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PubMed1976

Importance of full size complementary DNA in nucleic acid hybridization.

The size of the DNA product synthesized by RNA-directed DNA polymerase (isolated from avian myeloblastosis virus) was found to be important for complementary DNA (cDNA)-mRNA hybridization reactions. Incomplete cDNA to rabbit reticulocyte globin mRNA formed poor hybrids and presumably lacked sequences needed for hybridization. The size of the cDNA synthesized was influenced by the reaction conditions used. The complementary DNA product contained 10 S material when synthesis was done at high deoxynucleoside triphosphate concentrations (greater than 50 muM) while the product was smaller than the template when synthesis was at lower concentrations. The concentration and size (oligo(dT)6 to (dT)10) of primer had little or no effect on the product size. Increasing the concentration of 10 S globin mRNA caused the cDNA product to contain more small material. The cDNA synthesized at high deoxynucleoside triphosphate concentrations was fractionated into heavy, medium, and light fractions by alkaline sucrose density centrifugation. All hybridized to globin mRNA. The larger cDNAs had a higher TM when hybridized to globin mRNA, a lower dTMP/dCMP ratio (indicating that the poly(dT) region constituted a smaller fraction of the molecule), and gave increased protection of 125I-labeled mRNA from nuclease digestion. The full size cDNA was especially useful for studying the RNA transcribed from chromatin by RNA polymerase. The complement of the 5' end of the mRNA is contained only in full size cDNA; the 5' end is the part of the mRNA first transcribed by the RNA polymerase assuming correct transcription. Thus, full size cDNA can hybridize more effectively to the short RNA transcripts that are obtained than partial cDNA. RNA transcribed from rabbit bone marrow chromatin by Escherichia coli RNA polymerase hybridized twice as efficiently to complete cDNA as it did to partial cDNA demonstrating the usefulness of full size cDNA.

Animals↗

PubMed1992

Fluorescent-labeled oligonucleotides that exhibit a measurable signal in the presence of complementary DNA.

Oligonucleotide derivatives with a fluorescent dye were designed for exhibiting a measurable signal only when they bind to complementary DNA in aqueous solution. The oligonucleotide with a dansyl group at the specific 2'-sugar residue was synthesized by using the protected 2'-dansylaminouridine phosphorobisamidite. The dansyl-oligonucleotide conjugate binds to its complementary DNA to form duplex with a normal stability and exhibits enhanced fluorescence together with a blue-shift in emission maxima after the hybridization. Another possible candidate involved the use of pyrene-excimer emission upon forming ternary complex between two pyrene-labeled oligonucleotide probes with target DNA. A new and general method for introduction of a pyrene fluorophore into the 3'- or 5'-terminal hydroxyl group of oligonucleotides via different linkers was developed.

DNA↗

PubMed1997

p53 abnormalities in primary prostate cancer: single-strand conformation polymorphism analysis of complementary DNA in comparison with genomic DNA. The Cooperative Prostate Network.

