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J. Gen. Virol. 93, 2408–18. Evolution of the hepatitis E virus hypervariable region. 2012

Smith, D.B., Vanek, J., Ramalingam, S., Johannessen, I., Templeton, K. and Simmonds, P.

Notes: The authors of this study investigated the function of the hypervariable region (HVR) present in open reading frame 1 (ORF1) in the hepatitis E virus (HEV) by measuring the diversity of the HVR in HEV samples from acutely infected patients and in epidemiologically related samples. They sequenced HEV HVR PCR products from limited dilution cDNA from 8 patients PCR positive for ORF2 of HEV. HEV RNA was extracted from serum using a commercial kit, and then HEV RNA was amplified using the Access RT-PCR System. A second round of PCR was performed using GoTaq® polymerase. cDNA was generated using random hexamer or appropriate primers in the presence of Recombinant RNasin® Ribonuclease Inhibitor. (4242)

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Proc. Natl. Acad. Sci. USA 109, 13428-13433. CAG expansion induces nucleolar stress in polyglutamine diseases. 2012

Tsoi, H., Lau, T.C., Tsang, S.Y., Lau, K.F., and Chan, H.Y.

Notes: Polyglutamine diseases are neurodegenerative disorders associated with the presence of proteins containing polyglutamine repeats. These authors studied the mechanism of polygluatmine toxicity. Mutant RNAs carrying an expanded CAG repeat were shown to activate the nucleolar stress pathway and induce apoptosis. Expanded CAG RNAs were shown to interact with nucleolin, preventing it from binding to an upstream control element of the rRNA promoter and causing decreased rRNA transcription, which in turn induced apoptosis. Perturbations in rRNA transcription were identified by real-time PCR, and fluorescence in situ hybridization was used to determine that expanded CAG RNAs localized to the nucleolus. Hybridization solutions were supplemented with RNasin® Ribonuclease Inhibitor. ImProm-II™ Reverse Transcriptase was used in RT-qPCR assays. (4228)

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Nucl. Acids Res. 40, 6270–89. Mammalian HCA66 protein is required for both ribosome synthesis and centriole duplication. 2012

Bonnart C, Gérus M, Hoareau-Aveilla C, Kiss T, Caizergues-Ferrer M, Henry Y, Henras AK.

Notes: The authors of this study were investigating the relationship between ribosome biosynthesis and cell cycle progression. Specifically they were looking at the role of the protein HCA66, which is a component of the centromere, and required for centriole duplication in mammalian cells and required for nucleolar steps of 40S ribosomal subunit maturation. For studies that were conducted using HeLa cells, HeLa cell nuclear extract was prepared in the presence of Recombinant RNasin® Ribonuclease Inhibitor (0.5U/µl). Prior to lysis of transfected HeLa cells for sucrose gradient experiments, cells were placed in a buffer containing Recombinant RNasin® Ribonuclease Inhibitor (0.5U/µl), and for immunoprecipitation experiments involving transfected HeLa cells, cells were sonicated in the the presence of Recombinant RNasin® Ribonuclease Inhibitor (0.1U/µl). (4243)

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PLoS Genet. 8, e1002941. MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. 2012

Goodier, J.L., Cheung, L.E. and Kazazian, H.H. Jr.

Notes: To better understand the role MOV10 protein, a putative RNA helicase and component of the RNA–induced silencing complex (RISC), in reducing retrotransposon activity, 293T human embryonic kidney cells expressing MOV10 and one of three retrotransposons (LINE1 (L1), Alu or SVA) were lysed in a buffer that included RNasin® Ribonuclease Inhibitor, and FLAG-tagged L1 complexes immunoprecipitated and analyzed by mass spectrometry. Several retrotransposon assays were conducted using FuGENE® HD Transfection Reagent for transfected constructs into 293T, HeLa and HeLa-HA cells. (4255)

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J. Biol. Chem. 287, 21599-21614. Proteomic analysis of wild-type and mutant huntingtin-associated proteins in mouse brains identifies unique interactions and involvement in protein synthesis. 2012

Culver, B.P., Savas, J.N., Park, S.K., Choi, J.H., Zheng, S., Zeitlin, S.O., Yates, J.R., and Tanese, N.

