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PubMed1991

Similar conformers in the minus strands of divergent positive strand RNA phage.

Minus strand RNAs of phages MS2 and Q beta, prepared by in vitro transcription, were each separated into two forms on nondenaturing agarose gels. Only a single form of RNA was observed for minus strands denatured with glyoxal prior to agarose analysis, demonstrating that the two forms were conformers in each case. Truncated and elongated versions of these RNAs, analyzed under nondenaturing conditions, demonstrated that a region of RNA complementary to the A protein gene was at least partially responsible for the presence of these conformers in both MS2 and Q beta minus strands.

Chromatography, Agarose↗
PubMed1999

2-5A-DNA conjugate inhibition of respiratory syncytial virus replication: effects of oligonucleotide structure modifications and RNA target site selection.

To define more fully the conditions for 2-5A-antisense inhibition of respiratory syncytial virus (RSV), relationships between 2-5A antisense oligonucleotide structure and the choice of RNA target sites to inhibition of RSV replication have been explored. The lead 2-5A-antisense chimera for this study was the previously reported NIH8281 that targets the RSV M2 RNA. We have confirmed and extended the earlier study by showing that NIH8281 inhibited RSV strain A2 replication in a variety of antiviral assays, including virus yield reduction assays performed in monkey (EC90 = 0.02 microM) and human cells (EC90 = microM). This 2-5A-antisense chimera also inhibited other A strains, B strains and bovine RSV in cytopathic effect inhibition and Neutral Red Assays (EC50 values = 0.1-1.6 microM). The 2'-O-methylation modification of NIH8281 to increase affinity for the complementary RNA and provide nuclease resistance, the introduction of phosphothioate groups in the antisense backbone to enhance resistance to exo- and endonucleases, and the addition of cholesterol to the 3'-terminus of the antisense oligonucleotide to increase cellular uptake, all resulted in loss of activity. Of the antisense chimeras targeting other RSV mRNAs (NS1, NS2, P, M. G, F, and L), only those complementary to L mRNA were inhibitory. These results suggest that lower abundance mRNAs may be the best targets for 2-5A-antisense; moreover, the active 2-5A antisense chimeras in this study may serve as useful guides for the development of compounds with improved stability, uptake and anti-RSV activity.

Adenine Nucleotides↗
PubMed2003

Idiotype-anti-idiotype circuit in non-autoimmune mice after immunization with the epitope and complementary epitope 289-308aa of La/SSB: implications for the maintenance and perpetuation of the anti-La/SSB response.

BACKGROUND: Antibodies to La/SSB are usually found in sera of patients with Sjogren's Syndrome (SS) and Systemic Lupus Erythematosus (SLE). Recent work from our laboratory (Mol Med 2002;8:293-305) revealed that an active idiotypic network involving antibodies to epitopes of La/SSB and their anti-idiotypes exist in human sera. The anti-idiotypic antibodies were detected using complementary peptides to B-cell epitopes of the autoantigen. The principle of the complementary peptides is based on the 'molecular recognition' theory. According to this theory, translation of two complementary RNA strands (coding and non-coding strand) into protein, generate a pair of peptides, which bind each other with specificity and high affinity. AIM: To investigate antibody production and T-cell responses in non-autoimmune-susceptible animal strains which were immunized with the epitope 289-308aa of La/SSB as well as its complementary epitope. MATERIALS AND METHODS: Balb/c mice were immunized with a peptide corresponding to epitope 289-308aa (pep) or its complementary (cpep) peptide (5 animals/group). The sera were tested for the presence of antibodies to pep and cpep as well as for epitope spreading to recombinant human La/SSB and a major B-cell epitope of La/SSB spanning the region 349-364aa. Another group of animals was sacrificed on day 10 and T-cell responses against pep and cpep were evaluated in cells from lymph nodes and spleen. RESULTS: Immunizations with either pep or cpep led to the appearance of antibodies against the immunogen peptide by day 31 which subsequently was followed by antibody production to its complementary peptide by day 55. In two out of five animals immunized with the epitope 289-308aa, a spreading of the immune response to epitope 349-364aa was observed. In the remaining three animals, negative for antibodies to pep349-364, a specific treatment of sera, using cpep349-364 revealed that anti-idiotypic antibodies masked antibodies to pep349-364. In all immunization experiments high T-cell proliferative responses to both pep and cpep peptides were detected. CONCLUSIONS: Complementary peptides to epitopes of La/SSB can be utilized as probes to study the development of an idiotypic-anti-idiotypic network towards the major autoantigen. The ability of pep and cpep peptides to induce both B-cell and T-cell responses may provide useful insights into understanding further the initiation and maintenance of autoimmune response and create new tools for therapeutic intervention.

