Journal articles: 'Branched RNA'

1

Edmonds, Mary. "Branched RNA." BioEssays 6, no. 5 (May 1987): 212–16. http://dx.doi.org/10.1002/bies.950060505.

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2

Grøtli, Morten, Ramon Eritja, and Brian Sproat. "Solid-phase synthesis of branched RNA and branched DNA/RNA chimeras." Tetrahedron 53, no. 33 (August 1997): 11317–46. http://dx.doi.org/10.1016/s0040-4020(97)00731-x.

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3

Nakashima, Yuko, Hiroshi Abe, Naoko Abe, Kyoko Aikawa, and Yoshihiro Ito. "Branched RNA nanostructures for RNA interference." Chemical Communications 47, no. 29 (2011): 8367. http://dx.doi.org/10.1039/c1cc11780g.

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4

Aviñó, Anna, Sandra M. Ocampo, José Carlos Perales, and Ramon Eritja. "Branched RNA: A New Architecture for RNA Interference." Journal of Nucleic Acids 2011 (2011): 1–7. http://dx.doi.org/10.4061/2011/586935.

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Branched RNAs with two and four strands were synthesized. These structures were used to obtain branched siRNA. The branched siRNA duplexes had similar inhibitory capacity as those of unmodified siRNA duplexes, as deduced from gene silencing experiments of the TNF-α protein. Branched RNAs are considered novel structures for siRNA technology, and they provide an innovative tool for specific gene inhibition. As the method described here is compatible with most RNA modifications described to date, these compounds may be further functionalized to obtain more potent siRNA derivatives and can be attached to suitable delivery systems.

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5

Kierzek, Ryszard, David W. Kopp, Mary Edmonds, and Marvin H. Caruthers. "Chemical synthesis of branched RNA." Nucleic Acids Research 14, no. 12 (1986): 4751–64. http://dx.doi.org/10.1093/nar/14.12.4751.

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6

Lilley, David M. J. "Folding of branched RNA species." Biopolymers 48, no. 2-3 (1998): 101–12. http://dx.doi.org/10.1002/(sici)1097-0282(1998)48:2<101::aid-bip2>3.0.co;2-7.

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7

Wang, Yangming, and Scott K. Silverman. "Characterization of Deoxyribozymes That Synthesize Branched RNA†." Biochemistry 42, no. 51 (December 2003): 15252–63. http://dx.doi.org/10.1021/bi0355847.

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8

Wang, Yangming, and Scott K. Silverman. "Deoxyribozymes That Synthesize Branched and Lariat RNA." Journal of the American Chemical Society 125, no. 23 (June 2003): 6880–81. http://dx.doi.org/10.1021/ja035150z.

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9

Damha, Masad J., and Kelvin K. Ogilvie. "Synthesis and spectroscopic analysis of branched RNA fragments: messenger RNA splicing intermediates." Journal of Organic Chemistry 53, no. 16 (August 1988): 3710–22. http://dx.doi.org/10.1021/jo00251a010.

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10

Lönnberg, Tuomas A. "Can Phosphate-Branched RNA Persist under Physiological Conditions?" ChemBioChem 13, no. 18 (November 26, 2012): 2690–700. http://dx.doi.org/10.1002/cbic.201200629.

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11

Esslinger, Stephanie Maria, Björn Schwalb, Stephanie Helfer, Katharina Maria Michalik, Heidi Witte, Kerstin C. Maier, Dietmar Martin, et al. "DrosophilamiR-277 controls branched-chain amino acid catabolism and affects lifespan." RNA Biology 10, no. 6 (June 2013): 1042–56. http://dx.doi.org/10.4161/rna.24810.

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12

Garrey, Stephen M., Adam Katolik, Mantas Prekeris, Xueni Li, Kerri York, Sarah Bernards, Stanley Fields, Rui Zhao, Masad J. Damha, and Jay R. Hesselberth. "A homolog of lariat-debranching enzyme modulates turnover of branched RNA." RNA 20, no. 8 (June 11, 2014): 1337–48. http://dx.doi.org/10.1261/rna.044602.114.

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13

Döring, Jessica, and Thomas Hurek. "Dual coding potential of a 2′,5′-branched ribonucleotide in DNA." RNA 25, no. 1 (October 25, 2018): 105–20. http://dx.doi.org/10.1261/rna.068486.118.