Notes: These authors analyzed and compared affinity-purified protein complexes from brain homogenates of wild type and huntingtin (Htt) mutant mice by mass spectrometry. Brain tissue from FLAG-tagged wild-type and Htt mice was homogenized in HEPES buffer supplemented with protease inhibitors and RNasin®. After affinity purification, protein complexes were digested using Sequencing-Grade Modified Trypsin and ProteaseMAX™ Trypsin Enhancer prior to mass-spectrometry analysis. (4227)

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Appl. Environ. Microbiol. 78, 445–54. Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. 2012

Ma, K., Conrad, R. and Lu, Y.

Notes: The authors of this study investigated the microbial mechanisms associated with the reduction of methane production and emission from rice fields observed with intermittent field drainage. They looked in particular at the abundance of mcrA gene copies and transcripts from rice paddy soil fauna. The mcrA gene encodes the alpha subunit of methyl coenzyme M reductase. 

Total nucleic acid was extracted from soil samples using a phenol-chloroform procedure. For RNA analyses, DNA was hydrolyzed using RQ1 RNase-free DNase in the presence of 0.2µl Recombinant RNasin® Ribonuclease Inhibitor and then further purified using a commercial kit. cDNA synthesis was carried out using the Improm-II™ Reverse Transcription System, again in the presence of 1.0µl Recombinant RNasin® Ribonuclease Inhibitor. A clone library of transcripts was generated using the pGEM®-T Easy Vector System. The transcript standard for quantitative mcrA analysis was prepared from the in vitro transcript of a mcrA clone using the Riboprobe® in vitro Transcription Systems. (4241)

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Nucl. Acids Res. Dec 8, Epub ahead of print. Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts. 2011

Zhelyazkhova, P., Hammani, K., Rojas, M., Voelker, R., Vargas-Suárez, M., Börner, T., and Barkan, A.

Notes: Pentatricopeptide repeat (PPR) proteins are helical repeat proteins that bind specific RNA segments and protect the adjacent RNA by serving as a barrier to exoribonucleases. This study showed that protection by PPR or PPR-like proteins is the predominant mechanism for defining the positions of processed 5′ and intercistronic mRNA termini in land plant chloroplasts. The authors used RNasin® Ribonuclease Inhibitor in binding reactions between labeled RNA and PPR proteins prior to Gel mobility shift assays. They also used the pGEM®-T Vector to clone various 3´ RNA terminal sequences amplified by RT-PCR. (4185)

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Nucl. Acids Res. [Epub ahead of print]. RNA-binding protein HuR autoregulates its expression by promoting alternative polyadenylation site usage. 2011

Dai, W., Zhang, G. and Makeyev, E.V.