BACKGROUND: The reported frequency of mutation of the p53 tumor suppressor gene (also known as TP53) in human carcinomas of the prostate has varied widely, ranging from 3% to 42%. This variability may be a consequence of tumor heterogeneity and/or the use of different methods of analysis. Since p53 mutation has been associated with clinical outcome for a number of cancer types, determination of its true frequency in primary carcinomas of the prostate is important. PURPOSE: The principal aims of this study were as follows: 1) to validate the utility of detecting p53 gene mutations by means of polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis of complementary DNA (cDNA) (synthesized from prostate tissue RNA and 2) to study the concordance of RNA- and DNA-based PCR-SSCP assays in detecting p53 mutations in individual tumor fragments. METHODS: RNA and genomic DNA were isolated by means of standard techniques from specimens of 19 carcinomas of the prostate, selected on the basis of p53 data obtained in a previous analysis of cDNA (indicating that 14 were mutant and five were wild-type). RNA was converted into cDNA by means of reverse transcription (RT); the cDNA was then amplified by means of nonisotopic (i.e., nonradioactive) PCR, and the PCR products were subjected to SSCP analysis in polyacrylamide gels (RT-PCR-SSCP analysis). Genomic DNA was examined by means of SSCP analysis of isotopically labeled (32PO4) PCR products (DNA-PCR-SSCP analysis). In both approaches, the protein coding region of the p53 gene was divided into multiple, smaller fragments for study. PCR products exhibiting abnormal migration in SSCP gels were subjected to direct nucleotide sequencing or to cloning and sequencing of multiple clones. RESULTS: RT-PCR-SSCP and DNA-PCR-SSCP identified p53 gene abnormalities in 15 of the 19 selected carcinomas, including one previously reported to be wild-type for p53. Overall, PCR-SSCP analysis identified 18 p53 fragments with abnormalities; three carcinomas showed two abnormalities each. Six (33%) of the 18 abnormalities were detected by both RT-PCR-SSCP and DNA-PCR-SSCP, 10 (56%) were detected by RT-PCR-SSCP alone, and two (11%) were detected by DNA-PCR-SSCP alone. The 18 abnormalities were caused by 20 changes in the sequence of the p53 gene; in one carcinoma, double mutations in two individual p53 exons were identified. CONCLUSIONS AND IMPLICATIONS: PCR-SSCP analysis of both RNA and DNA allows the detection of more mutations than the analysis of either alone. Some primary carcinomas of the prostate contain more than one altered p53 gene, consistent with the possibility of intratumoral heterogeneity of mutation of this gene. For comprehensive analysis of p53 mutations in carcinomas of the prostate, and perhaps in other tumor tissues, SSCP analysis of cDNA should be used in combination with SSCP analysis of genomic DNA.

DNA, Complementary↗

PubMed1997

Nucleotide sequence of rat steroidogenic acute regulatory protein complementary DNA.

The steroidogenic acute regulatory (StAR) protein is a key regulator for the steroidogenesis in acute response to trophic hormone. A rat complementary DNA of the StAR protein was cloned and its complete nucleotide sequence was determined. The deduced amino acid sequence of the clone has an additional 86 amino acid stretch at amino terminus when it was compared with those sequences in other species. The other part of the amino acid sequence has 94% identity to mouse StAR protein sequence. Three transcripts (1.3 kb, 1.6 kb, and 3.5 kb) which are hybridizing to the clone were detected in testis, ovary and adrenal gland. When the cDNA was expressed in COS1 cells, 30 kDa and 47 kDa proteins specific to the anti-StAR antibody were detected.

Amino Acid Sequence↗

PubMed1994

Human very-low-density lipoprotein receptor complementary DNA and deduced amino acid sequence and localization of its gene (VLDLR) to chromosome band 9p24 by fluorescence in situ hybridization.

A complementary DNA for the very-low-density lipoprotein receptor (VLDLR) that codes for a protein of 873 amino acids was cloned from a human heart cDNA library. The mature protein of 846 amino acids, preceded by a 27-residue signal peptide, shares 97% amino acid sequence identity with the rabbit VLDLR. Like the low-density lipoprotein receptor, the VLDLR contains five different domains, all of which are highly conserved between human and rabbit. A tetrapeptide NPVY that potentially serves as a signal for clustering of the VLDLR on coated pits is present in the cytoplasmic domain, which is 100% conserved between human and rabbit. We localized the VLDLR gene to chromosome 9p24 by fluorescence in situ hybridization using the cloned cDNA as hybridization probe. The high amino acid sequence homology of the VLDLR between two mammalian species suggests that the receptor plays a fundamental role in lipoprotein metabolism and that energy metabolism mediated by triglyceride utilization may be an evolutionarily highly conserved mechanism.

Amino Acid Sequence↗

PubMed1994

Episomal expression of sense and antisense insulin-like growth factor (IGF)-binding protein-4 complementary DNA alters the mitogenic response of a human colon cancer cell line (HT-29) by mechanisms that are independent of and dependent upon IGF-I.

