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Results for “RNA, Complementary”

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At least 487 records · Page 27Linked to original sources

PubMed2001

Site-selective artificial ribonuclease using pinpoint RNA activation.

An acridine residue attached to the end or the inside of a DNA activates the target phosphodiester linkages in complementary RNA. Due to this pinpoint activation, the RNA is site-selectively and efficiently cleaved at these linkages by various free metal ions under mild condition. Spectroscopic analyses show that the acridine moiety is sandwiched between neighboring bases, and pushes the opposite nucleotide out of the hetero-duplex.

Acridines↗

PubMed1983

Transfer of the Epstein-Barr virus genes coding for small RNAs to human lymphoid cells with a vector carrying a dominant selectable marker.

Epstein-Barr virus (EBV)-negative, Burkitt-like lymphoma-derived cells were transformed with a transducing vector (pSV2-gpt) containing the Escherichia coli gene coding for xanthine-guanine phosphoribosyltransferase (XGPRT) and with a derivative of PSV2-gpt that carries the genes for the EBV-associated small RNAs on the EcoRI J fragment of B95-8 EBV DNA inserted at the unique EcoRI site (pJ-gpt). Cells transformed with PSV2-gpt and pJ-gpt express the E. coli gpt gene to approximately the same extent, judged by determinations of the XGPRT activity of cell extracts. Blot hybridisation experiments with restriction endonuclease-cleaved DNA from the transformants have revealed the presence of vector DNA sequences in the cells, at least some of which are most probably integrated into high mol. wt. chromosomal DNA. Northern blot hybridisation analysis of cytoplasmic RNA from pJ-gpt-transformed cells revealed the presence of an EcoRI J DNA complementary RNA species of the same size as the EBV DNA-encoded small RNAs found in EBV-transformed cells.

Burkitt Lymphoma↗

PubMed1985

Sequence of the nucleoprotein gene of influenza A/parrot/Ulster/73.

The nucleotide sequence of the nucleoprotein (NP) gene of the avian influenza A virus strain A/parrot/Ulster/73 (H7N1) has been determined. The gene (RNA segment 5) consists of 1565 bases. The only large open reading frame of the complementary RNA codes for a protein of 498 amino acids. A comparison of its sequence with that of three other influenza virus NPs shows that the NP of the parrot Ulster strain, although closely related to the NP of the other avian strain (A/FPV/Rostock/34), is definitely more closely related genetically to the NPs of the two human influenza strains, A/PR/8/34 and A/NT/60/68 than that of FPV. This raises the question how far the NP gene can cross the species barrier by reassortment and become adapted by mutation to the new host.

Amino Acid Sequence↗

PubMed1987

The cellular localization of preprotachykinin A messenger RNA in the bovine nervous system.

The cellular distribution of preprotachykinin A messenger RNA in the bovine nervous system was investigated by in situ hybridization and its tissue distribution by Northern and dot blotting. The latter results were compared with the levels of substance P-like immunoreactivity as determined by radio-immunoassay. The highest levels of preprotachykinin A messenger RNA were found in striatum and trigeminal ganglion, medium levels in retina and lower levels in hypothalamus, spinal cord, pituitary gland and adrenal medulla. The cellular localization of preprotachykinin A messenger RNA was obtained in striatum and trigeminal ganglion using either single-stranded DNA or complementary RNA probes labelled with 32P, 35S or 3H. Specific labelling of small trigeminal ganglion neurones and of medium-sized striatal nerve cells was observed with probes in the anti-messenger RNA sense orientation. Only background labelling was obtained with probes in the messenger RNA sense orientation. The technique was further validated by the demonstration that the same cells in the trigeminal ganglion were labelled by both in situ hybridization and immunohistochemistry. The present findings allow an unambiguous identification of the cellular sites of synthesis of preprotachykinin A messenger RNA; in situ hybridization should also prove a useful technique for investigating the regulation of neuropeptide biosynthesis at the cellular level.

Animals↗

PubMed2006

Inhibition of respiratory syncytial virus in cultured cells by nucleocapsid gene targeted deoxyribozyme (DNAzyme).