Notes: The full-length 3´ UTR of mouse RNA-binding protein HuR was amplified and cloned into psiCHECK™-1 Vector to create pEM429 plasmid. To generate radiolabeled RNA substrates for use in cleavage assays, RNA was synthesized from 1µg of linearized plasmid using 50µCi of [α-32P]UTP, 0.8mM Ribo m7G Cap Analog and T7 RNA Polymerase by incubating for 1.5 hours at 37°C. The RNAs were then treated with 1 unit of RQ1 RNase-Free DNase per 1µg of template DNA for 15 minutes at 37°C before extracting with phenol:chloroform, precipitating with ethanol and resuspending in DEPC-treated water. The cleavage assay used 60fmol of 32P-labeled substrate RNA with 10U Recombinant RNAsin Ribonuclease Inhibitor in a reaction incubated for 2.5 hours at 30°C. RNA probes were labeled with biotin using T7 or T3 RNA Polymerases with a biotin-UTP labeling NTP mixture and incubated for 2 hours at 37°C. The biotinylation reaction was then treated with RQ1 RNase-Free DNase following the same protocol used for radiolabeled RNA. To form HuR/RNA complexes, 2µg of biotinylated RNA was mixed with 100µg nuclear extract and 40 units Recombinant RNAsin® Ribonuclease Inhibitor in a total volume of 20µl, and incubated for 30 minutes at room temperature. For CstF-64/RNA complexes, 1µg of biotinylated RNA was used and the complexes were stabilized by UV crosslinking using 10U Recombinant RNAsin Ribonuclease Inhibitor during the UV treatment. NIH 3T3 cells were UV crosslinked and either total or nuclear RNA used for immunoprecipitation. After extraction the RNAs were treated with RQ1 RNase-Free DNase for 15 minutes at 37°C before RT-PCR using HuR-specific primers. Total RNA purified from cultured cells were incubated with 50U/ml RQ1 RNase-Free DNase at 37°C for 30 minutes before use in RT-qPCR. (4187)

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Genome Res. 20, 1590-604.
Next-generation sequencing identifies the natural killer cell microRNA transcriptome

T. A. Fehniger, T. Wylie, E. Germino, et al.

Notes: RNasin was used in the small RNA library preparation step before sequencing on an Illumina platform.


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J. Cell Sci. 123, 3789-3795. CLP-1 associates with MyoD and HDAC to restore skeletal muscle cell regeneration. 2010

Galatioto, J., Mascareno, E., and Siddiqui, M.A.

Notes: These authors investigated the role of the cardiac lineage protein 1 (CLP1/HEXIM1) in skeletal myogenesis. They showed that CLP1 knockout C2C12 cells were unable to differentiate, and then investigated the hypothesis that CLP1 associates with MyoD and HDAC proteins to downregulate cell cycle genes, such as cyclin D1, and allow expression of differentiation-specific genes. RNasin® Ribonuclease inhibitor was used in coimmunoprecipitation assays investigating the interaction between CLP1 and HDAC in C2C12 cells under differentiation and non-differentiation culture conditions. RNasin® was included during cell lysate preparation prior to coimmunoprecipitation assays with antibodies directed against various HDAC proteins. The authors also performed  a luciferase reporter assay using the Dual-Luciferase® Assay System to investigate the regulation of cyclin D1 expression by CLP1, MyoD and HDAC. A luciferase reporter-cyclin D1 construct was co-transfected with MyoD, HDAC and CLP1 constructs and the effect on luciferase expression examined under differentiation and non-differentiation conditions. In differentiation medium MyoD, CLP1 and HDAC5 acted synergistically to reduce cyclin D1 expression. (4225)

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Nucl. Acids Res. 38, e167. In situ reverse transcription: the magic of strength and anonymity. 2010

Ligasová, A., and Koberna, K.

Notes: This paper describes a method for detection of polyA RNA in permeablized cells and cell sections. The method is based on incorporation of 5-bromo-2´-deoxyuridine (BrdUTP) into cDNA by AMV reverse transcriptase. The BrdUTP was easily detectable in DNA-RNA duplexes, and undetectable in DNA-DNA duplexes, making it possible to use the method to detect RNA in situ. RNasin® Ribonuclease Inhibitor was used in the reverse transcriptase reaction mix. (4226)

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FASEB J. 21, 1893–1901. Low expression of COX-2, reduced cumulus expansion, and impaired ovulation in SULT1E1-deficient mice. 2007

Gershon, E., Hourvitz, A., Reikhav, S., Maman, E. and Dekel, N.