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14

Földesi, András, Peter Agback, Corin Glemarec, and Chattopadhyaya Jyoti. "Synthesis of tetrameric branched RNA-DNA conjugate & branched-RNA analogue & their comparative conformational studies by 500 MHz NMR spectroscopy." Tetrahedron 47, no. 34 (August 1991): 7135–56. http://dx.doi.org/10.1016/s0040-4020(01)96167-8.

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15

Bryson, David I., Wenyu Zhang, Patrick M. McLendon, Theresa M. Reineke, and Webster L. Santos. "Toward Targeting RNA Structure: Branched Peptides as Cell-Permeable Ligands to TAR RNA." ACS Chemical Biology 7, no. 1 (October 28, 2011): 210–17. http://dx.doi.org/10.1021/cb200181v.

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16

Hubbard, Lauren, Paula McSteen, John Doebley, and Sarah Hake. "Expression Patterns and Mutant Phenotype of teosinte branched1 Correlate With Growth Suppression in Maize and Teosinte." Genetics 162, no. 4 (December 1, 2002): 1927–35. http://dx.doi.org/10.1093/genetics/162.4.1927.

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Abstract The evolution of domesticated maize from its wild ancestor teosinte is a dramatic example of the effect of human selection on agricultural crops. Maize has one dominant axis of growth, whereas teosinte is highly branched. The axillary branches in maize are short and feminized whereas the axillary branches of teosinte are long and end in a male inflorescence under normal growth conditions. Previous QTL and molecular analysis suggested that the teosinte branched1 (tb1) gene of maize contributed to the architectural difference between maize and teosinte. tb1 mutants of maize resemble teosinte in their overall architecture. We analyzed the tb1 mutant phenotype in more detail and showed that the highly branched phenotype was due to the presence of secondary and tertiary axillary branching, as well as to an increase in the length of each node, rather than to an increase in the number of nodes. Double-mutant analysis with anther ear1 and tassel seed2 revealed that the sex of the axillary inflorescence was not correlated with its length. RNA in situ hybridization showed that tb1 was expressed in maize axillary meristems and in stamens of ear primordia, consistent with a function of suppressing growth of these tissues. Expression in teosinte inflorescence development suggests a role in pedicellate spikelet suppression. Our results provide support for a role for tb1 in growth suppression and reveal the specific tissues where suppression may occur.

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17

Fang, Li Tai, William M. Gelbart, and Avinoam Ben-Shaul. "The size of RNA as an ideal branched polymer." Journal of Chemical Physics 135, no. 15 (October 21, 2011): 155105. http://dx.doi.org/10.1063/1.3652763.

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18

Javadi-Zarnaghi, Fatemeh, and Claudia Höbartner. "Lanthanide Cofactors Accelerate DNA-Catalyzed Synthesis of Branched RNA." Journal of the American Chemical Society 135, no. 34 (August 14, 2013): 12839–48. http://dx.doi.org/10.1021/ja406162z.

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19

Damha, Masad J., and Kelvin K. Ogilvie. "Conformational properties of branched RNA fragments in aqueous solution." Biochemistry 27, no. 17 (August 23, 1988): 6403–16. http://dx.doi.org/10.1021/bi00417a032.

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20

Bell, Anthony J., Seema Chauhan, Sarah A. Woodson, and Neville R. Kallenbach. "Interactions of recombinant HMGB proteins with branched RNA substrates." Biochemical and Biophysical Research Communications 377, no. 1 (December 2008): 262–67. http://dx.doi.org/10.1016/j.bbrc.2008.09.131.

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21

Clark, Nathaniel E., Adam Katolik, Kenneth M. Roberts, Alexander B. Taylor, Stephen P. Holloway, Jonathan P. Schuermann, Eric J. Montemayor, et al. "Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1." Proceedings of the National Academy of Sciences 113, no. 51 (December 6, 2016): 14727–32. http://dx.doi.org/10.1073/pnas.1612729114.