Respiratory syncytial virus (RSV), which presents the primary cause of bronchiolitis and pneumonia among infants and causes significant morbidity and mortality in immunodeficient patients, remains a health problem worldwide. Unfortunately, an effective vaccine is currently unavailable and pharmacologic treatment needs further optimization for RSV disease. Because RSV is a non-segmented negative-strand RNA virus, it may be sensitive to the genome RNA cleaving by DNAzyme, an artificial nucleic acids molecule with high catalytic capability of cleaving complementary RNA molecules. Thus, RSV-targeted DNAzymes potentially present as a therapeutic candidate of RSV diseases. In this study, DNAzymes targeting the RSV genomic RNA or mRNA were designed and synthesized, one of which (DZn1133) did cleave RSV RNA in vitro, inhibit the transcription and expression of F viral gene, reduce the RSV yield by about 7 logs and protect more than 90% RSV-infected Hep-2 cells from a cytopathic effect at 8 microM. Moreover, 10 wild RSV strains isolated from clinic patients including both subgroups A and B were all suppressed by DZn1133 with greater anti-RSV activity than antisense DNA or ribavirin.

Base Sequence↗

PubMed1991

Identification and analysis of antisense RNA target regions of the human immunodeficiency virus type 1.

Antisense RNA, transcribed intracellularly from constitutive expression cassettes, inhibits the replication of the human immunodeficiency virus type 1 (HIV-1) as demonstrated by a quantitative microinjection assay in human SW480 cells. Infectious proviral HIV-1 DNA was co-microinjected together with a fivefold molar excess of plasmids expressing antisense RNA complementary to a set of ten different HIV-1 target regions. The most inhibitory antisense RNA expression plasmids were targeted against a 1 kb region within the gag open reading frame and against a 562 base region containing the coding sequences for the regulatory viral proteins tat and rev. Experimental evidence is presented that the antisense principle is the inhibitory mechanism in this assay system.

Cell Line↗

PubMed1993

In borna disease virus infected rabbit neurons 100 nm particle structures accumulate at areas of Joest-Degen inclusion bodies.

Borna disease virus infected rabbits were chosen to search for electronmicroscopic structures. Intensively investigated hippocampal neurons showed intranuclear inclusions; 100 nm particle-like structures surrounded by 20 nm granular forms were prominent. In connection with elsewhere reported in situ hybridization studies of virus-specific RNA to areas of the Joest-Degen inclusions we suggest that these particle structures may represent Borna virus. Jost-Degen (8) found intranuclear inclusion bodies in neurons to be pathognomonic for Borna disease (BD) in the horse. Half a century later these structures were suggested to represent BD virus (BDV)-specific antigen aggregates (15). A century later we characterized the virus to contain a single and negative stranded RNA of 8.5 kb, which transcribes in the nucleus (5) and could show that virus complementary RNA seems to hybridize spot-like to nuclear areas, probably representing the Jost-Degen inclusions (7). Electron microscopic (EM) findings on structures in BDV infected brain cells and about particle-like structures obtained from infected tissue culture cells have been reported by different groups (1, 2, 3, 4, 5, 6, 9, 11, 12, 13). The demonstration of crystalline aggregates and filament bundles in the cytoplasma and karyospheridia (nuclear bodies) were prominent. Such structures were seen in infected rabbits, hamsters, rats mice and naturally infected horses. The phenotypic description of filamentous structures, crystalline aggregates in the cytoplasma and large karyospheridia were prominent. Based on our experience with BDV infections in rabbits we selected this species for ultrastructural studies.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1992

Differential expression of a Clostridium acetobutylicum antisense RNA: implications for regulation of glutamine synthetase.

