SEARCH · Search PubMed

Results for “cDNA”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources

PubMed1999

Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain.

We have conducted a sequencing project of human cDNAs which encode large proteins in brain. For selection of cDNA clones to be sequenced in this project, cDNA clones have been experimentally examined by in vitro transcription/translation prior to sequencing. In this study, we tested an alternative approach for picking up cDNA clones having a high probability of carrying protein coding region. This approach exploited 5'-end single-pass sequence data and the GeneMark program for assessing protein-coding potential, and allowed us to select 74 clones out of 14,804 redundant cDNA clones. The complete sequence data of these 74 clones revealed that 45% of them encoded proteins consisting of more than 500 amino acid residues while all the clones thus selected carried possible protein coding sequences as expected. The results indicated that the GeneMark analysis of 5'-end sequences of cDNAs offered us a simple and effective means to select cDNA clones with protein-coding potential although the sizes of the encoded proteins could not be predicted.

5' Untranslated Regions↗

PubMed1991

Efficient cDNA cloning by direct phenotypic correction of a mutant human cell line (HPRT-) using an Epstein-Barr virus-derived cDNA expression vector.

Human cells are, in general, poor recipients of foreign DNA, which has severely hampered the cloning of genes by direct phenotypic correction of deficient human cell lines after DNA mediated gene transfer. In this communication a methodology is presented which largely circumvents this problems. The method relies on the use of a recently developed episomal Epstein-Barr-virus-derived cDNA expression vector (Belt et al. (1989) Gene 84, 407-417). The cloning of hypoxanthine phosphoribosyltransferase (HPRT) cDNA, corresponding to a low abundant mRNA in wild type cells is used as a model system. Size fractionated poly (A)+ RNA from wild type cells, which resulted in an approximately 10 fold enrichment in HPRT mRNA, was used to construct a cDNA library of 25,000 independent clones in the pECV25 vector. An HPRT deficient human cell line was transfected and subsequently selected with hygromycin B for DNA uptake. In a small scale experiment only 7000 hygromycin BR transfectants were sufficient to isolate 2 independent HATR clones which were shown to replicate episomes harbouring HPRT cDNA. The first insert had a 5' untranslated region (UTR) and a 3' UTR perfectly in agreement with published data. The second cDNA clone harboured an unusually long 5' UTR and a shorter 3' UTR due to alternative polyadenylation of the HPRT transcript which has not been previously recognized.

Base Sequence↗

PubMed1996

Restriction landmark cDNA scanning (RLCS): a novel cDNA display system using two-dimensional gel electrophoresis.

We have developed a new method, designated restriction landmark cDNA scanning (RLCS), which displays many cDNA species quantitatively and simultaneously as two-dimensional gel spots. In this method cDNA species of uniform length were prepared for each mRNA species using restriction enzymes. After the restriction enzyme sites were radiolabeled as landmarks, the labeled fragments were subjected to high resolution two-dimensional gel electrophoresis. In analyses of cDNA samples from adult mouse liver and brain (cerebral cortex, cerebellum and brain stem) we detected approximately 500 and >1000 discrete gel spots respectively of various intensities at a time. The spot patterns of the three brain regions were very similar, although not identical, but were quite different from the pattern for the liver. RNA blot hybridization analysis using several cloned spot DNAs as probes showed that differences in intensity of the spots among RLCS profiles correlated well with expression levels of the corresponding mRNA species in the brain regions. Because the spots and their intensities reflect distinct mRNA species and their expression level respectively, the RLCS is a novel cDNA display system which provides a great deal of information and should be useful for systematic documentation of differentially expressed genes.

Animals↗

PubMed1992

cDNA clones for mouse parotid proline-rich proteins. mRNA regulation by isoprenaline and the nucleotide sequence of proline-rich protein cDNA MP5.