HT-29 cells express and secrete insulin-like growth factor (IGF)-II and only one of the six IGF-binding proteins, IGFBP-4. In the present study, the physiological role of endogenous IGFBP-4 in regulating the growth response of HT-29 cells to exogenous and endogenous IGFs was examined. Both the basal and the IGF-stimulated growth of HT-29 cells was significantly increased over control values in the presence of IGFBP-4 antibody, suggesting that endogenous IGFBP-4 is a potent inhibitor of the mitogenic effects of endogenous and exogenous IGFs. In order to further confirm the inhibitory role of endogenous IGFBP-4, sense and antisense complementary DNA fragments of human IGFBP-4 were ligated into an episomal mammalian expression vector (pCEP4). Restriction mapping and Southern blot analysis were used to confirm directional cloning of the IGFBP-4 complementary DNA fragments in the sense and antisense directions in the pCEP4 vectors. HT-29 cells were transfected with either the control (no insert, C-P), sense (S-P), or antisense (AS-P) vectors and subjected to hygromycin selection. The functional nature of the transfectants was confirmed by measuring IGFBP-4 concentrations in the conditioned media (CM) of 10(7) cells by ligand and immunoblot analysis. IGFBP-4 concentrations were 7.4 +/- 1.7-fold higher in the CM of S-P cells compared to that in the CM of C-P cells, while IGFBP-4 concentrations in the CM of AS-P cells were significantly lower than those present in the CM of C-P cells. Both the basal and the IGF-I-stimulated growth of the AS-P cells was significantly higher than that of the C-P and S-P cells. The basal (non-stimulated) and the IGF-I-stimulated growth of the S-P cells was not significantly different from that of the C-P cells, suggesting that overexpression of IGFBP-4 was not inhibitory to the growth of the HT-29 cells. The basal growth of the S-P and C-P cells was significantly increased in the presence of IGFBP-4 antibody, once again suggesting that endogenous IGFBP-4 was a potent inhibitor of autocrine effects of endogenous factors (IGF-II). Addition of IGFBP-4 antibody had no significant effect on the basal growth of the AS-P cells, confirming that the difference between the growth response of the AS-P, C-P, and S-P cells was largely contributed by the difference in the endogenous secretion of IGFBP-4 by the cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Antibodies↗

PubMed1993

Molecular cloning of a unique complementary DNA of rat myosin regulatory light chain and its elevated expression in v-src-transformed rat culture cell lines.

We have isolated a complementary DNA (cDNA) clone, termed N14, from a cDNA library derived from normal rat fibroblast 3Y1 cells using a differential screening procedure. N14 cDNA was 1115 nucleotides in length and contained an open reading frame of 172 amino acid residues. The expression of N14 gene was significantly increased in Rous sarcoma virus-transformed 3Y1 cells (SR-3Y1) compared with that in parental 3Y1 cells. The high level of N14 gene expression was reduced by treatment with herbimycin A, indicating that the expression was dependent upon the activity of pp60v-src tyrosine kinase. A homology search revealed that the nucleotide sequence of N14 cDNA was nearly identical to that of the rat nonsarcomeric myosin regulatory light chain cDNA (RLC-B), with the exception of a 250-nucleotide insertion which is present between C at position +483 and G at position +484 in the RLC-B cDNA. Southern blot analysis indicated that N14 gene was present as a single copy in the rat genome. Therefore, these two mRNAs might be generated through the alternative splicing mechanism. However, a RNase protection assay revealed that RLC-B mRNA was not expressed in SR-3Y1 cells. In addition, the amount of N14 mRNA was also increased in other types of transformed cells, including v-mos-, simian virus 40-, and v-Ha-ras-transformed 3Y1 cells.

Alternative Splicing↗

PubMed2003

Progesterone induces cellular differentiation in MDA-MB-231 breast cancer cells transfected with progesterone receptor complementary DNA.

Progesterone is an important regulator of growth and differentiation in breast tissues. In this study, the effect of progesterone on cell differentiation was evaluated in the estrogen receptor-negative and progesterone receptor (PR)-negative MDA-MB-231 cell line which was transfected with PR-complementary DNA. Morphological changes were analyzed at the ultrastructural level by scanning and transmission electron microscopy. Progesterone-treated PR-transfected cells exhibited a more protracted and well spread morphology with an increase in organelles such as mitochondria and rough endoplasmic reticulum as compared to the rounded form of control vehicle (0.1% ethanol)-treated PR-transfected cells. Vehicle and progesterone-treated MDA-MB-231 cells transfected with the pSG5 plasmid (transfection control cells) had similar rounded morphology as control vehicle-treated PR-transfected cells. Immunofluorescence staining revealed that expression of E-cadherin, a differentiation marker, was more prominent in progesterone-treated cells. Expression of keratin and vimentin but not beta-catenin was up-regulated in progesterone treated cells when evaluated by immunoblotting. As signal transducers and activators of transcription (STAT) molecules have been implicated in mammary differentiation, we analyzed the expression of Stat 1, 3, 5a, and 5b proteins and found a significant up-regulation of the Stat 5b protein in progesterone-treated cells. We have provided in vitro evidence of the close association of PR with differentiation in breast cancer. It is likely that the Stat 5b protein may play a major role in progesterone-induced differentiation in breast cancer cells.

