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Results: 1 to 10 of 52

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The effect of hybridization-induced secondary structure alterations on RNA detection using backscattering interferometry.
Adams NM, Olmsted IR, Haselton FR, Bornhop DJ, Wright DW
(2013) Nucleic Acids Res 41: e103
MeSH Terms: Interferometry, Nucleic Acid Conformation, Nucleic Acid Hybridization, Nucleocapsid Proteins, Oligonucleotide Probes, Oligonucleotides, RNA, RNA Folding, RNA, Viral
Show Abstract · Added March 7, 2014
Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid probes that maximize BSI signal upon binding the respiratory syncytial virus nucleocapsid gene RNA biomarker. The number of base pairs formed upon the addition of oligonucleotide probes to a solution containing the viral RNA target correlated with the BSI signal magnitude. Using RNA folding software mfold, we found that the predicted number of unpaired nucleotides in the targeted regions of the RNA sequence generally correlated with BSI sensitivity. We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. We attribute this enhancement in BSI performance to the increased A-form character of the LNA:RNA hybrid. A limit of detection of 624 pM, corresponding to ∼10(5) target molecules, was achieved using nine distinct ∼23-mer DNA probes complementary to regions distributed along the RNA target. Our results indicate that BSI has promise as an effective tool for sensitive RNA detection and provides a road map for further improving detection limits.
0 Communities
2 Members
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9 MeSH Terms
Single molecule-sensitive probes for imaging RNA in live cells.
Santangelo PJ, Lifland AW, Curt P, Sasaki Y, Bassell GJ, Lindquist ME, Crowe JE
(2009) Nat Methods 6: 347-9
MeSH Terms: Actin-Related Protein 2, Actins, Animals, Avian Proteins, Bacterial Proteins, Biotin, Carbocyanines, Cell Line, Tumor, Cell Membrane Permeability, Cell Survival, Cells, Cultured, Chick Embryo, DNA-Binding Proteins, Fibroblasts, Fluorescent Dyes, Humans, Image Processing, Computer-Assisted, Microscopy, Confocal, Microscopy, Fluorescence, Molecular Probe Techniques, Oligonucleotide Probes, Poly(A)-Binding Proteins, RNA, RNA, Messenger, RNA-Binding Proteins, Respiratory Syncytial Virus, Human, Streptavidin, Streptolysins, T-Cell Intracellular Antigen-1
Show Abstract · Added August 6, 2012
To visualize native or non-engineered RNA in live cells with single-molecule sensitivity, we developed multiply labeled tetravalent RNA imaging probes (MTRIPs). When delivered with streptolysin O into living human epithelial cancer cells and primary chicken fibroblasts, MTRIPs allowed the accurate imaging of native mRNAs and a non-engineered viral RNA, of RNA co-localization with known RNA-binding proteins, and of RNA dynamics and interactions with stress granules.
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29 MeSH Terms
Molecular beacons can assess changes in expression and 3'-polyadenylation of human eNOS mRNA.
Jones R, Baker MB, Weber M, Harrison DG, Bao G, Searles CD
(2009) Am J Physiol Cell Physiol 296: C498-504
MeSH Terms: Animals, Cells, Cultured, Endothelial Cells, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, Gene Expression Regulation, Enzymologic, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Lovastatin, Lung, Mice, Nitric Oxide Synthase Type III, Nucleic Acid Hybridization, Oligonucleotide Probes, Physical Exertion, Polyadenylation, Polymerase Chain Reaction, RNA Interference, RNA, Messenger, Reproducibility of Results, Stress, Mechanical
Show Abstract · Added December 10, 2013
The endothelium plays an essential role in maintaining vascular homeostasis, and it fulfills this role by modulating intracellular signaling and gene expression in response to chemical and mechanical stimuli. Assessing changes in endothelial gene expression is essential to understanding how physiological and pathophysiological processes modulate vascular homeostasis. Here we describe the use of molecular beacons to rapidly and quantitatively assess expression and 3'-polyadenylation of a gene that is important for vascular homeostasis, endothelial nitric oxide synthase (eNOS). Single- and dual-fluorescence resonance energy transfer (FRET) molecular beacon hybridization assays were developed to measure changes in mRNA levels and 3'-polyadenylation, respectively, in primary human endothelial cell cultures subjected to laminar shear stress or statin treatment. Optimized beacon hybridization assays took approximately 15 min to perform, and eNOS mRNA levels were validated by quantitative real-time RT-PCR. Competitive inhibition assays and posttranscriptional silencing of eNOS expression were used to verify the specificity of molecular beacon fluorescence. Finally, the dual-FRET method was used to assess eNOS polyadenylation in tissues isolated from mice subjected to exercise training. These data demonstrate that molecular beacons can be used to rapidly and efficiently measure endothelial gene expression and 3'-polyadenylation. This approach could easily be adapted for studies of other endothelial genes and has promise for applications in live endothelial cells.