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Intron lariats are circular, branched RNAs (bRNAs) produced during pre-mRNA splicing. Their unusual chemical and topological properties arise from branch-point nucleotides harboring vicinal 2′,5′- and 3′,5′-phosphodiester linkages. The 2′,5′-bonds must be hydrolyzed by the RNA debranching enzyme Dbr1 before spliced introns can be degraded or processed into small nucleolar RNA and microRNA derived from intronic RNA. Here, we measure the activity of Dbr1 fromEntamoeba histolyticaby using a synthetic, dark-quenched bRNA substrate that fluoresces upon hydrolysis. Purified enzyme contains nearly stoichiometric equivalents of Fe and Zn per polypeptide and demonstrates turnover rates of ∼3 s−1. Similar rates are observed when apo-Dbr1 is reconstituted with Fe(II)+Zn(II) under aerobic conditions. Under anaerobic conditions, a rate of ∼4.0 s−1is observed when apoenzyme is reconstituted with Fe(II). In contrast, apo-Dbr1 reconstituted with Mn(II) or Fe(II) under aerobic conditions is inactive. Diffraction data from crystals of purified enzyme using X-rays tuned to the Fe absorption edge show Fe partitions primarily to the β-pocket and Zn to the α-pocket. Structures of the catalytic mutant H91A in complex with 7-mer and 16-mer synthetic bRNAs reveal bona fide RNA branchpoints in the Dbr1 active site. A bridging hydroxide is in optimal position for nucleophilic attack of the scissile phosphate. The results clarify uncertainties regarding structure/function relationships in Dbr1 enzymes, and the fluorogenic probe permits high-throughput screening for inhibitors that may hold promise as treatments for retroviral infections and neurodegenerative disease.

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22

FOELDESI, A., P. AGBACK, C. GLEMAREC, and J. CHATTOPADHYAYA. "ChemInform Abstract: Synthesis of Tetrameric Branched RNA-DNA Conjugate and Branched-RNA Analogue and Their Comparative Conformational Studies by 500 MHz NMR Spectroscopy." ChemInform 22, no. 50 (August 22, 2010): no. http://dx.doi.org/10.1002/chin.199150230.

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23

Ganeshan, K., T. Tadey, K. Nam, R. Braich, W. C. Purdy, J. D. Boeke, and M. J. Damha. "Novel Approaches to the Synthesis and Analysis of Branched RNA." Nucleosides, Nucleotides and Nucleic Acids 14, no. 3 (May 1, 1995): 1009–13. http://dx.doi.org/10.1080/15257779508012522.

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24

Lee, Christine S., Timothy P. Mui, and Scott K. Silverman. "Improved deoxyribozymes for synthesis of covalently branched DNA and RNA." Nucleic Acids Research 39, no. 1 (August 25, 2010): 269–79. http://dx.doi.org/10.1093/nar/gkq753.

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25

Béclin, Christophe, Stéphanie Boutet, Peter Waterhouse, and Hervé Vaucheret. "A Branched Pathway for Transgene-Induced RNA Silencing in Plants." Current Biology 12, no. 8 (April 2002): 684–88. http://dx.doi.org/10.1016/s0960-9822(02)00792-3.

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26

Wynn, Jessica E., and Webster L. Santos. "HIV-1 drug discovery: targeting folded RNA structures with branched peptides." Organic & Biomolecular Chemistry 13, no. 21 (2015): 5848–58. http://dx.doi.org/10.1039/c5ob00589b.

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27

Lafortune, Francois, Masad J. Damha, Xuejun Tang, Kenneth G. Standing, John B. Westmore, and Kelvin K. Ogilvie. "Time-of-flight Secondary Ion Mass Spectrometry of Branched RNA Fragrants: Messenger RNA Splicing Intermedistes." Nucleosides and Nucleotides 9, no. 3 (April 1990): 445–46. http://dx.doi.org/10.1080/07328319008045167.

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28

Casey, John L. "RNA Editing in Hepatitis Delta Virus Genotype III Requires a Branched Double-Hairpin RNA Structure." Journal of Virology 76, no. 15 (August 1, 2002): 7385–97. http://dx.doi.org/10.1128/jvi.76.15.7385-7397.2002.