Animals↗
PubMed2006

Properties of novel antisense oligonucleotides containing 2'-O-modified adenosine with a photo-reactive group.

In order to enhance the efficiency of antisense molecules for target RNA regulation, a novel photo-reactive antisense oligonucleotide was developed. We designed and synthesized a photo-reactive antisense oligonucleotide containing an adenosine in which 2'-OH was modified with 4,5',8-trimethylpsoralen (Ps) via an ethoxymethylene linkage (2'-Ps-eom). We evaluated the photo-cross-linking efficiency and sequence specificity toward complementary RNA (match-RNA). 2'-Ps-eom was selectively photo-cross-linked to the match-RNA. The photo-cross-linking efficiency was about 75% upon UVA-irradiation (365 nm) for 10 min. Previously, we reported oligonucleotides that had an adenosine anchoring Ps at 2'-O-position via a methylene linkage (2'-Ps-met). The photo-cross-linking efficiency of 2'-Ps-met and match-RNA was about 35% upon UVA-irradiation for 120 min. The photo-cross-linking efficiency of 2'-Ps-eom was dramatically enhanced in comparison with the one of 2'-Ps-met.

Adenosine↗
PubMed2001

2'-O,4'-C-ethylene-bridged nucleic acids (ENA) with nuclease-resistance and high affinity for RNA.

Novel nucleosides, 2'-O,4'-C-ethylene nucleosides and their corresponding phosphoramidites, were synthesized as building blocks for antisense oligonucleotides. The 2'-O,4'-C-ethylene linkage of these nucleosides, as well as the linkage of 2'-O,4'-C-methylene nucleosides which are known as bridged nucleic acids (BNA) or locked nucleic acids (LNA), restricts the sugar puckering to the N-conformation. The ethylene-bridged nucleic acids (ENA) showed a high binding affinity for the complementary RNA strand (delta Tm = degrees C/modification) and were approximately 400 and 80 times more nuclease-resistant than natural DNA and BNA/LNA, respectively. These results indicate that ENA have better antisense activity than BNA/LNA.

Base Sequence↗
PubMed1986

[Cloning of mRNA nucleotide sequences amplified during DNA replication in the regenerating liver].

A library of double-stranded cDNA has been constructed using the mRNA of regenerating rat liver 20 hr after partial hepatectomy. The differential screening of the library with the regenerating liver specific and the resting-liver-specific single-stranded cDNA probes has identified 11 cDNA clones which sequences are preferentially expressed in regenerating rat liver. The RNA dot blot hybridization has shown that levels of RNA complementary to these clones are 3 to 8-fold higher in dividing cells as compared with resting cells.

Animals↗
PubMed1989

Solid-phase synthesis and high-resolution NMR studies of two synthetic double-helical RNA dodecamers: r(CGCGAAUUCGCG) and r(CGCGUAUACGCG).