Notes: The authors investigated the role of estrogen inactivation by the SULT1E1-encoded estrogen sulfotransferase in ovulation in mice. Semiquantitative RT-PCR was used to characterize the temporal and tissue-specific expression of SULT1E1 mRNA in ovulating mice. First-strand cDNA synthesis was performed at 37°C for 2 hours using 7.5µg of total RNA, 1µl (0.5µg) of oligo(dT)15, 40 units of RNasin® Ribonuclease Inhibitor and 200 units of M-MLV Reverse Transcriptase. (3913)

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Infect. Immun. 75, 3478–89. Reversal of the antichlamydial activity of putative type III secretion inhibitors by iron. 2007

Slepenkin, A., Enquist, P.A., Hägglund, U., de la Maza, L.M., Elofsson, M. and Peterson, E.M.

Notes: The authors screened members of a class of acylated hydrazones of salicylaldehydes (INPs) to characterize their ability to inhibit growth of Chlamydia by affecting the type III secretion (T3S) system, a potent virulence mechanism. Expression levels of various T3S genes and gene markers of early, middle and late developmental cycles were examined by RT-PCR in Chlamydia trachomatis-infected HeLa 229 cells in the presence and absence of INPs. HeLa229 RNA was isolated at 4, 8, 24 and 36 hours postinfection, treated with RQ1 RNase-Free DNase and amplified using the Access RT-PCR System in the presence of 0.5 units of RNasin RNase Inhibitor. Each set of experiments included a no-reverse transcriptase control reaction to control for DNA contamination and a positive control reaction using the Positive Control RNA with Carrier and control primers supplied with the kit. (3795)

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J. Biol. Chem. 281, 7364-73. Human arsenic methyltransferase (AS3MT) pharmacogenetics. Gene resequencing and functional genomics studies. 2006

Wood, T.C., Salavagionne, O.E., Mukherjee, B., Wang, L., Klumpp, A.F., Thomae, B.A., Eckloff, B.W., Schaid, D.J., Wieben, E.D. and Weinshilboum, R.M.

Notes: Human arsenic methyltransferase (AS3MT) was cloned and mutated to produce allozymes for further analysis. COS-1 cells were transfected with constructs encoding the wildtype enzyme and the synthetic allozymes using TransFast™ Transfection Reagent. The wildtype enzyme and allozymes were transcribed and translated using TNT® T7 Coupled Reticulocyte Lysate System in the presence of RNasin® Ribonuclease Inhibitor. (3383)

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J. Immunol. 176, 27-35. Hydrolytic and nonenzymatic functions of acetylcholinesterase comodulate hemopoietic stress responses. 2006

Grisaru, D., Pick, M., Perry, C., Sklan, E.H., Almog, R., Goldberg, I., Naparstek, E., Lessing, J.B., Soreq, H. and Deutsch, V.

Notes: Expression levels of transcription factors critical for hemopoiesis in bone marrow were determined using real-time quantitative PCR. First, total RNA was isolated from mouse bone marrow, treated with DNase I, then reverse transcribed using the ImProm-II™ Reverse Transcription System. Each reaction included 2.4µl of 25mM MgCl2, 4µl of 5X buffer, 1µl of reverse transcriptase, 1µl of dNTP mix (10mM each), 1µl of 50µM random hexamers, 0.5µl of RNasin® Ribonuclease Inhibitor (20U), and 2µl of sample RNA (200ng/µl). (3454)

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Clin. Chem. 52, 634-642. Quantification of mRNA in whole blood by assessing recovery of RNA and efficiency of cDNA synthesis. 2006

Mitsuhashi, M., Tomozawa, S., Endo, K. and Shinagawa, A.

Notes: The authors developed a method to reverse transcribe poly(A)+ RNA from leukocytes without using oligo(dT) immobilized on a 96-well plate. Four RNA targets, as well as a synthetic control RNA, were reverse transcribed using MMLV Reverse Transcriptase (1X reverse transcription buffer [50mM KCl, 10mM Tris-HCl (pH 8.3), 5.5mM MgCl2, 1nL/µL Tween 20], 1.25 mM each dNTP and 4 units of Recombinant RNasin® Ribonuclease Inhibitor), then quantitated by real-time quantitative PCR. The authors varied the concentration of MMLV Reverse Transcriptase, incubation time, and primer/template ratio] to obtain the maximum yield. Small quantities of MMLV Reverse Transcriptase were sufficient to reverse transcribe short synthetic RNA and abundant RNAs, but approximately 100 units was required for other RNAs. The synthetic control RNA was synthesized using the T7 RiboMAX™ Express Large Scale RNA Production System. (3456)