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ABSTRACT RNA editing at the amber/W site plays a central role in the replication scheme of hepatitis delta virus (HDV), allowing the virus to produce two functionally distinct forms of the sole viral protein, hepatitis delta antigen (HDAg), from the same open reading frame. Editing is carried out by a cellular activity known as ADAR (adenosine deaminase), which acts on RNA substrates that are at least partially double stranded. In HDV genotype I, editing requires a highly conserved base-paired structure that occurs within the context of the unbranched rod structure characteristic of HDV RNA. This base-paired structure is disrupted in the unbranched rod of HDV genotype III, which is the most distantly related of the three known HDV genotypes and is associated with the most severe disease. Here I show that RNA editing in HDV genotype III requires a branched double-hairpin structure that deviates substantially from the unbranched rod structure, involving the rearrangement of nearly 80 bp. The structure includes a UNCG RNA tetraloop, a highly stable structural motif frequently involved in the folding of large RNAs such as rRNA. The double-hairpin structure is required for editing, and hence for virion formation, but not for HDV RNA replication, which requires the unbranched rod structure. HDV genotype III thus relies on a dynamic conformational switch between the two different RNA structures: the unbranched rod characteristic of HDV RNA and a branched double-hairpin structure that is required for RNA editing. The different mechanisms of editing in genotypes I and III underscore their functional differences and may be related to pathogenic differences as well.

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29

Pratico, E. D., and S. K. Silverman. "Ty1 reverse transcriptase does not read through the proposed 2',5'-branched retrotransposition intermediate in vitro." RNA 13, no. 9 (July 13, 2007): 1528–36. http://dx.doi.org/10.1261/rna.629607.

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30

Sabarinathan, Radhakrishnan, Christian Anthon, Jan Gorodkin, and Stefan Seemann. "Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures." Genes 9, no. 12 (December 4, 2018): 604. http://dx.doi.org/10.3390/genes9120604.

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Self-contained structured domains of RNA sequences have often distinct molecular functions. Determining the boundaries of structured domains of a non-coding RNA (ncRNA) is needed for many ncRNA gene finder programs that predict RNA secondary structures in aligned genomes because these methods do not necessarily provide precise information about the boundaries or the location of the RNA structure inside the predicted ncRNA. Even without having a structure prediction, it is of interest to search for structured domains, such as for finding common RNA motifs in RNA-protein binding assays. The precise definition of the boundaries are essential for downstream analyses such as RNA structure modelling, e.g., through covariance models, and RNA structure clustering for the search of common motifs. Such efforts have so far been focused on single sequences, thus here we present a comparison for boundary definition between single sequence and multiple sequence alignments. We also present a novel approach, named RNAbound, for finding the boundaries that are based on probabilities of evolutionarily conserved base pairings. We tested the performance of two different methods on a limited number of Rfam families using the annotated structured RNA regions in the human genome and their multiple sequence alignments created from 14 species. The results show that multiple sequence alignments improve the boundary prediction for branched structures compared to single sequences independent of the chosen method. The actual performance of the two methods differs on single hairpin structures and branched structures. For the RNA families with branched structures, including transfer RNA (tRNA) and small nucleolar RNAs (snoRNAs), RNAbound improves the boundary predictions using multiple sequence alignments to median differences of −6 and −11.5 nucleotides (nts) for left and right boundary, respectively (window size of 200 nts).

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31

Tedin, K., and F. Norel. "Comparison of ΔrelA Strains of Escherichia coli and Salmonella enterica Serovar Typhimurium Suggests a Role for ppGpp in Attenuation Regulation of Branched-Chain Amino Acid Biosynthesis." Journal of Bacteriology 183, no. 21 (November 1, 2001): 6184–96. http://dx.doi.org/10.1128/jb.183.21.6184-6196.2001.

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ABSTRACT The growth recovery of Escherichia coli K-12 andSalmonella enterica serovar Typhimurium ΔrelAmutants were compared after nutritional downshifts requiring derepression of the branched-chain amino acid pathways. Because wild-type E. coli K-12 and S. enterica serovar Typhimurium LT2 strains are defective in the expression of the genes encoding the branch point acetohydroxy acid synthetase II (ilvGM) and III (ilvIH) isozymes, respectively, ΔrelA derivatives corrected for these mutations were also examined. Results indicate that reduced expression of the known global regulatory factors involved in branched-chain amino acid biosynthesis cannot completely explain the observed growth recovery defects of the ΔrelA strains. In the E. coli K-12 MG1655 ΔrelA background, correction of the preexisting rph-1 allele which causes pyrimidine limitations resulted in complete loss of growth recovery. S. enterica serovar Typhimurium LT2 ΔrelA strains were fully complemented by elevated basal ppGpp levels in an S. enterica serovar Typhimurium LT2 ΔrelA spoT1 mutant or in a strain harboring an RNA polymerase mutation conferring a reduced RNA chain elongation rate. The results are best explained by a dependence on the basal levels of ppGpp, which are determined byrelA-dependent changes in tRNA synthesis resulting from amino acid starvations. Expression of the branched-chain amino acid operons is suggested to require changes in the RNA chain elongation rate of the RNA polymerase, which can be achieved either by elevation of the basal ppGpp levels or, in the case of the E. coli K-12 MG1655 strain, through pyrimidine limitations which partially compensate for reduced ppGpp levels. Roles for ppGpp in branched-chain amino acid biosynthesis are discussed in terms of effects on the synthesis of known global regulatory proteins and current models for the control of global RNA synthesis by ppGpp.