Ten-micromole solid-phase RNA synthesis has been successfully performed on an automated nucleic acid synthesizer with coupling efficiencies up to 99%, using the tert-butyldimethylsilyl group to protect the 2'-hydroxyl. The tert-butyldimethylsilyl group was easily removed by tetrabutylammonium fluoride under conditions in which virtually no 2'- to 3'-isomerization was found to occur. By use of this approach, the self-complementary RNA dodecamers r(CGCGAAUUCGCG) and r(CGCGUAUACGCG) were synthesized on an automated nucleic acid synthesizer, purified by TLC, and studied by high-resolution NMR. Imino protons were assigned from one-dimensional nuclear Overhauser effects. The nonexchangeable base, H1', and H2' protons were assigned by the sequential NOESY connectivity method. The NOE data from these two oligomers were analyzed qualitatively and compared to the ideal A- and B-type helix models of Arnott et al. (1972a,b). The internucleotide H6/H8 NOEs to the preceding H1' in r(CGCGUAUACGCG) were found to be sequence-dependent and probably reflect the roll angles between adjacent bases. The internucleotide H6/H8 to H2' NOEs of these oligomers correspond very well to an A-type conformation, but the interstrand adenine H2 NOEs to the following H1' were much stronger than those predicted from the fiber model. These srong interstrand NOEs can be rationalized by base pair slide to favor more interstrand base overlap, as predicted by Callidine and Drew (1984).

Base Composition↗
PubMed1993

Transgenic plants that express genes including the 3' untranslated region of the turnip yellow mosaic virus (TYMV) genome are partially protected against TYMV infection.

In order to evaluate new possibilities for protecting plants against virus infection by interference with viral replication, two chimeric genes were constructed in which the (+) strand 3'-terminal 100 nucleotides (nt) of the noncoding region of the turnip yellow mosaic virus (TYMV) genome were placed downstream from the sense or antisense cat coding region. The two chimeric genes were then introduced into the genome of rapeseed (Brassica napus) using an Agrobacterium rhizogenes vector system. Plants expressing high levels of either chimeric gene showed partial protection against infection by TYMV RNA or virions. One interesting feature of the protection is that a proportion of the inoculated transgenic plants does not become infected. Protection was overcome when the inoculum concentration was increased. RNA complementary to the initial transcript was detected after infection.

Base Sequence↗
PubMed1978

Sequence organization and transcription at two heat shock loci in Drosophila.

The heat shock loci of Drosophila melanogaster chromosome subdivisions 87A and 87C have been studied by using cloned DNA. Both sites contain a number of copies of a 2,4-kilobase (kb) region homologous to mRNA for the 70,000-dalton heat shock protein. In situ hybridization to chromosomal RNA shows that transcripts of this sequence accumulate at both sites after temperature elevation. At 87C there is a 1.5-kb repeated sequence homologous to another heat shock RNA. One cloned segment includes two to three tandem copies of this sequence located 0.8 kb from the beginning of a 2.4-kb message region. RNA complementary to the 1.5-kb repeat acccumulates at 87C after temperature elevation, but does not code for any known heat shock protein. In the sibling species D. simulans, there are sequences located and transcribed at 87A and 87C that are homologous to the melanogaster 2.4-kb message sequence. The 1.5-kb repeat, however, is absent from 87C in simulans and no heat shock RNA homologous to it can be detected.

Animals↗
PubMed1980

Transcription and processing of a yeast tRNA gene containing a modified intervening sequence.

The tRNA(3) (Leu) gene from yeast contains an intervening sequence of 32 nucleotides not present in mature tRNA. This sequence is transcribed and subsequently removed during the maturation of the RNA. To probe the involvement of this region of the gene in transcription and processing of the pre-tRNA(3) (Leu), the yeast DNA was cloned in plasmid pBR322 and a 21-base-pair DNA fragment corresponding to the lac operator was inserted into the intervening sequence. Insertion was done at a cleavage site for the restriction endonuclease Hpa I that occurs 19/20 base pairs from the 5' end of the intervening sequence. The parent and modified plasmids were then transcribed in a Xenopus germinal vesicle extract. RNA-fingerprint analysis of the transcription products revealed that both the tRNA(3) (Leu) gene and its modified counterpart were accurately transcribed. Transcription products corresponding to mature tRNA(3) (Leu) and pre-RNA(3) (Leu) with the normal and lac-containing intervening sequence were identified. Precursors extended at their 5' and 3' ends were also present. Both parent and modified genes were transcribed efficiently, and the various products accumulated in similar amounts, indicating that no deleterious effects on transcriptional competence, stability of the transcripts, or processing result from insertion of the 21-base-pair lac operator DNA. Incubation of pre-tRNA molecules that contained intervening sequences but were 5' and 3' mature with a yeast ribosomal wash fraction resulted in excision of the intervening sequence and, in the presence of ATP, ligation of the resulting half-tRNA molecules. The presence of RNA complementary to lac operator DNA neither inhibited the excision and splicing activities nor altered the site of the junction.