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Proc. Natl. Acad. Sci. USA 103, 2827–32. The U(L)41 protein of herpes simplex virus 1 degrades RNA by endonucleolytic cleavage in absence of other cellular or viral proteins. 2006

Taddeo, B., Zhang, W. and Roizman, B.

Notes: In this study, an in vitro assay was performed to examine the ribonuclease activity of the herpes simplex virus virion host shutoff (vhs) protein. To test whether a purified GST-vhs fusion protein exhibited RNase activity, the entire 3’ UTR of human IEX-1 mRNA (a known target of vhs) was labeled with 32P and then incubated at 30°C with either GST-vhs or GST alone. Samples were taken at various time points and analyzed by denaturing polyacrylamide gel electrophoresis and autoradiography. The GST-vhs fusion protein displayed RNase activity. When RNasin® Plus RNase Inhibitor was added to the reaction, no degradation products were seen, confirming that the nuclease activity of GST-vhs could be blocked by an RNase inhibitor. (3391)

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Clin. Exp. Immunol. 131, 144–51. Contribution of Vα24+Vβ11+ natural killer T cells in Wilsonian hepatitis. 2005

Kinebuchi, M., Matsuura, A., Ohya, K., Abo, W. and Kitazawa, J.

Notes: To prepare single rat NK cells for reverse transcription, the cells were sorted by flow cytometry and lysed using 0.5% NP-40, 2.2µl of 5X M-MLV Reverse Transcriptase Buffer, 0.3µl of 0.1mol/l DTT, 5.5µl DEPC-treated water and 1U of RNasin® Plus RNase Inhibitor. After a 30-minute incubation on ice, the lysates were heated to 65°C for 90 seconds, cooled to 22°C for 3 minutes and placed back on ice. For the RT reaction, 1U RNasin® Plus RNase Inhibitor, 60 U of M-MLV Reverse Transcriptase, 2.5mmol/l dNTPs and 100µM primers were added to these single-cell lysates. (3390)

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Mol. Cell. Biol. 25, 621–636. Mutations in the RNA polymerase III subunit Rpc11p that decrease RNA 3’ cleavage activity increase 3’-terminal oligo(U) length and La-dependent tRNA processing. 2005

Huang, Y., Intine, R.V., Mozlin, A., Hasson, S. and Maraia, R.J.

Notes: RNasin® Plus RNase Inhibitor was added to RNA-DNA ligation reactions and in vitro transcription reactions to protect RNA molecules in both reactions.  For in vitro transcription reactions, 1 unit of RNasin® Plus RNase Inhibitor was added to the reaction buffer.   (3257)

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Oncogene 23, 8920-30. Fibronectin and type IV collagen activate ERα AF-1 by c-Src pathway: effect on breast cancer cell motility. 2004

Sisci, D., Aquila, S., Middea, E., Gentile, M., Maggiolini, M., Mastroiami, F., Montanaro, D. and Ando, S.