The Clostridium acetobutylicum glutamine synthetase (GS) DNA region is characterized by a downstream promoter, P3, oriented toward the glnA gene, which controls the transcription of an RNA complementary to the start of the glnA mRNA. Expression of the predicted 43-base antisense RNA was demonstrated in C. acetobutylicum and Escherichia coli cells containing the cloned glnA DNA. Antisense RNA transcription from P3 was not regulated by nitrogen in E. coli cells, but the expression of antisense RNA was associated with decreased levels of GS activity. In C. acetobutylicum, GS activity and the transcription of glnA mRNA and antisense RNA were regulated by nitrogen. GS activity and glnA mRNA were repressed in cells grown in nitrogen-rich medium. Repression ratios for GS activity varied from 1.6 to 9.0, depending on the sampling time. The relative number of glnA transcripts was approximately 25% lower in cells grown for 72 h in nitrogen-rich medium than in cells grown in nitrogen-limiting medium. This finding contrasted with the expression of antisense RNA, which was repressed in nitrogen-limiting medium but induced in nitrogen-rich medium. The relative number of antisense RNA transcripts was increased approximately sixfold in cells grown in nitrogen-rich medium. There was a 1.6-fold excess of antisense RNA over glnA mRNA under conditions that repressed GS activity. Under conditions that induced GS activity, glnA mRNA transcripts exceeded antisense RNA transcripts by fivefold.

Base Sequence↗

PubMed1999

Crystal structure of an RNA duplex r(G GCGC CC)2 with non-adjacent G*U base pairs.

The crystal structure of a self-complementary RNA duplex r(GGGCGCUCC)2with non-adjacent G*U and U*G wobble pairs separated by four Watson-Crick base pairs has been determined to 2.5 A resolution. Crystals belong to the space group R3; a = 33.09 A,alpha = 87.30 degrees with a pseudodyad related duplex in the asymmetric unit. The structure was refined to a final Rworkof 17.5% and Rfreeof 24.0%. The duplexes stack head-to-tail forming infinite columns with virtually no twist at the junction steps. The 3'-terminal cytosine nucleosides are disordered and there are no electron densities, but the 3' penultimate phosphates are observed. As expected, the wobble pairs are displaced with guanine towards the minor groove and uracil towards the major groove. The largest twist angles (37.70 and 40.57 degrees ) are at steps G1*C17/G2*U16 and U7*G11/C8*G10, while the smallest twist angles (28.24 and 27.27 degrees ) are at G2*U16/G3*C15 and C6*G12/U7*G11 and conform to the pseudo-dyad symmetry of the duplex. The molecule has two unequal kinks (17 and 11 degrees ) at the wobble sites and a third kink at the central G5 site which may be attributed to trans alpha (O5'-P), trans gamma (C4'-C5') backbone conformations. The 2'-hydroxyl groups in the minor groove form inter-column hydrogen bonding, either directly or through water molecules.

Base Pairing↗

PubMed1993

Antisense oligonucleotides made of 2'-O-alkylRNA: their properties and applications in RNA biochemistry.

Oligo(2'-O-alkylribonucleotides) have been developed recently as novel oligonucleotide analogues with properties that enhance their use as antisense probes. They possess high chemical stability and are resistant to hydrolysis by DNA- or RNA-specific nucleases. Many forms of oligo(2'-O-alkylribonucleotides) hybridise specifically and efficiently to complementary RNA sequences, forming stable duplexes that are not substrates for cleavage by RNAse H. In combination with prosthetic reporter groups, such as biotin, DNP or fluorophores, oligo(2'-O-alkylribonucleotides) have important applications in a wide range of biochemical studies on RNA function and structure.

Alkylation↗

PubMed1986

Nucleotide sequence of the Bunyamwera virus M RNA segment: conservation of structural features in the Bunyavirus glycoprotein gene product.

The complete nucleotide sequence of the Bunyamwera virus M RNA segment was determined from four overlapping cDNA clones and by primer extension. The RNA segment is 4458 bases in length, and encodes a single gene product in the viral complementary RNA. The predicted protein is 1433 amino acids long (mol wt 162,065), contains four potential glycosylation sites, and is relatively cysteine rich. It is presumed that the three proteins G1, G2, and NSM which have been mapped to the M RNA segment are synthesized as a precursor polyprotein which is subsequently proteolytically cleaved. A putative hydrophobic signal sequence at the amino terminus and a hydrophobic anchor sequence at the carboxy terminus of the predicted protein have been identified, in addition to internal regions of hydrophobicity of unknown function. The nucleotide and amino acid sequences of the Bunyamwera virus M segment have been compared with those of the snowshoe hare virus M segment (Y. Eshita and D. H. L. Bishop, Virology 137, 227-240, 1984). Common features include the overall architecture of the RNAs, single cysteine-rich primary gene products, and conservation of hydrophobic domains in the gene products. When aligned the amino acid sequences are 43% homologous, and 66 of 70 cysteine residues can be matched. The evolutionary significance of these findings is discussed.