1 Communities
1 Members
0 Resources
21 MeSH Terms
Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2'-SeMe-uridine for crystallographic phasing of nucleic acid structures.
Pallan PS, Egli M
(2007) Nat Protoc 2: 647-51
MeSH Terms: Chromatography, High Pressure Liquid, Crystallography, Molecular Structure, Nucleic Acids, Oligonucleotide Probes, Selenomethionine, Uridine
Show Abstract · Added March 5, 2014
This protocol describes a method for introducing an anomalously scattering atom into oligonucleotides at the 2'-position of uridine by conventional solid-phase synthesis. The 2'-SeMe ribose modification is particularly attractive for derivatization of RNA to facilitate crystal structure determination. The estimated time for the synthesis and HPLC purification of oligonucleotides with incorporated 2'-SeMe-uridine residues is approximately 46 h for 'trityl on' and approximately 32 h for 'trityl off' methods, respectively.
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7 MeSH Terms
HIV-1 Nef mediates post-translational down-regulation and redistribution of the mannose receptor.
Vigerust DJ, Egan BS, Shepherd VL
(2005) J Leukoc Biol 77: 522-34
MeSH Terms: Amino Acid Sequence, Base Sequence, Cell Line, Flow Cytometry, Gene Products, nef, HIV-1, HeLa Cells, Humans, Lectins, C-Type, Macrophages, Mannose-Binding Lectins, Molecular Sequence Data, Mutagenesis, Site-Directed, Oligonucleotide Probes, Protein Processing, Post-Translational, Receptors, Cell Surface, Recombinant Fusion Proteins, Transfection, nef Gene Products, Human Immunodeficiency Virus
Show Abstract · Added March 22, 2016
Human immunodeficiency virus (HIV) has derived a variety of means to evade the host immune response. HIV-derived proteins, including Tat, Nef, and Env, have all been reported to decrease expression of host molecules such as CD4 and major histocompatibility complex I, which would assist in limiting viral replication. The mannose receptor (MR) on the surface of macrophages and dendritic cells (DC) has been proposed to function as an effective antigen-capture molecule, as well as a receptor for entering pathogens such as Mycobacterium tuberculosis and Pneumocystis carinii. Regulation of this receptor would therefore benefit HIV in removing an additional arm of the innate immune system. Previous work has shown that MR function is reduced in alveolar macrophages from HIV-infected patients and that surface MR levels are decreased by the HIV-derived protein Nef in DC. In addition, several laboratories have shown that CD4 is removed from the surface of T cells in a manner that might be applicable to decreased MR surface expression in macrophages. In the current study, we have investigated the role of Nef in removing MR from the cell surface. We have used a human macrophage cell line stably expressing the MR as well as human epithelial cells transiently expressing CD4 and a unique CD4/MR chimeric molecule constructed from the extracellular and transmembrane domains of CD4 and the cytoplasmic tail portion of the MR. We show that the MR is reduced on the cell surface by approximately 50% in the presence of Nef and that the MR cytoplasmic tail can confer susceptibility to Nef in the CD4/MR chimera. These data suggest that the MR is a potential intracellular target of Nef and that this regulation may represent a mechanism to further cripple the host innate immune system.
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19 MeSH Terms
Use of high specific activity StarFire oligonucleotide probes to visualize low-abundance pre-mRNA splicing intermediates in S. pombe.
Behlke MA, Dames SA, McDonald WH, Gould KL, Devor EJ, Walder JA
(2000) Biotechniques 29: 892-7
MeSH Terms: Oligonucleotide Probes, RNA Precursors, RNA Splicing, RNA, Fungal, Schizosaccharomyces
Show Abstract · Added March 5, 2014
An oligonucleotide labeling system was developed that can produce radiolabeled hybridization probes with tenfold or more higher specific activity than is obtained by traditional 5'-end-labeling with polynucleotide kinase. Yet the system is as rapid and simple as kinase labeling. The reaction uses the Klenow fragment of E. coli DNA polymerase to add alpha-32P-dA residues to the 3'-end of an oligonucleotide in a primer-extension reaction. Unlike other methods of radioactive tailing (e.g., terminal transferase), a single species is produced of both known length and known specific activity. The reaction is efficient, and over 90% of probe molecules are routinely labeled. Using this method of labeling, an oligonucleotide was shown to be tenfold more sensitive in detecting target DNA sequences in a dot blot hybridization assay, compared to the same oligonucleotide labeled using polynucleotide kinase. Northern blots of Schizosaccharomyces pombe RNA were probed with an oligonucleotide specific for intron 1 of the tf2d gene, a TATA-box binding transcription factor. Kinase-labeled tf2d probe detected only unspliced RNA, while the same oligonucleotide labeled using the new method detected both unspliced tf2d RNA and rare pre-mRNA splicing intermediates.