cDNA clones for mRNA sequences regulated by isoprenaline in mouse parotid glands were identified by differential colony hybridisation and all hybridised to a diagnostic proline-rich protein (PRP) oligonucleotide. They were divided into two cross-hybridisation groups, A and B, which were shown by hybrid-selected translations to encode acidic PRP and basic PRP, respectively. The A-type subgroup consisted of sequences homologous to the previously identified mouse PRP genes MP2 and MP3. The B-type subgroup comprised clones for the previously identified cDNA pUMP125 (MP4) as well as other PRP sequences. Six of the B-type clones contained a novel PRP cDNA (MP5) and these were sequenced. The composite MP5 cDNA was 897 nucleotides long and contained an open reading frame capable of encoding a 260-residue-long salivary PRP precursor (30% Pro, 19% Gln and 18% Gly), containing nine variant repeat units of consensus PGNQQGPPPQGGPQQ(GPP)R(PPQ). MP5 was 80% identical to the sequence of MP4 and had a high degree of similarity (60%) at its 3'-untranslated region to rat salivary glutamate/glutamine-rich protein (GRP) cDNA. Two MP5 clones contained a 273-bp intron-like insertion in the 3' untranslated region, being derived, therefore, from incompletely spliced MP5 transcripts. Northern blotting showed that, although PRP mRNA species were induced by isoprenaline, a B-type PRP mRNA was present in normal parotid glands. RNA dot-blots probed with PRP-gene-specific oligonucleotides established that MP3, MP4 and MP5 PRP mRNA were all induced by isoprenaline.

Amino Acid Sequence↗

PubMed2004

Fabrication of high quality cDNA microarray using a small amount of cDNA.

DNA microarray technology has become an essential part of biological research. It enables the genome-scale analysis of gene expression in various types of model systems. Manufacturing high quality cDNA microarrays of microdeposition type depends on some key factors including a printing device, spotting pins, glass slides, spotting solution, and humidity during spotting. UsingEthe Microgrid II TAS model printing device, this study defined the optimal conditions for producing high density, high quality cDNA microarrays with the least amount of cDNA product. It was observed that aminosilane-modified slides were superior to other types of surface modified-slides. A humidity of 30+/-3% in a closed environment and the overnight drying of the spotted slides gave the best conditions for arraying. In addition, the cDNA dissolved in 30% DMSO gave the optimal conditions for spotting compared to the 1X ArrayIt, 3X SSC and 50% DMSO. Lastly, cDNA in the concentration range of 100-300 ng/ micro l was determined to be best for arraying and post-processing. Currently, the printing system in this study yields reproducible 9000 spots with a spot size 150 mm diameter, and a 200 nm spot spacing.

DNA, Complementary↗

PubMed2006

[Preparation of the cDNA microarray on the differential expressed cDNA of senescence-accelerated mouse's hippocampus].

Alzheimer' s disease (AD) is the most common form of dementia in the elderly. AD is an invariably fatal neurodegenerative disorder with no effective treatment. Senescence-accelerated mouse prone 8 (SAMP8) is a model for studying age-related cognitive impairments and also is a good model to study brain aging and one of mouse model of AD. The technique of cDNA microarray can monitor the expression levels of thousands of genes simultaneously and can be used to study AD with the character of multi-mechanism, multi-targets and multi-pathway. In order to disclose the mechanism of AD and find the drug targets of AD, cDNA microarray containing 3136 cDNAs amplified from the suppression subtracted cDNA library of hippocampus of SAMP8 and SAMR1 was prepared with 16 blocks and 14 x 14 pins, the housekeeping gene beta-actin and G3PDH as inner conference. The background of this microarray was low and unanimous, and dots divided evenly. The conditions of hybridization and washing were optimized during the hybridization of probe and target molecule. After the data of hybridization analysis, the differential expressed cDNAs were sequenced and analyzed by the bioinformatics, and some of genes were quantified by the real time RT-PCR and the reliability of this cDNA microarray were validated. This cDNA microarray may be the good means to select the differential expressed genes and disclose the molecular mechanism of SAMP8's brain aging and AD.

Aging↗

PubMed1989

Construction of a rat T-cell hybridoma cDNA expression library and isolation of a cDNA clone for the rat T-cell differentiation marker RT6.2.