Amino Acid Sequence↗

PubMed1995

Growth inhibition of MCF-7 breast cancer cells by stable expression of an insulin-like growth factor I receptor antisense ribonucleic acid.

Insulin-like growth factors (IGFs) play an important role in cellular proliferation, and IGF action appears to be involved in tumorigenesis. To determine the role of the IGF-I receptor in breast cancer cell growth, we stably transfected MCF-7 breast cancer cells with a construct encoding an antisense RNA complementary to the region surrounding the translation initiation site of the IGF-I receptor messenger RNA (mRNA). Control cells were transfected with vector alone. Clones expressing the antisense RNA exhibited a 30% reduction in endogenous IGF-I receptor mRNA levels and a significant reduction in receptor protein levels, as measured by both ligand binding assays and Western blot analysis. Antisense-expressing clones expressed approximately 30,000 receptors/cell compared with approximately 48,000-58,000 receptors/cell in control (neo) cells (P < 0.05). Although endogenous RNA:RNA hybrids were demonstrable in antisense-expressing cells, our results suggest that the major effect of the antisense may be the reduction in mRNA levels and not via an inhibition of translation. The reduction in receptor expression reduced both IGF-I- and serum-stimulated cellular proliferation. The maximum cell number reached at 96 h in the presence of IGF-I (100 ng/ml) was significantly reduced in antisense-expressing clones (22,000-30,000) compared with that in control (neo) cells (39,000-42,000). Furthermore, IGF-I-induced c-fos gene expression was reduced by 30% in the clones expressing the antisense RNA. These results strongly support a role for the IGF-I receptor in the proliferation of human breast cancer cells and suggest that strategies using this type of technology may prove useful in cancer therapy.

Breast Neoplasms↗

PubMed1996

Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus.

Hepatitis C virus (HCV) is the major etiological agent of non-A, non-B post-transfusion hepatitis. Its genome, a (+)-stranded RNA molecule of approximately 9.4 kb, encodes a large polyprotein that is processed by viral and cellular proteases into at least nine different viral polypeptides. As with other (+)-strand RNA viruses, the replication of HCV is thought to proceed via the initial synthesis of a complementary (-) RNA strand, which serves, in turn, as a template for the production of progeny (+)-strand RNA molecules. An RNA-dependent RNA polymerase has been postulated to be involved in both of these steps. Using the heterologous expression of viral proteins in insect cells, we present experimental evidence that an RNA-dependent RNA polymerase is encoded by HCV and that this enzymatic activity is the function of the 65 kDa non-structural protein 5B (NS5B). The characterization of the HCV RNA-dependent RNA polymerase product revealed that dimer-sized hairpin-like RNA molecules are generated in vitro, indicating that NS5B-mediated RNA polymerization proceeds by priming on the template via a 'copy-back' mechanism. In addition, the purified HCV NS5B protein was shown to perform RNA- or DNA oligonucleotide primer-dependent RNA synthesis on templates with a blocked 3' end or on homopolymeric templates. These results represent a first important step towards a better understanding of the life cycle of the HCV.

Animals↗

PubMed1994

Stabilizing effects of the RNA 2'-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2'-O-methylated adenosines.