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32

Zhang, Aiguo, Larry Pastor, Quan Nguyen, Yuling Luo, Wen Yang, Michael Flagella, Rajesh Chavli, et al. "Small Interfering RNA and Gene Expression Analysis Using a Multiplex Branched DNA Assay without RNA Purification." Journal of Biomolecular Screening 10, no. 6 (September 2005): 549–56. http://dx.doi.org/10.1177/1087057105277414.

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The authors have developed a novel multiplex detection system that quantitatively measures the expression level of 11 messenger RNAs (mRNAs) directly from cell lysates or tissue homogenates without RNA purification. The system incorporates branched DNA (bDNA) technology from Bayer and a multiplex bead array platform from Luminex. In this study, a 21-nt synthetic small interfering RNA (siRNA; specifically designed to knockdown interleukin-8 [IL-8] expression) was delivered into HeLa cells. Using the multiplex bDNA assay, gene expression levels were measured simultaneously from cell lysates for 11 genes. After treating the HeLa cells for 20 h with phorbol myristate acetate (PMA), IL-8 mRNA levels were induced by almost 50-fold; transfection with 30 nM IL-8-specific siRNA reduced the PMA-induced IL-8 mRNA by 80%. In addition, PMA induced mRNA expression in IL-1α (3-fold) and IL-6 (4-fold); however, the IL-8 siRNA did not affect the expression of either of these 2 cytokine genes, indicating that the siRNA was selective for IL-8 mRNA expression. Three housekeeping genes’ expression levels were measured under all conditions tested. The multiplex bDNA assay provides a powerful tool for quantitative multiplex gene expression analysis directly from cell lysates, which could be extremely valuable for conservation of rare or difficult-to-obtain samples.

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33

Bryson, David I., Wenyu Zhang, W. Keith Ray, and Webster L. Santos. "Screening of a branched peptide library with HIV-1 TAR RNA." Molecular BioSystems 5, no. 9 (2009): 1070. http://dx.doi.org/10.1039/b904304g.

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34

Liu, Di, Cody W. Geary, Gang Chen, Yaming Shao, Mo Li, Chengde Mao, Ebbe S. Andersen, Joseph A. Piccirilli, Paul W. K. Rothemund, and Yossi Weizmann. "Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures." Nature Chemistry 12, no. 3 (January 20, 2020): 249–59. http://dx.doi.org/10.1038/s41557-019-0406-7.

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35

Zhang, Wenyu, David I. Bryson, Jason B. Crumpton, Jessica Wynn, and Webster L. Santos. "Branched peptideboronic acids (BPBAs): a novel mode of binding towards RNA." Chem. Commun. 49, no. 24 (February 7, 2013): 2436–38. http://dx.doi.org/10.1039/c3cc00243h.

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36

Yamori, Yuka, Masafumi Hamakawa, Ryota Hidese, Moeko Fukuda, Haruyuki Atomi, Wakao Fukuda, and Shinsuke Fujiwara. "Branched-chain polyamine stabilizes RNA polymerase at elevated temperatures in hyperthermophiles." Amino Acids 52, no. 2 (May 17, 2019): 275–85. http://dx.doi.org/10.1007/s00726-019-02745-y.

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37

Benzaria, Samira, Dorothée Bardiot, Tony Bouisset, Clément Counor, Céline Rabeson, Claire Pierra, Richard Storer, et al. "2′-C-Methyl Branched Pyrimidine Ribonucleoside Analogues: Potent Inhibitors of RNA Virus Replication." Antiviral Chemistry and Chemotherapy 18, no. 4 (August 2007): 225–42. http://dx.doi.org/10.1177/095632020701800406.