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2 Members
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5 MeSH Terms
The effects of hormone replacement therapy on hypothalamic neuropeptide gene expression in a primate model of menopause.
Abel TW, Voytko ML, Rance NE
(1999) J Clin Endocrinol Metab 84: 2111-8
MeSH Terms: Animals, Carboxylic Ester Hydrolases, Estrogen Replacement Therapy, Female, Hypothalamus, In Situ Hybridization, Macaca fascicularis, Menopause, Microglia, Models, Biological, Neurokinin B, Neurons, Oligonucleotide Probes, Ovariectomy, Pro-Opiomelanocortin
Show Abstract · Added March 5, 2014
Menopause is associated with increased neurokinin B (NKB) gene expression and decreased proopiomelanocortin (POMC) gene expression in the human hypothalamus. In the present study, young, ovariectomized cynomolgus monkeys were used in a model of menopause to examine the effects of hormone replacement therapy (HRT) on hypothalamic neuropeptide gene expression. A secondary goal was to determine whether HRT produces signs of estrogen toxicity in the primate hypothalamus by examining POMC neurons and microglial cells. In situ hybridization was performed using synthetic, radiolabeled, 48-base oligonucleotide probes. Alpha-napthyl butyrate esterase histochemistry was used to visualize microglial cells. Both estrogen and estrogen plus progesterone treatments produced a marked suppression of the number of infundibular neurons expressing NKB gene transcripts. In contrast, HRT had no effect on the POMC system of neurons or the number of microglial cells in the infundibular nucleus. These results provide strong support for the hypothesis that the increased NKB gene expression in the hypothalamus of postmenopausal women is secondary to estrogen withdrawal. Conversely, these data suggest that the dramatic decline in the numbers of neurons expressing POMC gene transcripts in older women is caused by factors other than ovarian failure. Finally, we found no evidence that HRT, in doses designed to mimic currently prescribed regimens, produces signs of estrogen toxicity in the primate infundibular nucleus.
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15 MeSH Terms
Expression of angiogenesis-related genes and progression of human ovarian carcinomas in nude mice.
Yoneda J, Kuniyasu H, Crispens MA, Price JE, Bucana CD, Fidler IJ
(1998) J Natl Cancer Inst 90: 447-54
MeSH Terms: Animals, Blotting, Northern, Endothelial Growth Factors, Female, Fibroblast Growth Factor 2, Gelatinases, Gene Expression Regulation, Neoplastic, Immunohistochemistry, In Situ Hybridization, Interleukin-8, Lymphokines, Matrix Metalloproteinase 2, Metalloendopeptidases, Mice, Mice, Nude, Neovascularization, Pathologic, Oligonucleotide Probes, Ovarian Neoplasms, RNA, Messenger, RNA, Neoplasm, Vascular Endothelial Growth Factor A, Vascular Endothelial Growth Factors
Show Abstract · Added March 5, 2014
BACKGROUND - By the time patients are diagnosed with ovarian carcinoma, peritoneal dissemination of the tumor often has occurred. The progressive growth and spread of ovarian carcinoma depend, in part, on the formation of an adequate blood supply. We determined whether the expression of genes that regulate distinct steps in angiogenesis (i.e., the formation of new blood vessels) was associated with the pattern and progressive growth of human ovarian carcinomas implanted in the peritoneal cavity of nude mice.
METHODS - Five different human ovarian carcinomas were injected individually into the peritoneal cavity of female NCr-nu/nu nude mice. The expression of basic fibroblast growth factor, vascular endothelial growth factor/vascular permeability factor (VEGF/VPF), interleukin 8 (IL-8), and collagenase type IV (MMP-2 [matrix metalloproteinase-2] and MMP-9) was determined by northern blot analysis, in situ hybridization of messenger RNA, and immunohistochemical analysis. Blood vessel distribution and density, macrophage infiltration pattern, and stromal reaction were determined by immunohistochemical analysis with specific antibodies.
