SEARCH · PubMed Health

Results for “DNA, Complementary”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 1,423 records · Page 79Linked to original sources

PubMed1998

Sequences of cDNAs encoding calmodulin, and partial structures of calmodulin kinase, and a calcium channel of kdr-resistant and -susceptible German cockroaches, Blattella germanica.

Complementary DNA sequences of genes encoding calmodulin, partial structures of calmodulin-dependent protein kinase II (CaM-kinase II) and an L-type-like calcium channel al subunit (IVS5-IVS6-EF hand region) were identified and compared between susceptible and kdr strains of German cockroach, Blattella germanica. For this purpose, polymerase chain reactions (PCR) were used to obtain their sequences using cDNA from poly(A) + RNA isolated from their heads and thoraces. No mutation differences were found in all three sequences of calcium-regulating proteins between susceptible and strain. Northern blot analysis, however, showed reduced expressions of CaM-kinase II mRNA in two kdr strains. Western blot analysis with an antibody preparation against CaM-kinase II on protein levels confirmed the above strain difference in the titer of this enzyme. In contrast, the levels of calmodulin as well as that of an L-type-like calcium channel gene expression were not different between susceptible and kdr strains.

Amino Acid Sequence↗

PubMedDate not supplied

Cucumber mosaic virus from Ixora: infectious RNA transcripts confirm deficiency in satellite support and unusual symptomatology.

A cucumber mosaic virus isolate from an Ixora plant originating in the Philippines and first described 20 years ago (CMV-Ix) by Waterworth and Povish differs from other characterized CMV strains in its anomalous satellite support and in several biological and molecular properties. We describe the preparation of infectious transcripts from cloned complementary DNA and the characterization of progeny virus. The results confirm that CMV-Ix has a more limited host range than most CMV isolates. Virions of CMV-Ix are smaller than those of the control CMV-S, independent of the type of negative stain used. Furthermore, CMV-Ix from transcripts supports the replication of the satellite T-CARNA 5 but not of D-CARNA 5.

Cloning, Molecular↗

PubMed2000

Synthesis and hybridization properties of polyamide based nucleic acid analogues incorporating pyrrolidine-derived nucleoamino acids.

Ndelta-Fmoc protected nucleoamino acids of type I (Base = T, C, A) have been synthesized and employed as building blocks for the construction of novel polyamide based nucleic acid analogues. Homopyrimidine oligomer A binds to complementary RNA with significant affinity and in a sequence-specific fashion, while no binding was observed to complementary DNA.

Amino Acids↗

PubMed2003

Oligonucleotides containing a new type of acyclic, achiral nucleoside analogue: 1-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]thymine.

An achiral, acyclic nucleoside analogue has been incorporated once or twice in oligodeoxyribonucleotides by the phosphoramidite method, and conditions found which allow deprotection of the oligonucleotides containing a sensitive modified allylic unit. The binding affinity of the modified oligonucleotides towards complementary DNA and RNA was reduced compared to unmodified DNA (DeltaT(m) -2 to -6.5 degrees C). An oligonucleotide with two modifications at the 3'-end showed considerable resistance towards cleavage with a 3'-exonuclease.

Animals↗

PubMed1997

Use of cDNA-expressed human cytochrome P450 enzymes to study potential drug-drug interactions.