Blotting, Western↗

PubMed1977

Determination of the sequence homology between the four RNA species of cucumber mosaic virus by hybridization analysis with complementary DNA.

The method of Taylor etal., (11) has been used to transcribe complementary DNA probes from the four major RNA species of cucumber mosaic virus (RNAs 1 - 4 in order of decreasing molecular weight). Analysis of the kinetics of hybridization of these probes in homologous and heterologous complementary DNA-RNA hybridization reactions has shown that the sequence of the smallest RNA (RNA 4), which contains the coat protein gene, is present within RNA 3. RNAs 1 and 2 are unique RNA molecules while each has a region of approximately 300 nucleotides in common with RNA 4.Images

Base Sequence↗

PubMed1980

Cloning of DNA complementary to bovine prolactin mRNA.

We have cloned DNA complementary to mRNA coding for bovine prolactin (bPrl). Double-stranded cDNA prepared from bovine pituitary mRNA was inserted into the Pst I site of plasmid bPR322 by the dC x dG tailing technique and amplified in E. coli chi 1776. A recombinant plasmid containing bPrl cDNa was identified by hybridization to cloned rat Prl cDNA. It contains cDNA corresponding to the region of the mRNA coding for the carboxy terminal 101 amino acids of bPrl, as well as 42 nucleotides in the 3' untranslated region of the mRNA. Nucleotide sequencing confirmed the amino acid sequencing of this region of bPrl, and permitted the assignment of asparagine or glutamic acid at seven previously equivocal loci. Codon use in bPrl mRNA is comparable to that found in rat and human Prl mRNA's and differs from that in bovine, rat, and human growth hormone mRNA's.

Amino Acid Sequence↗

PubMed1984

Bovine beta-crystallin complementary DNA clones. Alternating proline/alanine sequence of beta B1 subunit originates from a repetitive DNA sequence.

A library of recombinant plasmids carrying complementary DNA sequences synthesized from bovine lens messenger RNAs was constructed. Clones coding for five different beta-crystallin subunits: beta B1, beta B3, beta Bp, beta s, beta A3 (and beta A1), were identified by means of hybridization selection, followed by one- and two-dimensional gel electrophoresis of the translational products. Under rather stringent conditions each of these clones hybridizes with its corresponding mRNA and does not show significant cross-hybridization with mRNAs coding for other beta-crystallins, except in the case of the homologous beta A3 and beta A1-crystallins. The beta A3 and beta A1 subunits seem to be encoded by one mRNA using two different AUG codons as start position for translation. We have also determined the nucleotide sequence of a beta B1-crystallin cDNA (pBL beta B1) which enabled us to deduce the complete amino acid sequence of the protein. The beta B1-crystallin, a characteristic component of the high molecular weight crystallin aggregate (beta H), is internally homologous both at DNA and protein level as has been reported for gamma- and other beta-crystallins. This is in agreement with the idea that these proteins had a common ancestral precursor gene that internally duplicated. The G + C content of the coding sequence of beta B1 is very high: 67% overall and even 84.2% for the first 170 nucleotides, due to a remarkable non-random codon usage. A proline/alanine repetition in the N-terminal domain of the protein is encoded by a repetitive "simple" DNA sequence.

Alanine↗

PubMed1988

Restoration of excitation-contraction coupling and slow calcium current in dysgenic muscle by dihydropyridine receptor complementary DNA.

Microinjection of an expression plasmid that carries complementary DNA encoding the receptor for dihydropyridine calcium channel blockers of skeletal muscle restores both excitation-contraction coupling and slow calcium current in cultured skeletal muscle cells from mice with muscular dysgenesis. This suggests that the dihydropyridine receptor in the transverse tubule membrane of skeletal muscle functions both as the voltage sensor for excitation-contraction coupling and as the slow calcium channel.