Base Sequence↗
PubMed1976

Elimination of the sarcoma genome from murine sarcoma virus transformed cat cells.

Cat cells transformed by Moloney murine sarcoma virus contain virus-specific sequences in their RNA and DNA. Cloned, spontaneous revertant cell lines derived from clones of these cells had no evidence of the sarcoma genome in the cell RNA or DNA as judged by RNA-complementary DNA or DNA-complementary DNA hybridizations. ?This is apparently the first report of loss of a transforming genome in a revertant cell line.

Cell Line↗
PubMed1994

Identification and characterization of an antisense RNA transcript (gfg) from the human basic fibroblast growth factor gene.

Basic fibroblast growth factor (bFGF) is an autocrine growth factor that is overexpressed in glial tumor cells and promotes their unregulated proliferation. We have previously reported that increased messenger RNA (mRNA) stability contributes to the elevated steady state levels of bFGF mRNA in human U87-MG glioma cells. Stability of bFGF mRNA is regulated by a natural antisense transcript in Xenopus oocytes, but the mammalian equivalent of this transcript has not previously been described. We were interested in identifying the human equivalent of this antisense transcript in order to study its role in bFGF mRNA stability. Analysis of the 3'-untranslated region of the 6.7-kilobase human bFGF mRNA revealed two areas of greater than 75% homology to exons 3 and 4 of the Xenopus antisense transcript, separated by 4300 basepairs of nonhomologous sequence. We used reverse transcription-polymerase chain reaction to amplify, clone, and sequence a 301-basepair fragment of the antisense splice variant from U87-MG cells. The clone (gfg-1) is 73% identical to the Xenopus sequence, with a conserved splice junction and an open reading frame. Strand-specific gfg-1 complementary RNA probes detect a 1.5-kilobase mRNA transcript in normal rat tissues and human T47D breast cancer cells, which contain very low levels of bFGF mRNA. In contrast, antisense transcript expression was undetectable by Northern hybridization in U87-MG cells, which overexpress the bFGF sense mRNA. The reciprocal relationship between bFGF sense and antisense expression suggests that antisense transcripts may regulate bFGF expression in mammalian cells, and that disruption of normal sense/antisense mRNA ratios may lead to overexpression of bFGF in some tumors.

Animals↗
PubMed1996

Distribution of aromatase P450 transcripts and adipose fibroblasts in the human breast.

The fibroblast component of adipose tissue is the primary extraglandular site of aromatase P450 (P450arom) expression, which is responsible for the conversion of C19 steroids to estrogens. Previously, we have shown positive correlations between the level of P450arom transcripts and the ratio of fibroblasts to mature adipocytes in adipose tissue samples proximal to breast tumors. The present study was conducted to determine the distribution of P450arom messenger ribonucleic acid (RNA) levels and fibroblast to adipocyte ratios in disease-free breasts of premenopausal women. Adipose tissue samples were collected from 3 regions (outer, upper, and inner) of both breasts of 13 women undergoing reduction mammoplasty. The histological composition of adipose tissue (n = 12) was determined by morphometry using a computerized image analysis program. We used a competitive RT-PCR method employing rat P450arom complementary RNA as an internal standard to quantify adipose P450arom transcripts in tissue total RNA samples (n = 11). Overall, 67% of the highest fibroblast to adipocyte ratios and 64% of the highest P450arom transcript levels were detected in an outer breast region, whereas in only 1 patient were the highest values detected in an inner region. Parametric ANOVA showed significant differences between the fibroblast content of the regions [p(F) = 0.037]. This distribution pattern directly correlates with the most common or the least common sites of carcinoma in the breast, the outer and inner regions, respectively. Moreover, a direct relationship was demonstrated between adipose fibroblasts and P450arom transcripts within the breast, in that regions with the highest fibroblast to adipocyte ratios contained the highest P450arom transcript levels (by ANOVA of contrast variables, P = 0.0009). These results suggest that, similar to our previous findings in the breast bearing a tumor, adipose tissue aromatase expression in the disease-free breast is determined by the local ratio of fibroblasts to adipocytes.