BACKGROUND: The stability of hybrids of 2'-O-methyl-ribonucleotides with complementary RNA is considerably higher than that of the corresponding DNA.RNA duplexes. The 2'-O-modified ribonucleotides are thus an attractive class of compounds for antisense applications. Understanding how these substituents stabilize the structure of the hybrid duplex may be important in the design of ribonucleotides with novel properties. RESULTS: The crystal structure of a dimer of the self-complementary DNA strand d(GCGT)O2'mer(A)d(TACGC), which has a 2'-O-methylated ribonucleotide incorporated at position 5, was determined at 2.1 A resolution. This strand forms a duplex with an overall A-type conformation; the methyl groups of the two modified adenosines point into the relatively wide minor groove. Both 2'-methoxy groups are hydrogen-bonded to solvent molecules. These results allowed us to build a model of a fully 2'-O-methylated RNA double helix. CONCLUSIONS: Insertion of 2'-O-modified RNA residues into a stretch of DNA can nucleate a local A-type conformation, in part because modification with a bulky residue at this position stabilizes a C3'-endo type sugar pucker. The increased stability of fully 2'-O-methylated RNA may result from hydrophobic interactions between substituents in the minor groove. As the 2'-O-methyl groups are directed into the minor groove, it may be worthwhile to introduce tailor-made 2'-O-substituents into RNA; it might be possible to design groups that both stabilize the hybrid duplexes and carry a nuclease function, further improving the efficacy of these modified RNAs in antisense applications.

Adenosine↗

PubMed1984

A transcript from the S segment of the Germiston bunyavirus is uncapped and codes for the nucleoprotein and a nonstructural protein.

Analysis of the RNAs present in BHK-21 cells infected with Germiston virus showed that the transcripts from the L and M segments have a size similar to that of their template, whereas two types of complementary RNA are transcribed from the S segment. One, S1, is a full-length "plus" RNA strand (antigenome), and the other, S2, is an incomplete plus RNA strand which serves as mRNA for at least the synthesis of the N protein and a virus-specific nonstructural polypeptide, p12. The 5' ends of these two transcripts appeared to be identical and complementary to the 3' ends of the viral RNA. Our results suggest that transcription of the S fragment either stops 100 to 150 nucleotides from the 5' end of the template, generating an S2 molecule, or continues, generating an S1 molecule. Neither the S1 antigenome nor the S2 mRNA molecules were polyadenylated at their 3' ends or capped at their 5' ends.

Animals↗

PubMed1979

The use of R-looping for structural gene identification and mRNA purification.

A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs by gel filtration chromatography in the presence of a high concentration of salt. The complementary RNAs are released from the R-loops by heating, and are assayed by gel electrophoresis or cell free translation to determine their purity and to identify the proteins for which they code. We have demonstrated that recombinant DNAs containing sequences for abundant or moderately abundant mRNAs of Saccharomyces cerevisiae can be identified by this means.

Base Sequence↗

PubMed1972

Loss of simian virus 40 DNA-RNA hybrids from nitrocellulose membranes; implications for the study of virus--host DNA interactions.

Complete hybrids of simian virus 40 (SV40)DNA and its complementary RNA (cRNA) are not retained on nitrocellulose membranes. At saturating cRNA concentrations, retention of the hybrids indicates incomplete homology between DNA and RNA, probably due to incorporation of host DNA in the viral DNA; this effect is most pronounced when DNA is produced in cells infected at high multiplicity. Hybrids between DNA of Chinese hamster cells transformed by SV40 and cRNA are retained if the DNA fragments are long, but they are lost if the DNA is sheared to less than the length of an SV40 DNA molecule. Hence, in cells examined with about six SV40 genomes per cell, each genome is individually integrated. The results may explain previous discrepancies in the estimation of the number of viral genomes in transformed cells.

Animals↗

PubMed1996

Antisense oligonucleotide containing an internal, non-nucleotide-based linker promote site-specific cleavage of RNA.

We have designed and synthesized a series of novel antisense methylphosphonate oligonucleotide (MPO) cleaving agents that promote site-specific cleavage on a complementary RNA target. These MPOs contain a non- nucleotide-based linking moiety near the middle of the sequence in place of one of the nucleotide bases. The region surrounding the unpaired base on the RNA strand (i.e. the one directly opposite the non-nucleotide-linker) is sensitive to hydrolytic cleavage catalyzed by ethylenediamine hydrochloride. Furthermore, the regions of the RNA comprising hydrogen bonded domains are resistant to cleavage compared with single-stranded RNA alone. Several catalytic moieties capable of supporting acid/base hydrolysis were coupled to the non-nucleotide-based linker via simple aqueous coupling chemistries. When tethered to the MPO in this manner these moieties are shown to catalyze site-specific cleavage on the RNA target without any additional catalyst.

Base Sequence↗