Complementary DNA (cDNA)-expressed human cytochrome P450 enzymes provide a reproducible, consistent source of single enzymes for many types of studies. The use of single enzymes systems, relative to multienzyme systems, has distinct advantages and disadvantages depending on the specific application. cDNA-expressed materials have advantages in the analysis of cytochrome P450 form-selective metabolism of a drug or drug candidate. This analysis can be accomplished by direct incubation of the drug with microsomes prepared from cells expressing a single cytochrome P450 form coupled with analysis of either metabolite formation or loss of parent compound. This approach allows the unambiguous assignment of specific biotransformations to specific enzymes. However, extending these data to the balance of enzymes present in human liver microsomes can be problematic. New approaches for relating rates of metabolism for cDNA-expressed enzymes to human liver microsomes metabolism are being developed (Crespi, 1995). In addition, cDNA-expressed enzymes can be used to study the cytochrome P450 form-selective inhibition by drugs or drug candidates. This analysis is accomplished through the study of the inhibition of the metabolism of a model substrate by the drug or drug candidate. Through these analyses, apparent Ki values can be obtained and compared to Ki values for known, clinically significant inhibitors of the same enzyme. For this application, cDNA-expressed, single enzyme systems have distinct advantages because of greater flexibility in the choice of model substrates and the lack of competing pathways of metabolism. Specific data for the use of cDNA-expressed CYP2C9, CYP2D6, and CYP3A4 are presented.

Aryl Hydrocarbon Hydroxylases↗

PubMed2001

Molecular cloning and sequence of gilthead sea bream (Sparus aurata) alpha-skeletal actin: tissue and developmental expression.

In the present study, the Sparus aurata alpha-skeletal actin was cloned from a mixed larvae complementary DNA library. The clone isolated was 1523 bp long with an open reading frame of 1134 bp coding for a 377-amino acid protein. The deduced amino acid sequence of sea bream alpha-actin is identical to Fugu alpha-actin-1. The expression of alpha-actin was initiated at the onset of segmentation. In adult fish, alpha-actin is expressed predominantly in white and red muscle.

Actins↗

PubMed1999

Predicting oligonucleotide affinity to nucleic acid targets.

A computer program, OligoWalk, is reported that predicts the equilibrium affinity of complementary DNA or RNA oligonucleotides to an RNA target. This program considers the predicted stability of the oligonucleotide-target helix and the competition with predicted secondary structure of both the target and the oligonucleotide. Both unimolecular and bimolecular oligonucleotide self structure are considered with a user-defined concentration. The application of OligoWalk is illustrated with three comparisons to experimental results drawn from the literature.

Base Sequence↗

PubMed1994

Cis,cis-muconate lactonizing enzyme from Trichosporon cutaneum: evidence for a novel class of cycloisomerases in eucaryotes.

The absolute stereochemical courses of cis,cis-muconate lactonizing enzyme (MLE;EC 5.5.1.1) from Trichosporon cutaneum (TcMLE) and chloromuconate cycloisomerase (MLE II; EC 5.5.1.7) from Pseudomonas sp B13 have been determined from 1H NMR measurements. Both cycloisomerases convert cis,cis-muconate to (4S)-muconolactone by a syn lactonization, the absolute stereochemical outcome of which is identical to that observed with MLE from Pseudomonas putida. The regiochemical courses of cyclization of 3-halo-cis,cis-muconates by TcMLE and MLE II have been characterized and shown to differ in a halogen substituent dependent manner, suggesting at least a different active site architecture of the two MLEs. Moreover, the regiochemical preferences of MLE II and TcMLE parallel results previously observed for the nonenzymatic lactonization of the 3-halomuconates at pH 1-6 and in concentrated HCl, respectively, in which alternate mechanisms of cyclization were proposed [Pieken, W. A., & Kozarich, J. W. (1990) J. Org. Chem. 55, 3029-3035]. Complementary DNA clones encoding TcMLE have been isolated from phenol induced T. cutaneum cDNA using the polymerase chain reaction. The deduced amino acid sequence does not exhibit any similarity to that of MLE from P. putida. It does however, exhibit moderate sequence similarity (21% residue identity, 14 gaps) with 3-carboxy-cis,cis-muconate lactonizing enzyme (CMLE; EC 5.5.1.5) from Neurospora crassa, which catalyzes a regiochemically analogous and stereochemically identical lactonization reaction with 3-carboxymuconate. The limited data available suggest that the fungal CMLE and yeast MLE are representative of a unique class of eucaryotic cycloisomerases which have evolved convergently with the bacterial MLEs.