RESULTS - Three of the carcinomas produced both solid lesions and ascitic tumors, whereas the remaining two produced only solid lesions. Two of the carcinomas produced rapidly progressive disease, two produced slow disease, and one produced intermediate disease. The formation of ascites was directly associated with expression of VEGF/ VPF, and survival was inversely associated with expression of IL-8. In rapidly growing tumors, the number of blood vessels was high throughout the lesion; in contrast, in slow-growing tumors, most vessels (and infiltrating macrophages) were located at the periphery.
CONCLUSIONS - The expression of various genes that regulate angiogenesis in human ovarian carcinomas is associated with the pattern of the disease and its progression. Therefore, targeting specific genes that regulate angiogenesis could offer new approaches to the treatment of ovarian cancer.
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22 MeSH Terms
Disruption of PAX6 function in mice homozygous for the Pax6Sey-1Neu mutation produces abnormalities in the early development and regionalization of the diencephalon.
Grindley JC, Hargett LK, Hill RE, Ross A, Hogan BL
(1997) Mech Dev 64: 111-26
MeSH Terms: Animals, Base Sequence, DNA-Binding Proteins, Diencephalon, Eye Proteins, Female, Gene Expression Regulation, Developmental, Homeodomain Proteins, Homozygote, In Situ Hybridization, Mice, Mice, Inbred ICR, Models, Biological, Mutagenesis, Insertional, Mutation, Olfactory Bulb, Oligonucleotide Probes, PAX6 Transcription Factor, Paired Box Transcription Factors, Phenotype, Pregnancy, RNA, Messenger, Repressor Proteins, Tectum Mesencephali
Show Abstract · Added April 14, 2010
Pax6 expression in the diencephalon of the mouse embryo is restricted both antero-posteriorly and dorso-ventrally, with changes in level occurring at prosomere boundaries. Small eye (Pax6Sey-1Neu) mice homozygous for Pax6 mutations have multiple defects in early forebrain development. In the diencephalon of Pax6Sey-1Neu/Pax6Sey-1Neu mice there is an apparent enlargement of the zona limitans (the boundary region between prosomeres p2 and p3), and a blurring of the p1-p2 boundary. PAX6 function is also required for the normal development of the posterior commissure at the midbrain-p1 boundary. In the posterior diencephalon PAX6 appears to regulate its own transcription, and that of Wnt7b. In p2 and p3, ventral markers are expressed more dorsally than normal, and this is accompanied in p3 by a reduction in the size of the zona incerta. Thus, PAX6 is essential for the normal development and regionalization of the diencephalon.
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24 MeSH Terms
Amphetamine and dopamine-induced immediate early gene expression in striatal neurons depends on postsynaptic NMDA receptors and calcium.
Konradi C, Leveque JC, Hyman SE
(1996) J Neurosci 16: 4231-9
MeSH Terms: Amphetamine, Animals, Base Sequence, Binding Sites, Calcium, Corpus Striatum, Dizocilpine Maleate, Dopamine, Gene Expression, Genes, Immediate-Early, Male, Molecular Sequence Data, Neurons, Oligonucleotide Probes, Rats, Rats, Sprague-Dawley, Receptors, Dopamine D1, Receptors, N-Methyl-D-Aspartate, Synapses
Show Abstract · Added May 27, 2014
Amphetamine and cocaine induce the expression of both immediate early genes (IEGs) and neuropeptide genes in rat striatum. Despite the demonstrated dependence of these effects on D1 dopamine receptors, which activate the cyclic AMP pathway, there are several reports that amphetamine and cocaine-induced IEG expression can be inhibited in striatum in vivo by NMDA receptor antagonists. We find that in vivo, the NMDA receptor antagonist MK-801 inhibits amphetamine induction of c-fos acutely and also prevents downregulation of IEG expression with chronic amphetamine administration. Such observations raise the question of whether dopamine/glutamate interactions occur at the level of corticostriatal and mesostriatal circuitry or within striatal neurons. Therefore, we studied dissociated striatal cultures in which midbrain and cortical presynaptic inputs are removed. In these cultures, we find that dopamine- or forskolin-mediated IEG induction requires Ca2+ entry via NMDA receptors but not via L-type Ca2+ channels. Moreover, blockade of NMDA receptors diminishes the ability of dopamine to induce phosphorylation of the cyclic AMP responsive element binding protein CREB. Although these results do not rule out a role for circuit-level dopamine/glutamate interactions, they demonstrate a requirement at the cellular level for interactions between the cyclic AMP and NMDA receptor pathways in dopamine-regulated gene expression in striatal neurons.
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19 MeSH Terms