The phosphatidylinositol-linked T-cell surface protein RT6 occurs in two alloantigenic forms, RT6.1 and RT6.2. A lambda gt11 cDNA expression library was constructed from the RT6.2+ T-T hybridoma cell line EpD3 and screened with RT6-specific antisera. One of nine independent positive clones obtained in an initial screening of 500,000 recombinant phages was able to select antibodies capable of immunoprecipitating RT6.2 as well as RT6.1. Northern and Southern blot analyses with the cDNA insert of this clone provide additional strong evidence for its RT6.2 specificity. The 330 bp cDNA insert of this clone hybridizes with a 1.6 kb mRNA species present in RT6.2+ and RT6.1+ but absent from RT6- T-cell lines. In Southern blot analyses this insert detects a DNA restriction fragment length polymorphism between genomic DNAs from RT6.1 and RT6.2 rat strains. In addition, these analyses indicate that RT6.1 and RT6.2 are each encoded by a single gene and provide no evidence for the existence of additional RT6 alleles or a closely related gene family. Preliminary sequence analyses suggest that the RT6.2-specific partial cDNA found in these studies represents an internal EcoRI fragment of the corresponding cDNA and encodes part of the presumptive leader and the N-terminal domain of RT6.2. The immunological reactivity of the corresponding fusion protein indicates that the N-terminal domain of RT6.2 contains an allotype-specific epitope as well as at least one additional epitope shared with the alloantigenic counterpart RT6.1.

Animals↗

PubMed1993

Isolation of cDNA clones mapping around DXS178: a search for human X-linked agammaglobulinaemia gene using yeast artificial chromosomes, cosmids and direct cDNA selection.

X-linked agammaglobulinaemia (XLA) was previously mapped using genetic linkage analysis to Xq22. No recombinants have been found so far between the XLA locus and DXS178 in over 30 informative meioses. Two overlapping yeast artificial chromosomes (YACs), which cover a region of approximately 1000 kb around DXS178 and form part of a larger YAC contig, were hybridised to an ordered cosmid library constructed from a human fibroblast cell line with karyotype 49,XXXXX. Positive cosmids were gridded in high density arrays onto nylon filters and rescreened with a series of YACs, YAC end probes and additional markers from the region to assign cosmids into intervals. A 640 kb-YAC hybridising to p212 (DXS178) was used for direct selection of PCR-amplified cDNA from two cDNA libraries. To identify the cosmids containing transcribed sequences the enriched cDNA from each library was radiolabelled and hybridised back to positive clones which mapped to the region of interest. These clones were then hybridised to the subcloned enriched cDNA sublibraries. Candidate cDNA clones were isolated, grouped within the region of interest and their position was confirmed by mapping back to the cosmids.

Agammaglobulinemia↗

PubMed1993

Cloning and sequencing of a cDNA encoding Saccharomyces cerevisiae carnitine acetyltransferase. Use of the cDNA in gene disruption studies.

cDNA encoding for carnitine acetyltransferase (CAT) of yeast S. cerevisiae was isolated by screening a yeast cDNA lambda gt11 library with antibody. The whole coding sequence was obtained from the cDNA and from a YEP 13 DNA clone identified using the cDNA as probe. The coding sequence consists of 670 residues, which amounts to a molecular mass of 77,300 kDa. This cDNA was used successfully to disrupt the gene for the mitochondrial isoenzyme of CAT, which was shown by measuring the enzyme activity and by immunoblot. The acetylcarnitine content of these cells decreased significantly. A search in the PIR protein data base revealed that besides the known carnitine acyltransferases, choline acyltransferases are highly homologous to yeast CAT. The mitochondrial CAT-deficient (CAT-) cells were able to grow on different fermentable and nonfermentable carbon sources, even on acetate at the same rate as the parental strain. In contrast to these, 13C NMR studies revealed significant differences between parental and CAT- cells. In CAT-cells [3-13C]pyruvate was converted mainly to lactate and acetate, whereas in the parental cells alanine and tricarboxylic acid cycle intermediates were found as the main products of pyruvate metabolism beside acetate. These results suggest diminished flux through the pyruvate dehydrogenase complex in the absence of mitochondrial CAT in yeast cells.

Amino Acid Sequence↗

PubMed1998

cDNA excision in stable retroviral cDNA transfectants is prevented by R removal.

The present study provides evidence on the occurrence of DNA rearrangement between the redundant 5' and 3' R domains of equine infectious anemia virus (EIAV) Tat cDNA. This was correlated with a gradual loss of cDNA copy number concomitantly with a decrease in gene expression. Removal of the 5' RU5 abolished rearrangement and stabilized Tat expression in EIAV tat cDNA transfectants. Our data suggest that prior removal of the 5' R from cloned retroviral cDNAs can impede DNA rearrangement, thus preventing cDNA excision that frequently occurs and hinders permanent expression of retroviral cDNAs in stable transfectants.