Amino Acid Sequence↗

PubMed1994

Human cyclophilin C: primary structure, tissue distribution, and determination of binding specificity for cyclosporins.

A complementary DNA (cDNA) for human cyclophilin C (Cyp-C) was isolated from a human kidney cDNA library. Northern blot experiments with several human tissues and cell lines revealed that Cyp-C is less abundant than Cyp-A. The amount of Cyp-C mRNA was 10-fold lower than that of Cyp-A in kidney. Expression of human Cyp-C in the kidney is not significantly elevated compared to pancreas, skeletal muscle, heart, lung, and liver. This argues against a previously postulated specific role for Cyp-C in the nephrotoxic effects of CsA in humans, based on the studies of its relative abundance in murine kidney. It is present in extremely low concentrations in brain and in the Jurkat T cell line. The binding of recombinant human Cyp-A, -B, and -C to cyclosporin A (CsA) was studied by immunochemical methods. The relative affinity of Cyp-C for CsA is lower by a factor of 2 than that of Cyp-A, which itself is 10-fold lower than that of Cyp-B. Cross-reactivity studies with a series of Cs derivatives showed that Cyp-C binds CsA with a fine specificity similar to that of Cyp-A and Cyp-B. Cs amino acid residues 1, 2, 10, and 11 seemed essential for the interaction with all three Cyp subtypes. However, Cyp-C tolerates a greater variety of structures on Cs at position 2 than Cyp-A does, suggesting that this residue of CsA might not be in tight contact with Cyp-C. This was confirmed by modeling of human Cyp-C on the structure of the complex formed by Cyp-A and CsA. The knowledge of the fine specificity of human Cyps for CsA and of their expression levels may provide better insights into how CsA acts on its different target proteins in vivo.

Amino Acid Isomerases↗

PubMed1998

Characterization of molecular defects in isovaleryl-CoA dehydrogenase in patients with isovaleric acidemia.

Isovaleryl-CoA dehydrogenase (IVD) is a homotetrameric mitochondrial flavoenzyme which catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA. PCR of IVD genomic and complementary DNA was used to identify mutations occurring in patients with deficiencies in IVD activity. Western blotting, in vitro mitochondrial import, prokaryotic expression, and kinetic studies of IVD mutants were conducted to characterize the molecular defects caused by the amino acid replacements. Mutations leading to Arg21Pro, Asp40Asn, Ala282Val, Cys328Arg, Val342Ala, Arg363Cys, and Arg382Leu replacements were identified. Western blotting of fibroblast extracts and/or in vitro mitochondrial import experiments indicate that the seven precursor IVD mutant peptides, and a previously identified IVD Leu13Pro mutant, are synthesized and imported into mitochondria. While the IVD Leu13Pro, Arg21Pro, and Cys328Arg mutant peptides are rapidly degraded following mitochondrial import, the other mutant peptides exhibit greater mitochondrial stability, though less than the wild-type enzyme. Active IVD Ala282Val, Val342Ala, Arg363Cys, and Arg382Leu mutants were less stable than wild type when produced in Escherichia coli. The Km values of purified IVD Ala282Val, Val342Ala, and Arg382Leu mutants are 27.0, 2. 8, and 6.9 microM isovaleryl-CoA, respectively, compared to 3.1 microM for the wild type, using the electron-transfer flavoprotein (ETF) fluorescence quenching assay. The catalytic efficiency per mole of FAD content of these three mutants is 4.8, 17.0, and 17.0 microM-1*min-1, respectively, compared to 170 microM-1*min-1 for wild type.

Amino Acid Metabolism, Inborn Errors↗

PubMed2003

Structure-switching signaling aptamers.