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RNA viruses are the agents of numerous widespread and often severe diseases. Their unique RNA-dependent RNA polymerase (RDRP) is essential for replication and, thus, constitutes a valid target for the development of selective chemotherapeutic agents. In this regard, we have investigated sugar-modified ribonucleoside analogues as potential inhibitors of the RDRP. Title compounds retain ‘natural’ pyrimidine bases, but possess a β-methyl substituent at the 2′-position of the D- or L-ribose moiety. Evaluation against a broad range of RNA viruses, either single-stranded positive (ssRNA), single-stranded negative (ssRNA−) or double-stranded (dsRNA), revealed potent activities for D-2′- C-methyl-cytidine and -uridine against ssRNA+, and dsRNA viruses. None of the L-enantiomers were active. Moreover, the 5′-triphosphates of the active D-enantiomers were found to inhibit the bovine virus diarrhoea virus polymerase. Thus, the 2′-methyl branching of natural pyrimidine ribonucleosides transforms physiological molecules into potent, broad-spectrum antiviral agents that merit further development.

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38

Schwer, Beate, Fahad Khalid, and Stewart Shuman. "Mechanistic insights into the manganese-dependent phosphodiesterase activity of yeast Dbr1 with bis-p-nitrophenylphosphate and branched RNA substrates." RNA 22, no. 12 (October 7, 2016): 1819–27. http://dx.doi.org/10.1261/rna.058552.116.

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39

Carrocci, Tucker J., Lea Lohe, Matthew J. Ashton, Claudia Höbartner, and Aaron A. Hoskins. "Debranchase-resistant labeling of RNA using the 10DM24 deoxyribozyme and fluorescent modified nucleotides." Chemical Communications 53, no. 88 (2017): 11992–95. http://dx.doi.org/10.1039/c7cc06703h.

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40

Wynn, Jessica E., Wenyu Zhang, Denis M. Tebit, Laurie R. Gray, Marie-Louise Hammarskjold, David Rekosh, and Webster L. Santos. "Effect of intercalator and Lewis acid–base branched peptide complex formation: boosting affinity towards HIV-1 RRE RNA." MedChemComm 7, no. 7 (2016): 1436–40. http://dx.doi.org/10.1039/c6md00171h.

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41

Linnstaedt, S. D., W. K. Kasprzak, B. A. Shapiro, and J. L. Casey. "The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels." RNA 15, no. 6 (April 21, 2009): 1177–87. http://dx.doi.org/10.1261/rna.1504009.

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42

Lilley, David M. J. "Analysis of branched nucleic acid structure using comparative gel electrophoresis." Quarterly Reviews of Biophysics 41, no. 1 (February 2008): 1–39. http://dx.doi.org/10.1017/s0033583508004678.

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AbstractElectrophoresis in polyacrylamide gels provides a simple yet powerful means of analyzing the relative disposition of helical arms in branched nucleic acids. The electrophoretic mobility of DNA or RNA with a central discontinuity is determined by the angle subtended between the arms radiating from the branchpoint. In a multi-helical branchpoint, comparative gel electrophoresis can provide a relative measure of all the inter-helical angles and thus the shape and symmetry of the molecule. Using the long–short arm approach, the electrophoretic mobility of all the species with two helical arms that are longer than all others is compared. This can be done as a function of conditions, allowing the analysis of ion-dependent folding of branched DNA and RNA species. Notable successes for the technique include the four-way (Holliday) junction in DNA and helical junctions in functionally significant RNA species such as ribozymes. Many of these structures have subsequently been proved correct by crystallography or other methods, up to 10 years later in the case of the Holliday junction. Just as important, the technique has not failed to date. Comparative gel electrophoresis can provide a window on both fast and slow conformational equilibria such as conformer exchange in four-way DNA junctions. But perhaps the biggest test of the approach has been to deduce the structures of complexes of four-way DNA junctions with proteins. Two recent crystallographic structures show that the global structures were correctly deduced by electrophoresis, proving the worth of the method even in these rather complex systems. Comparative gel electrophoresis is a robust method for the analysis of branched nucleic acids and their complexes.

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43

Bussière, F., J. Ouellet, F. Côté, D. Lévesque, and J. P. Perreault. "Mapping in Solution Shows the Peach Latent Mosaic Viroid To Possess a New Pseudoknot in a Complex, Branched Secondary Structure." Journal of Virology 74, no. 6 (March 15, 2000): 2647–54. http://dx.doi.org/10.1128/jvi.74.6.2647-2654.2000.