Animals↗

PubMed1992

Molecular cloning and expression of a full-length complementary DNA encoding the guinea pig adrenocortical estrogen sulfotransferase.

Complementary DNA for the guinea pig adrenocortical estrogen sulfotransferase (EST) has been cloned and expressed. Oligonucleotides, based on amino acid sequences of the purified 34-kilodalton protein, were synthesized and used to generate a specific probe by polymerase chain reaction for screening a guinea pig adrenal cDNA library. The polymerase chain reaction rapid amplification of cDNA ends procedure was employed to obtain the 3' and 5' cDNA ends, and a full-length cDNA was constructed. The cloned cDNA consists of 1192 base pairs and encodes a protein of 296 amino acids with a calculated molecular mass of 35,161 daltons. A computer search of the protein data banks revealed significant homology with several sulfotransferases: 71% with bovine placental estrogen sulfotransferase, 52% with rat liver phenol sulfotransferase, 35% with rat liver hydroxysteroid sulfotransferase, and 36% with rat liver senescence marker protein 2. The EST cDNA was inserted into the pcDNA I eukaryotic expression vector and transfected into COS-7 cells. The successful expression of EST cDNA in COS-7 cells was ascertained by Western blot analysis using antibody generated against the protein used to obtain the original amino acid sequence. Additionally, the expressed protein was clearly functional. Only after transfection with EST cDNA was there detectable estradiol sulfotransferase activity in COS-7 cell cytosol. The expressed EST had a single pI of 6.4, whereas native guinea pig adrenocortical EST exhibits four primary charge isoforms. The majority of adrenocortical EST activity focuses as a broad bimodal band in the pH range of 6.6-6.2; additionally, three other discrete immunocross-reactive isoforms are present with pIs of 5.5, 5.4, and 5.2. Antibodies generated against each individual isoform cross-react with all the other isoforms and with the expressed protein. These isoforms were previously reported to be isomers of a pregnenolone-binding protein; however it is now evident that the isoforms and antibodies raised against them are EST specific. Under high stringency hybridization conditions, EST mRNA was only detected in the adrenal gland, where two mRNA species of 1.4 and 1.8 kilobases were evident; when low stringency conditions were used, a faint 1.4-kilobase band was also detected in the liver. Primer extension analysis revealed that the multiple mRNAs do not arise from differential transcription initiation sites, and genomic Southern blot analysis indicated that the multiple mRNAs arise from a single gene.

Adrenal Cortex↗

PubMed1988

Molecular cloning of the complementary DNA for a human folate binding protein.

The complementary DNA for a human folate binding protein has been cloned from a lambda gt11-cDNA library prepared from cultured KB cells. A number of clones were selected by immunoscreening with a monospecific antiserum and by oligonucleotide probes corresponding to the NH2-terminal sequence of the folate binding protein. A partial nucleotide sequence of the cDNA was determined directly from the lambda gt11 phage and after subcloning into M13. The 18 amino acids deduced from the initial 19 codons were exactly the same as the amino acid sequence obtained by peptide analysis of the purified protein providing proof that this clone is the folate binding protein cDNA.

Amino Acid Sequence↗

PubMed1996

Nucleotide sequence analysis of a complementary DNA coding for a Blomia tropicalis allergen.

Blomia tropicalis is a mite of allergenic importance in tropical and subtropical areas. A clone (Bt11a) from a B. tropicalis complementary DNA library was expressed in lambda phage and analyzed by plaque radioimmunoassay. The recombinant allergen produced by this clone was bound by IgE in 16 of 32 sera from individuals with asthma with a positive RAST response and none of 3 control sera from healthy individuals with negative RAST response to B. tropicalis. The cDNA insert was amplified by polymerase chain reaction with use of universal primers. A 582-base-pair (bp) fragment was cloned into a pCR II vector. The complete sequence of both strands was determined by using T7, SP6, and internal primers. The sequence shows a 432 bp reading frame with a 34 bp 5' untranslated region and a 116 bp 3' untranslated region with a poly A tail. Analysis of the sequence suggests that it encodes a putative signal peptide of 20 residues and a 124-residue mature protein allergen of 14,206 Da. The nucleotide and the inferred amino acid sequences did not show homology to any known sequence. No potential N-linked glycosylation site was found. The recombinant protein appears to represent a major allergen of the mite B. tropicalis.