Aptamers are single-stranded nucleic acids with defined tertiary structures for selective binding to target molecules. Aptamers are also able to bind a complementary DNA sequence to form a duplex structure. In this report, we describe a strategy for designing aptamer-based fluorescent reporters that function by switching structures from DNA/DNA duplex to DNA/target complex. The duplex is formed between a fluorophore-labeled DNA aptamer and a small oligonucleotide modified with a quenching moiety (denoted QDNA). When the target is absent, the aptamer binds to QDNA, bringing the fluorophore and the quencher into close proximity for maximum fluorescence quenching. When the target is introduced, the aptamer prefers to form the aptamer-target complex. The switch of the binding partners for the aptamer occurs in conjunction with the generation of a strong fluorescence signal owing to the dissociation of QDNA. Herein, we report on the preparation of several structure-switching reporters from two existing DNA aptamers. Our design strategy is easy to generalize for any aptamer without prior knowledge of its secondary or tertiary structure, and should be suited for the development of aptamer-based reporters for real-time sensing applications.

Adenosine Triphosphate↗

PubMed2000

Molecular cloning, characterization, and expression of a cDNA coding Copper/Zinc superoxide dismutase from black porgy.

A full-length complementary DNA (cDNA) clone encoding a putative copper/zinc superoxide dismutase (Cu/Zn-SOD) was amplified by a Polymerase Chain Reaction (PCR) based technique from cDNA synthesized from black porgy, Acanthopagrus schlegeli, mRNA. Nucleotide sequence analysis of this cDNA clone revealed that it comprised a complete open reading frame coding for 154 amino acid residues. The deduced amino acid sequence showed slightly higher identity (72.8-78.1%) with shark and swordfish Cu/Zn-SOD than with Cu/Zn-SOD from mammalian (68.1-70.7%) and plant (55.5-56.5%) sources. The residues required for coordinating copper and zinc are conserved as they are among all reported Cu/Zn-SOD sequences. The deduced amino acid sequence lacks mitochondria targeting sequence, which suggests that the black porgy cDNA clone encodes a cytosolic Cu/Zn-SOD. The coding region of Cu/Zn-SOD from black porgy was introduced into an expression vector, pET-20b(+), and transformed into Escherichia coli AD494(DE3)pLysS. A predominant achromatic zone was detected by activity staining of native PAGE. This indicates that the Cu/Zn-SOD cDNA clone can express active Cu/Zn-SOD enzyme in E. coli.

Amino Acid Sequence↗

PubMed2000

Cloning and expression of a cDNA coding for catalase from zebrafish (Danio rerio).

A full-length complementary DNA (cDNA) clone encoding a catalase was amplified by the rapid amplication of cDNA ends-polymerase chain reaction (RACE-PCR) technique from zebrafish (Danio rerio) mRNA. Nucleotide sequence analysis of this cDNA clone revealed that it comprised a complete open reading frame coding for 526 amino acid residues and that it had a molecular mass of 59 654 Da. The deduced amino acid sequence showed high similarity with the sequences of catalase from swine (86.9%), mouse (85.8%), rat (85%), human (83.7%), fruit fly (75.6%), nematode (71.1%), and yeast (58.6%). The amino acid residues for secondary structures are apparently conserved as they are present in other mammal species. Furthermore, the coding region of zebrafish catalase was introduced into an expression vector, pET-20b(+), and transformed into Escherichia coli expression host BL21(DE3)pLysS. A 60-kDa active catalase protein was expressed and detected by Coomassie blue staining as well as activity staining on polyacrylamide gel followed electrophoresis.

Amino Acid Sequence↗

PubMed2001

Synthesis and properties of peptide nucleic acids containing a psoralen unit.

We prepared the psoralen PNA unit from 8-methoxypsoralen and synthesized various PNAs containing psoralen by a typical (t)()Boc method. PNAs containing psoralen (P-PNA) at strand end formed a stable duplex with complementary DNA. The hybridization of P-PNA with complementary DNA resulted in a considerable decrease of the psoralen fluorescence.

Base Sequence↗

PubMed2003

Synthesis and incorporation into PNA of fluorinated olefinic PNA (F-OPA) monomers.

