method has the capability to provide accurate sequencing information in a fraction of the time and labor in comparison with current automated sequencing techniques. When such procedures are used, DNA sequencing may become a routine tool for identifying clinically important mutations for diagnosis and prognosis of patients with genetic, malignant, infectious, and other diseases.

Autoanalysis↗
PubMed1998

Sequence assembly with CAFTOOLS.

Large-scale genomic sequencing requires a software infrastructure to support and integrate applications that are not directly compatible. We describe a suite of software tools built around the Common Assembly Format (CAF), a comprehensive representation of a sequence assembly as a text file. These tools form the backbone of sequencing informatics at the Sanger Centre and the Genome Sequencing Center. The CAF format is intentionally flexible, and our Perl and C libraries, which parse and manipulate it, provide powerful tools for creating new applications as well as wrappers to incorporate other software. The tools are available free by anonymous FTP from ftp://ftp.sanger.ac.uk/pub/badger/.

Algorithms↗
PubMed1995

Partial DNA sequence of a beta-lactamase produced by a Shigella flexneri strain.

A probe was constructed by radioactive labelling, and enzymatically a DNA fragment of plasmid pMAM-1, which codes for a beta-lactamase in Shigella flexneri UCSM 129, was obtained by amplification of a small part of the gene using the polymerase chain reaction technique (PCR). Since previous published work indicated that this beta-lactamase was of the TEM type, the primers used to amplify the gene were two highly conserved DNA regions in all TEM beta-lactamases. A 500 bp DNA probe was obtained which, by hybridization assays, facilitated the identification of restriction fragments of the plasmid containing the beta-lactamase gene. Two DNA fragments were sequenced by the Sanger method adapted to the PCR technique, and the sequence obtained showed a 100% homology with beta-lactamases TEM-1, TEM-2, TEM-13 and TEM-19. An intragenic restriction site, detected for Pst I, suggested that there is only one copy of the beta-lactamase gene per plasmid copy.

Amino Acid Sequence↗
PubMed2005

Emerging technologies in DNA sequencing.

Demand for DNA sequence information has never been greater, yet current Sanger technology is too costly, time consuming, and labor intensive to meet this ongoing demand. Applications span numerous research interests, including sequence variation studies, comparative genomics and evolution, forensics, and diagnostic and applied therapeutics. Several emerging technologies show promise of delivering next-generation solutions for fast and affordable genome sequencing. In this review article, the DNA polymerase-dependent strategies of Sanger sequencing, single nucleotide addition, and cyclic reversible termination are discussed to highlight recent advances and potential challenges these technologies face in their development for ultrafast DNA sequencing.

Animals↗
PubMed1991

[Determination of the primary structure of Eco-R1-fragment No. 5 of the rat tyrosine aminotransferase gene in the "Applied Biosystems" 370 automatic sequencer].

EcoRI-fragment No. 5 of the rat tyrosine aminotransferase gene containing exons K, L, intron 11, and a part of the 3'-nontranslatable region was digested with several restriction endonucleases (BspRI, Sau3A, BamHI, Ecl136II, AluI), the subfragments obtained were cloned into M13mp19 and sequenced using the Sanger technique with dye-labelled primers on the automated sequencer "Applied Biosystems", model 370A. The sequences were combined by means of a PC-GENE package and original programs to yield the primary structure (1064 b. p.) of the above fragment No. 5, adjacent to the previously sequenced EcoRI-fragment No. 4 (3677 b.p.).

Amino Acid Sequence↗
PubMed1992

Nucleotide sequencing of 5' and 3' termini of bovine viral diarrhea virus by RNA ligation and PCR.

Genomic RNA was extracted from cytopathic (CP) bovine viral diarrhea virus (BVDV) strain NADL, CP strain 72, and noncytopathic (NCP) strain SD-1 purified by ultracentrifugation. Assuming the presence of a cap structure, de-blocking of the 5' capped end of the genomic RNA was done by treatment with tobacco acid pyrophosphatase (TAP). Following decapping, the RNA molecules were ligated using T4 RNA ligase and the ligated tandem RNA templates were then amplified by primer-directed amplification (PCR). cDNA synthesis was done using reverse transcriptase with random primers and cDNA amplification was done using a negative sense primer 231-248 and a positive sense primer 12434-12451. The nucleotide sequence of the amplified product was determined by double-stranded sequencing using the Sanger di-deoxy chain termination method and an additional 'CCCCC' nucleotide sequence was identified at the ligation site. Following dATP tailing of cDNA and amplification across the 5' terminus and nucleotide sequencing, no additional nucleotides were identified on the 5' terminus. The 5' terminus as published by Collett et al., 1988b was confirmed as previously reported. Therefore, the 3' terminus includes an additional 'CCCCC' nucleotide sequence to that previously reported. Identical results were obtained when the BVDV genomic RNA was not decapped prior to RNA ligation and amplification.

Animals↗
PubMed2000

[Cloning and sequence analysis of SSU rRNA gene of cutaneous leishmaniasis pathogen from Xinjiang of China].

OBJECTIVE: By sequencing of SSU rRNA gene cloning from Xinjiang cutaneous leishmaniasis pathogen (XJCLP) to provide evidence for identification of the pathogen. METHODS: By PCR assay with primers R222 and R333, the specific fragment had been produced from SSU rRNA gene of XJCLP, L. infantum, L. tropica and cloned into pGEM-T Easy vector. The clones were sequenced by the Sanger dideoxy-mediated chain termination method, analysis of SSU rRNA gene sequences from XJCLP, L. tropica, L. infantum with DNASIS. RESULTS: Sequence analysis showed that the specific fragment of SSU rRNA gene from XJCLP, L. infantum, L. tropica, were all 394 bp in length. There were 391 bases identical and three point mutations between the sequences of XJCLP and L. tropica, the similarity being 99.2%; 390 bases identical and three point mutations and one insertion/deletion between the sequences of XJCLP and L. infantum, the similarity being 99.0%. One insertion/deletion between the sequences of L. tropica and L. infantum, the similarity being 99.7%. The primary and secondary structures of SSU rRNA gene from XJCLP differed from those of L. infantum and L. tropica. A retrieval from GenBank confirmed that these 394 bp sequence are new gene sequences. CONCLUSION: The primary and secondary structures of SSU rRNA gene from XJCLP, L. infantum, L. tropica were different. 394 bp sequence from SSU rRNA gene of XJCLP is a new gene sequence.

Animals↗