Adult↗

PubMed1999

Construction and sequence analysis of subtraction complementary DNA libraries from human preimplantation embryos.

PURPOSE: Because stage-specific genetic expression in human preimplantation development is not sufficiently studied, we have undertaken the construction of a subtraction complementary DNA (cDNA) library enriched for transcripts specific for human blastocysts. METHODS: For this purpose individual pools of cDNAs synthesized from four hatched blastocysts and three cleaving 8- to 10-cell embryos were exposed to suppression subtractive hybridization to minimize the presence of transcripts of housekeeping genes and other genes of maternal origin known to be expressed earlier in preimplantation development. Random clones of this library were sequenced and analyzed using the BLAST algorithm. RESULTS: The resulting subtraction library had a complexity of 3 x 10(5) and an average size of inserts of about 0.8 kb. Sequencing of random library clones revealed the following human genes: CD9 antigen, fatty acid binding protein, ferritin heavy chain, amyloid precursor, MAP kinase messenger RNAs, DNA clone 127H14, messenger RNA for diacylglycerol kinase, a sequence homologous to C1 inhibitor, messenger RNA for the KIAA0145 gene, and others. CONCLUSIONS: The presence of these genes in human preimplantation development suggests expression specific to the blastocyst stage.

Algorithms↗

PubMed2004

Complementary DNA cloning of rat spetex-1, a spermatid-expressing gene-1, encoding a 63 kDa cytoplasmic protein of elongate spermatids.

We used differential display in combination with complementary DNA (cDNA) cloning approach to isolate a novel rat gene designated as spetex-1, which had an open reading frame of 1,668-length nucleotides encoding a protein of 556 amino acids. Spetex-1 mRNA was highly expressed in testis, and weekly expressed in lung, intestine, and spleen. Spetex-1 expression in the rat testes was detected first at 3 weeks in postnatal development and continued to be detected up to adulthood. A search in the databases showed that the amino acid sequence of spetex-1 was 82% identical to that of its mouse homologue found in the databases. Both rat spetex-1 and the mouse homologue contained Ser-X (X = His, Arg, or Asn) repeats in the middle portion of the proteins. In situ hybridization revealed that spetex-1 mRNA was expressed in haploid spermatids of step 7-18 within the seminiferous epithelium. Immunohistochemical analysis with confocal laser-scanning microscopy demonstrated that spetex-1 protein was not expressed in spermatogonia, spermatocytes, and round spermatids in adult rat testis, but was specifically detected in the residual cytoplasm of elongate spermatids of step 15-18 as well as in residual bodies engulfed by Sertoli cells. We interpreted these data as a potential role of spetex-1 in spermatogenesis, especially in cell differentiation from late elongate spermatids to mature spermatozoa.

Amino Acid Sequence↗

PubMed1998

Cloning of a full-length insulin-like growth factor-I complementary DNA in the goldfish liver and ovary and development of a quantitative PCR method for its measurement.

Five forms of insulin-like growth factor-I (IGF-I) complementary DNA (cDNA) were isolated by PCR from goldfish liver and ovary, using primers based on common carp IGF-I sequence. In the goldfish liver, we cloned and sequenced three IGF-I forms (1,2, and 3), and elucidated the full-length cDNA sequence using the 5'-and 3'-RACE. Two IGF-I forms (1 and 2) were cloned from the goldfish ovary and were found to have differences with respect to both size and nucleotide sequence compared to liver IGF-I. The entire liver IGF-I form 1 sequence was found to be 833 nucleotides long, containing a 483-nucleotide open reading from encoding 161 amino acids. The deduced amino acid sequence of the mature peptide was compared to IGF-I sequences of other vertebrates, and found to have 97 and 93% similarity to carp and salmon IGF-I, respectively, In this study we also developed a competitive quantitative PCR method and demonstrated an increase in IGF-I expression following treatments with growth hormone or gonadotropin-releasing hormone in the goldfish liver.

Amino Acid Sequence↗