Notes: MCF-7 cells were incubated for 24 hours in PRF-SFM and then detached and plated on uncoated dishes or dishes coated with 2μg/cm2 poly-L-Lysine (P-Lys) in PBS, 30μg/ml fibronectin (Fn) in PBS or 30μg/ml type IV Collagen (Col) in 10mM acetic acid. The cells plated on uncoated dishes were treated both with and without 10nM estradiol (E2). After 24 hours, total cellular RNA was extracted and reverse transcribed using M-MLV reverse transcriptase. Briefly, reverse transcription was performed on 1μg of total RNA in a final volume of 10μl by incubation at 37°C for 30 min with 200U of M-MLV reverse transcriptase, 0.4μg oligo-dT, 0.5μM dNTP and 24U RNasin® Ribonuclease Inhibitor, followed by heat denaturation for 5 minutes at 95°C. Subsequent PCR analysis was performed on 1μl of the RT product in a final volume of 25μl. Primers were used to amplify the 210bp fragment of PS2 and the 304 bp fragment of cathepsin D. Amplification of 408bp of ribosomal RNA 36B4 was performed as control. The PCR mixture consisted of 1.25U GoTaq® DNA Polymerase, 1X PCR buffer (10mM Tris-HCl, 50mM KCl), 2.5mM MgCl2, 0.2mM each dNTP, 0.6μM of each PS2 primer or cathepsin D primer and 0.2μM of each 36B4 primer. PCR was performed for 20 cycles at 95°C for 1 minute, 59°C for 2 minutes and 72°C for 1 minute. Ten microliters of the PCR products were separated on a 1.2% agarose gel. (3377)

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Clin. Can. Res. 9, 3080-3097. Gene expression profiling of malignant mesothelioma 2003

Singhal, S., Wiewrodt, R., Malden, L.D., Amin, K.M., Matzie, K., Friedberg, J., Kucharczuk, J.C., Lizky, L.A., Johnson, S.W., Kaiser, L.R., Albelda, S.M.

Notes: RNA was extracted from 300mg malignant mesothelioma tissue samples and treated with DNase in the presence of RNasin® Ribonuclease Inhibitor. The RNA was incubated with oligo(dT) primers and reverse transcribed in the presence of radiolabeled nucleotides. The labeled cDNA was hybridized to preprinted microarrays containing 4132 human genes. (2715)

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Nat. Biotechnol. 20, 738-742. Amine-modified random primers to label probes for DNA microarrays. 2002

Xiang, C.C., Kozhich, O.A., Chen, M., Inman, J., Phan, Q.N., Chen, Y., and Brownstein, M.J.

Notes: In this paper, the authors describe a method to label probes for microarrays. The used the RNasin® Ribonuclease Inhibitor in the probe production process. (2499)

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Mol. Cell. Neurosci. 19, 447-458. AMPA Receptor-Mediated Modulation of Inward Rectifier K+ Channels in Astrocytes of Mouse Hippocampus 2002

Schroder, W., Seifert, G., Huttman, K., Hinterkeuser, S., Steinhauser, C.

Notes: The patch-clamp technique was combined with RT-PCR in acute hippocampal brain slices. After recording, each cell was harvested to perform transcript analysis and identify subunits that underlie inwardly rectifying K+ currents. The recording pipette solution was supplemented with recombinant RNasin Ribonuclease Inhibitor. After recording channel activity, cell contents were harvested through the recording pipette. RT-PCR was performed on cell contents. (2426)

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Infect. Immun. 70, 4389–4398. Characterization of Pit, a Streptococcus pneumoniae iron uptake ABC transporter. 2002

Brown, J.S., Gilliland, S.M., Ruiz-Albert, J. and Holden, D.W.

Notes: The authors describe using the Wizard® Genomic DNA Purification kit and the SV Total RNA Isolation System to isolate genomic DNA and total RNA, respectively, from Streptococcus pneumoniae. The researchers also added RNasin® Ribonuclease Inhibitor to purified total RNA before storing it and using it for later RT-PCR reactions performed with the Access RT-PCR System. (2835)

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Cell Death Differ. 9, 1334-1342. Differential subcellular localization of functionally divergent survivin splice mutants 2002

Mahotka, C., Liebmann, J., Wenzel, M., Suschek, C.V., Schmitt, M., Gabbert, H.E., Gerharz, C.D.

Notes: Promega reverse transcription buffer, AMV reverse transcriptase, and RNAsin® RNAse inhibitor were used in reverse transcription reactions of total RNA from HepG2 heptatoma cells. PCR products were cloned into the pGEMT vector. (2613)

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