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ABSTRACT We have investigated the secondary structure of peach latent mosaic viroid (PLMVd) in solution, and we present here the first description of the structure of a branched viroid in solution. Different PLMVd transcripts of plus polarity were produced by using the circularly permuted RNA method and the exploitation of RNA internal secondary structure to position the 5′ and 3′ termini and studied by nuclease mapping and binding shift assays using DNA and RNA oligonucleotides. We show that PLMVd folds into a complex, branched secondary structure. In general, this structure is similar to that reported previously, which was based on sequence comparison and computer modelling. The structural microheterogeneity is apparently limited to only some small domains. More importantly, this structure includes a novel pseudoknot that is conserved in all PLMVd isolates and seems to allow folding into a very compact form. This pseudoknot is also found in chrysanthemum chlorotic mottle viroid, suggesting that it is a unique feature of the viroid members of the PLMVd subgroup.

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44

Damha, Masad J., Kanjana Ganeshan, Robert H. E. Hudson, and Steven V. Zabarylo. "Solid-phase synthesis of branched oligoribonucleotides related to messenger RNA splicing intermediates." Nucleic Acids Research 20, no. 24 (1992): 6565–73. http://dx.doi.org/10.1093/nar/20.24.6565.

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45

Dhundale, A., T. Furuichi, M. Inouye, and S. Inouye. "Mutations that affect production of branched RNA-linked msDNA in Myxococcus xanthus." Journal of Bacteriology 170, no. 12 (1988): 5620–24. http://dx.doi.org/10.1128/jb.170.12.5620-5624.1988.

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46

WalkerPeach, Cindy R., Matthew Winkler, Dwight B. DuBois, and Brittan L. Pasloske. "Ribonuclease-resistant RNA Controls (Armored RNA) for Reverse Transcription-PCR, Branched DNA, and Genotyping Assays for Hepatitis C Virus." Clinical Chemistry 45, no. 12 (December 1, 1999): 2079–85. http://dx.doi.org/10.1093/clinchem/45.12.2079.

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Abstract Background: Comparison and evaluation of molecular diagnostic assays for the detection and quantification of hepatitis C virus (HCV) RNA have been limited by the lack of RNA controls and calibrators. Armored RNA® technology is a means for producing RNA that is completely protected from plasma ribonucleases. This method produces recombinant pseudoviral particles that are noninfectious and contain predefined RNA sequences. Methods: A consensus 412-base sequence from the 5′NCR/Core region of HCV subtype 2b was derived from 34 individually sequenced HCV genotype 2b variants. A DNA fragment encoding the consensus HCV-2b sequence was synthesized de novo, cloned, and expressed as an Armored RNA control. The resulting HCV-2b Armored RNA (AR-HCV-2b) contained the complete HCV-2b consensus RNA sequence encapsidated within a protective protein coat. Results: AR-HCV-2b was fully recoverable from human plasma incubated at 4 °C for >300 days. The particles were tested in three clinical assay formats: AmplicorTM HCV Monitor 1.0, QuantiplexTM HCV RNA 2.0, and INNO-LiPATM HCV II. When added into seronegative, nonviremic plasma, AR-HCV-2b showed reproducible signals and linear dilutions in both the Amplicor and Quantiplex assays. AR-HCV-2b was correctly identified as subtype 2b in the INNO-LiPA line probe assay. Conclusion: The HCV-2b Armored RNA control is a versatile, durable, ribonuclease-resistant viral RNA control that is compatible in three different clinical assay formats.

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Nair, Baiju G., Yue Zhou, Kyoji Hagiwara, Masashi Ueki, Takashi Isoshima, Hiroshi Abe, and Yoshihiro Ito. "Enhancement of synergistic gene silencing by RNA interference using branched “3-in-1” trimer siRNA." Journal of Materials Chemistry B 5, no. 22 (2017): 4044–51. http://dx.doi.org/10.1039/c7tb00846e.

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Nanostructured RNA carrying three different siRNAs was assembled to silence three target genes (Axin, APC, and GSK-3β) in the Wnt/β-catenin signaling pathway. This nanostructured ‘3-in-1’ siRNA showed high activity at a low concentration due to the long-term resistance, and enhancing the effect of RNA interference.