DNA, Complementary↗

PubMed2000

Cloning and analysis of the mouse Fanconi anemia group A cDNA and an overlapping penta zinc finger cDNA.

Despite the cloning of four disease-associated genes for Fanconi anemia (FA), the molecular pathogenesis of FA remains largely unknown. To study FA complementation group A using the mouse as a model system, we cloned and characterized the mouse homolog of the human FANCA cDNA. The mouse cDNA (Fanca) encodes a 161-kDa protein that shares 65% amino acid sequence identity with human FANCA. Fanca is located at the distal region of mouse chromosome 8 and has a ubiquitous pattern of expression in embryonic and adult tissues. Expression of the mouse cDNA in human FA-A cells restores the cellular drug sensitivity to normal levels. Thus, the expression pattern, protein structure, chromosomal location, and function of FANCA are conserved in the mouse. We also isolated a novel zinc finger protein, Zfp276, which has five C(2)H(2) domains. Interestingly, Zfp276 is situated in the Fanca locus, and the 3'UTR of its cDNA overlaps with the last four exons of Fanca in a tail-to-tail manner. Zfp276 is expressed in the same tissues as Fanca, but does not complement the mitomycin C (MMC)-sensitive phenotype of FA-A cells. The overlapping genomic organization between Zfp276 and Fanca may have relevance to the disease phenotype of FA.

Adult↗

PubMed1993

The alternative 5'-end of the Drosophila melanogaster epidermal growth factor receptor cDNA (DER) is part of the D14-3-3 cDNA.

A portion of the cDNA reported as a novel cDNA encoding the Drosophila melanogaster homolog of the bovine 14-3-3 protein by Swanson and Ganguly [Gene 113 (1992) 183-190] already exists in the database. It was originally reported as an alternative 5' end of the D. melanogaster homolog of the epidermal growth factor receptor (DER). Schejter and Shilo [Cell 56 (1989) 1093-1164] later reported that this finding was due to a cloning artifact that joined the 14-3-3 cDNA onto the DER cDNA.

14-3-3 Proteins↗

PubMed1989

Synthesis and characterization of a bovine hexokinase 1 cDNA probe by mixed oligonucleotide primed amplification of cDNA using high complexity primer mixtures.

Hexokinase (EC 2.7.1.1) catalyzes the first step in glucose metabolism, using ATP for the phosphorylation of glucose to glucose 6-phosphate. A portion of the HK1 gene was cloned by mixed oligonucleotide primer amplification of cDNA using primers of high complexity. The amino acid sequence for a partial fragment of bovine cardiac muscle HK was determined and used to create primer mixtures of 256- and 1024-fold complexity. Two products were generated from bovine cardiac muscle cDNA which show 82% nucleotide and 93% amino acid identity with a region of rat brain HK1 and cDNA. This work demonstrates that extension and amplification of cDNA probes may be successful even when amino acid sequence data indicate substantial codon degeneracy.

Amino Acid Sequence↗

PubMed1999

Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database.

We propose a prediction method for human full-length cDNA by comparing sequence data between human genome shotgun sequence and mouse full-length cDNA. The human genome which is homologous to the mouse full-length cDNA is selected by a homology search program, and the predicted exons are connected at the exon-intron junction which gives the best homology score to the mouse full-length cDNA. The accuracy of the predicted human full-length coding region is 83.3%, and the false positive rate is 16.7%. Five human full-length proteins out of 20 proteins are correctly predicted.

Animals↗

PubMed1987

Isolation of full-length putative rat lysophospholipase cDNA using improved methods for mRNA isolation and cDNA cloning.

We have cloned a full-length putative rat pancreatic lysophospholipase cDNA by an improved mRNA isolation method and cDNA cloning strategy. These new methods allow the construction of a cDNA library from the adult rat pancreas in which the majority of recombinant clones contained complete sequences for the corresponding mRNAs. A previously recognized but unidentified long and relatively rare cDNA clone containing the entire sequence from the cap site at the 5' end to the poly(A) tail at the 3' end of the mRNA was isolated by single-step screening of the library. The size, amino acid composition, and the activity of the protein expressed in heterologous cells strongly suggest this mRNA codes for lysophospholipase [Van den Bosch, H., Aarsman, A. J., DeJong, G. N., & Van Deenen, L. M. (1973) Biochim. Biophys. Acta 296, 94-104].