Adipose Tissue↗
PubMed2002

Differential expression and cellular localization of activin and inhibin mRNA in the rainbow trout ovary and testis.

An inhibin cDNA from rainbow trout consisted of 1305 bp, which coded for 352 amino acid residues. The deduced amino acid sequence of mature inhibin was 50 to 60% identical to mammalian sequences. Distribution of inhibin alpha and activin beta A and beta B in different ovarian and testis compartments was studied in rainbow trout by in situ hybridization with complementary RNA probes. In testis tissue, inhibin alpha and activin beta A and beta B were expressed only in the testicular interstitia between the seminal lobules, where Sertoli cells and Leydig cells are distributed. The localizations and intensities of the reactions were constant throughout the maturation of the testis. Within ovarian tissue, the theca cell layers of follicles showed strong reactions of Dig-labeled antisense mRNA probes hybridizing against inhibin alpha and activin beta A and beta B in all samples over the same sampling period. In regressing oocytes, a positive reaction was observed in the granular cell layer of the follicles.

Activins↗
PubMed2005

Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines.

Substitution of oxygen atoms by sulfur at various locations in the nucleic acid framework has led to analogs such as the DNA phosphorothioates and 4'-thio RNA. The phosphorothioates are excellent mimics of DNA, exhibit increased resistance to nuclease degradation compared with the natural counterpart, and have been widely used as first-generation antisense nucleic acid analogs for applications in vitro and in vivo. The 4'-thio RNA analog exhibits significantly enhanced RNA affinity compared with RNA, and shows potential for incorporation into siRNAs. 2-Thiouridine (s2U) and 5-methyl-2-thiouridine (m5s2U) are natural nucleotide analogs. s2U in tRNA confers greater specificity of codon-anticodon interactions by discriminating more strongly between A and G compared with U. 2-Thio modification preorganizes the ribose and 2'-deoxyribose sugars for a C3'-endo conformation, and stabilizes heteroduplexes composed of modified DNA and complementary RNA. Combination of the 2-thio and sugar 2'-O-modifications has been demonstrated to boost both thermodynamic stability and nuclease resistance. Using the 2'-O-[2-(methoxy)ethyl]-2-thiothymidine (m5s2Umoe) analog, we have investigated the consequences of the replacement of the 2-oxygen by sulfur for base-pair geometry and duplex conformation. The crystal structure of the A-form DNA duplex with sequence GCGTAT*ACGC (T* = m5s2Umoe) was determined at high resolution and compared with the structure of the corresponding duplex with T* = m5Umoe. Notable changes as a result of the incorporation of sulfur concern the base-pair parameter 'opening', an improvement of stacking in the vicinity of modified nucleotides as measured by base overlap, and a van der Waals interaction between sulfur atoms from adjacent m5s2Umoe residues in the minor groove. The structural data indicate only minor adjustments in the water structure as a result of the presence of sulfur. The observed small structural perturbations combined with the favorable consequences for pairing stability and nuclease resistance (when combined with 2'-O-modification) render 2-thiouracil-modified RNA a promising candidate for applications in RNAi.

Base Pairing↗
PubMed1999

Synthesis and properties of RNA analogs-oligoribonucleotide N3'-->P5' phosphoramidates.