[structure: see text] A fluorinated OPA monomer containing the base thymine ((Z)-t-F-OPA) was synthesized in 12 steps, featuring a highly selective allylic over homoallylic Mitsunobu substitution for the introduction of the nucleobase. F-OPA modified PNA decamers were prepared by the MMTr/acyl protection strategy. The thermal stability of duplexes of PNA decamers containing (Z)-t-F-OPA units with antiparallel complementary DNA was measured. We found a strong dependence of stability from the sequential position of the (Z)-t-F-OPA units, ranging from DeltaT(m) of +2.4 to -8.1 degrees C/modification relative to unmodified PNA.

Alkenes↗

PubMed2003

(1S,2R/1R,2S)-ainocyclohexyl glycyl thymine PNA: synthesis, monomer crystal structures, and DNA/RNA hybridization studies.

[structure: see text] The synthesis of ethyl cis-(1S,2R/1R,2S)-2-aminocyclohex-1-yl-N-(thymin-1-yl-acetyl) glycinate (10a and 10b) via enzymatic resolution of the key racemic intermediate trans-2-azido cyclohexanols 3 is reported. The crystal structures of 10 show equatorial disposition of the tertiary amide group, with the torsion angle beta in the range 60-70 degrees. The PNA oligomers incorporating these show differential effects in hybridizing with complementary DNA and RNA.

Burkholderia cepacia↗

PubMed1998

Molecular characterization of a single mitochondria-associated double-stranded RNA in the green alga Bryopsis.

Mitochondria from the green alga Bryopsis sp. very often contained a 4.5 kb double-stranded RNA (dsRNA) at a defined level. Complementary DNA probes derived from the mitochondrial dsRNA hybridized with none of the algal chloroplast dsRNAs of 1.7 to 2.2 kb, but did hybridize with a similar-sized dsRNA among several dsRNAs from the mitochondria of B. maxima. Sequence analysis of the mitochondrial dsRNA from Bryopsis sp. revealed only two large, overlapping, open reading frames (ORFs) on one strand if UGA was taken as a non-termination codon, suggesting the independent phylogenetic evolution of the mitochondrial dsRNA. Consensus sequence for RNA-dependent RNA polymerase was found within the longer ORF (2472 bp) of the dsRNA. The overlapping 52 bp of the ORFs in different reading frames is suggestive of the occurrence of a -1 ribosomal frameshift in the mitochondrial translation system. The observed simple genetic structures suggest that the algal mitochondrial dsRNA might be deficient in a gene for movement from cell to cell in host plants and, hence, has a plasmid-like nature that is distinct from that of infectious plant viruses. The nature and origin of the endogenous dsRNAs of various sizes and their relationships are discussed.

Amino Acid Sequence↗

PubMed2000

Characterisation of complementary DNAs from the expressed sequence tag analysis of life cycle stages of Laminaria digitata (Phaeophyceae).

Laminariales (Phaeophyceae, Heterokonta) are characterised by a heteromorphic digenetic life cycle with a filamentous, microscopic gametophyte and a highly evolved, macroscopic sporophyte. With the ultimate goal of comparing gene expression in each life cycle stage, complementary DNA libraries were constructed from sporophytes and gametophytes of Laminaria digitata. A set of ca. 500 expressed sequence tags (EST) was generated from each life history phase, by single-run partial sequencing of randomly picked cDNA clones. Comparison of the EST deduced amino acid sequences with database protein sequences assigned a putative identity for 39% of the 412 gametophyte clones and 48% of the 493 sporophyte clones sequenced thus far. These data represent more than 152 different proteins now probably identified in L. digitata. Several of those newly identified proteins are of interest to our understanding of the molecular physiology of kelps, for example their carbon-concentrating mechanisms, cell wall biosynthesis and halogen metabolism. EST analysis also confirmed that genes with long 3'-UTRs are widespread in Laminariales and the study of 5'-UTRs allowed the identification of a Kozak consensus sequence, c(A/C)A(A/C)CAUGGc(G/T). Several potential developmentally regulated differences in gene expression are discussed.

Algal Proteins↗