Amino Acid Sequence↗

PubMed1989

Identification of a new P450 expressed in human lung: complete cDNA sequence, cDNA-directed expression, and chromosome mapping.

A cDNA coding for a P450 expressed in human lung was isolated from a lambda gt11 library constructed from human lung mRNA using a cDNA probe to rat P450 IVA1. The cDNA-deduced amino acid sequence of this P450, designated IVB1, consisted of 511 amino acids and had a calculated molecular weight of 59,558. The IVB1 amino acid sequence bore 51%, 53%, and 52% similarities to rat IVA1, IVA2, and rabbit P450p-2, respectively. Comparison of the primary amino acid sequence of human IVB1 with rat IVA and rabbit p-2 P450 sequences revealed a region of absolute sequence identity of 17 amino acids between residues 304 and 320. However, the functional significance of this conserved sequence is unknown. Human IVB1 also appears to be related to P450 isozyme 5 that has been extensively characterized in rabbits. The IVB1 cDNA was inserted into a vaccinia virus expression vector and the enzyme expressed in human cell lines. The expressed enzyme had an absorption spectrum with a lambda max at 450 nm when reduced and complexed with carbon monoxide, typical of other cytochrome P450s. Unlike rabbit P450 isozyme 5, however, human IVB1 was unable to activate the promutagen 2-aminofluorene. Human lung microsomal P450s were also unable to metabolize this compound despite the presence of IVB1 mRNA in three out of four human lungs analyzed. In contrast to its expression in lung, IVB1 mRNA was undetectable in livers from 14 individuals, including those from which the lungs were derived. IVB1-related mRNA was also expressed in rat lung and was undetectable in untreated rat liver.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1999

Isolation of rice allergenic cDNA clones from a rice cDNA library by immunoscreening with a polyclonal antibody specific to 16 kD rice allergenic protein.

Clinical cases of type-1 hypersensitive reaction to rice (Oryza sativa) have been reported in western countries as well as in Japan. Among rice proteins, 14-16 kD globulin proteins encoded by multiple gene family have been identified as major rice allergens. In this study, a rice cDNA library was constructed using lambda UniZap vector and screened with a rat anti-16 kD globulin protein polyclonal antibody in order to isolate Korean rice allergenic cDNA clones. Five independent cDNA clones, termed RAK1-5, were obtained after second rounds of plaque assay and immunoblot analysis. These clones encoded 13-19 kD recombinant proteins upon IPTG induction, which were identified by the polyclonal antibody in immunoblot analysis. DNA sequencing analysis showed that RAK1-4 have 99% sequence homology with RA5b, and RAK5 is closely related with RA14c. This result indicated that RA5b gene is widely distributed in our cDNA library among other possible rice allergenic genes, and more study is needed to isolate heterogeneous or novel rice allergen genes.

Allergens↗

PubMed1995

Molecular cloning and functional expression of Neurospora deoxyhypusine synthase cDNA and identification of yeast deoxyhypusine synthase cDNA.

Deoxyhypusine synthase catalyzes the formation of deoxyhypusine residue on the eIF-5A precursor using spermidine as the substrate. We have purified deoxyhypusine synthase from Neurospora crassa to apparent homogeneity (Tao, Y., and Chen, K. Y. (1995) J. Biol. Chem. 270, 383-386). We have now cloned and characterized the deoxyhypusine synthase cDNA using a reverse genetic approach. Conceptual translation of the nucleotide sequence of the cloned 1258-base pair cDNA revealed an open reading frame containing 353 amino acids with a predicted M(r) of 38,985. The deoxyhypusine synthase cDNA was subcloned into the expression vector pQE60 to produce a 40,000-dalton recombinant protein on SDS-PAGE which exhibited deoxyhypusine synthase activity. A GenBank search showed that the Neurospora deoxyhypusine synthase cDNA possessed significant sequence homology to a previously uncharacterized yeast sequence (accession number U00061 (1994)). The yeast sequence encodes a protein of 387 amino acids that shows 69% of total amino acid identity and 80% of total amino acid similarity to the Neurospora enzyme. Sequence alignment and hydropathy analysis suggest that the yeast sequence represents deoxyhypusine synthase.

Amino Acid Sequence↗