The synthesis and characterization of RNA mimetics, uniformly modified oligoribonucleotide N3'-->P5' phosphoramidates containing all four natural bases (uracil, cytosine, adenine and guanine) as well as thymidine and 2,6-diaminopurine, are described. These RNA analogs contain N3'-->P5' phosphoramidate internucleotide linkages which replaced natural RNA O3'-->P5' phosphodiester groups. These oligonucleo-tides were constructed from novel monomeric units (2'- t -butyldimethylsilyl)-3'-(monomethoxyltrityl)-amino-nucleoside-5'- phos phoramidites, the preparation of which is also presented. Several mixed base 9-13mer oligoribonucleotide phosphoramidates were synthesized with step-wise coupling yields of 96-98%. Thermal denaturation experiments demonstrated that ribo-N3'-->P5' phosphoramidates form stable duplexes with a complementary RNA strand. Thus, the melting temperature ( T (m)) of a duplex formed by a 13mer ribo-N3'-->P5' phosphoramidate (84 degrees C) was higher than that observed for the isosequential natural RNA oligomer (64.0 degrees C), or for the 2'-deoxy-N3'-->P5' phosphoramidate counterpart (71.7 degrees C). Moreover, substitution of adenine by 2, 6-diaminopurine in an oligoribophosphoramidate pentamer resulted in a very significant increase in the duplex melting temperature ( approximately 7 degrees C per base substitution). The RNA phosphoramidates also showed similar rates of hydrolysis by both RNase A and RNase T(1)as compared to natural RNA oligomers. The data presented indicate that this class of RNA analogs may be used as structural and functional RNA mimetics.

Chromatography, High Pressure Liquid↗
PubMed1993

Prevention of experimental autoimmune myasthenia gravis by manipulation of the immune network with a complementary peptide for the acetylcholine receptor.

Myasthenia gravis (MG) and experimental autoimmune myasthenia gravis (EAMG) are caused, in part, by the production of autoantibodies against the main immunogenic region, amino acids 61-76, of the alpha chain of the acetylcholine receptor (AChR). Theoretically, induction of anti-idiotypic (Id) antibodies (Abs) should be a highly specific treatment for the disease by virtue of their potential ability to neutralize Abs to the AChR. We have tested this idea by attempting to evoke such anti-Id Abs by immunization with a peptide (termed RhCA 67-16) encoded by RNA complementary to the Torpedo AChR main immunogenic region and determining whether such treatment will prevent the development of EAMG. Immunization with RhCA 67-16, but not a control peptide termed PBM 9-1, was found to elicit the production of anti-Id Abs that blocked recognition of native Torpedo AChR by its Ab. This anti-Id Ab activity was ablated by incubation of the anti-RhCA 67-16 serum with RhCA 67-16, but PBM 9-1, prior to the assay for Ab binding to AChR. The anti-Id Ab-inducing activity of RhCA 67-16 was confirmed by the ability to produce a rat monoclonal Ab to RhCA 67-16 that showed anti-Id activity for polyclonal rat Ab reactive with AChR residues 67-76. Most importantly, RhCA 67-16 immunization also prevented the development of EAMG in Lewis rats challenged with Torpedo AChR (25% incidence versus 90% in the controls) and diminished the AChR Ab levels in animals injected with low doses of AChR. Our results suggest a therapy for MG and perhaps other autoimmune diseases through the induction of anti-Id Abs by peptide immunogens.

Amino Acid Sequence↗
PubMed1978

The primary sequence of rabbit alpha-globin mRNA.

The rabbit alpha-globin DNA insertion in the chimeric plasmid pHb 72 (Liu et al., 1977) has been sequenced by the method of Maxam and Gilbert (1977). This has enabled us to determine the messenger RNA(mRNA) sequence beginning in the 5' untranslated region 9 nucleotides before the initiation codon and extending through the first 361 nucleotides of the translated region. The data reported here overlap and are in complete agreement with sequences determined by Baralle (1977) for the 5' end of the mRNA and by Proudfoot et al. (1977) for the 3' end. Our sequence is also in agreement with the partial complementary RNA (cRNA) sequencing data which we reported previously (Paddock et al., 1977), this work marks the completion of the primary sequence of the rabbit alpha-globin mRNA. These observations reaffirm the high fidelity with which gene copies can be synthesized in vitro, cloned in a bacterial plasmid and maintained in the host. The general features of the mRNA nucleotide sequence are duscussed with particular attention given to the base composition and codon preferences observed and to comparison of this sequence with other completed mRNA gene sequences. A new computer program has been used to search for the most stable base-pairing arrangement of the completed mRNA.

Amino Acid Sequence↗