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Sund, C., A. Földesi, S. Yamakage, P. Agback, and J. Chattopadhyaya. "New regiospecific synthesis of branched tetra-, nona- & deca-RNA modelling the lariat formed in RNA splicing reactions." Tetrahedron 47, no. 32 (August 1991): 6305–36. http://dx.doi.org/10.1016/s0040-4020(01)86562-5.

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Faust, Russell A., Keith Henry, Peter Dailey, Holly Melroe, Christopher Sullivan, Alejo Erice, Ashley T. Haase, and Lawrence R. Boies. "Outpatient Biopsies of the Palatine Tonsil: Access to Lymphoid Tissue for Assessment of Human Immunodeficiency Virus RNA Titers." Otolaryngology–Head and Neck Surgery 114, no. 4 (April 1996): 593–98. http://dx.doi.org/10.1016/s0194-59989670252-8.

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OBJECTIVES: Our objective was to assess the feasibility of using tonsillar lymphoid biopsy specimens obtained on an outpatient basis to quantitate a patient's lymphoid human immunodeficiency virus (HIV) RNA titers. DESIGN: A pilot cohort study was performed. PATIENTS: We evaluated ten HIV-seropositive patients who ranged in age from 26 to 48 years and had CD4+ cell counts ranging from 110 to 833 at enrollment. MAIN OUTCOME MEASURES: The main outcome measures were tolerance and safety of outpatient tonsil biopsies and quantitation of HIV RNA titers in tonsillar lymphoid biopsy specimens, plasma, and peripheral blood mononuclear cells determined by a new method of HIV RNA signal amplification with branched DNA probes. RESULTS: Outpatient tonsil biopsies were well tolerated and were performed without complications. Nine of 10 tonsil biopsies from the HIV-seropositive patients examined were positive for significant concentrations of HIV RNA, ranging from 10 6 to 10 9 HIV RNA equivalents per gram of tissue. All of the HIV RNA-positive tonsillar lymphoid specimens had HIV RNA titers that were 10 2 to 10 4 times greater than those recovered from plasma (per milliliter) of the same patient obtained at the time of biopsy. CONCLUSIONS: Sufficient tonsillar tissue can be obtained in an outpatient clinic setting to quantitate lymphoid HIV titers by the new branched-DNA signal amplification method with relative ease and without complication. The biopsy method described here affords ready access to the lymphoreticular system, which may help to advance our understanding of the pathogenesis of myriad immune diseases without the need for excisional node biopsies.

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Gao, Feng, Wojciech Kasprzak, Vera A. Stupina, Bruce A. Shapiro, and Anne E. Simon. "A Ribosome-Binding, 3′ Translational Enhancer Has a T-Shaped Structure and Engages in a Long-Distance RNA-RNA Interaction." Journal of Virology 86, no. 18 (July 3, 2012): 9828–42. http://dx.doi.org/10.1128/jvi.00677-12.

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Many plant RNA viruses contain elements in their 3′ untranslated regions (3′ UTRs) that enhance translation. The PTE (Panicum mosaic virus-like translational enhancer) ofPea enation mosaic virus(PEMV) binds to eukaryotic initiation factor 4E (eIF4E), but how this affects translation from the 5′ end is unknown. We have discovered a three-way branched element just upstream of the PEMV PTE that engages in a long-distance kissing-loop interaction with a coding sequence hairpin that is critical for the translation of a reporter construct and the accumulation of the viral genomein vivo. Loss of the long-distance interaction was more detrimental than elimination of the adjacent PTE, indicating that the RNA-RNA interaction supports additional translation functions besides relocating the PTE to the 5′ end. The branched element is predicted by molecular modeling and molecular dynamics to form a T-shaped structure (TSS) similar to the ribosome-binding TSS ofTurnip crinkle virus(TCV). The PEMV element binds to plant 80S ribosomes with aKd(dissociation constant) of 0.52 μM and to 60S subunits with aKdof 0.30 μM. Unlike the TCV TSS, the PEMV element also binds 40S subunits (Kd, 0.36 μM). Mutations in the element that suppressed translation reduced either ribosome binding or the RNA-RNA interaction, suggesting that ribosome binding is important for function. This novel, multifunctional element is designated a kl-TSS (kissing-loop T-shaped structure) to distinguish it from the TCV TSS. The kl-TSS has sequence and structural features conserved with the upper portion of most PTE-type elements, which, with the exception of the PEMV PTE, can engage in similar long-distance RNA-RNA interactions.

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Journal articles on the topic 'Branched RNA'

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