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Journal articles on the topic 'RNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

OHNO, Hirohisa, and Hirohide SAITO. "RNA/RNP Nanotechnology for Biological Applications." Seibutsu Butsuri 56, no. 1 (2016): 023–26. http://dx.doi.org/10.2142/biophys.56.023.

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2

Shi, Rui-Zhu, Yuan-Qing Pan, and Li Xing. "RNA Helicase A Regulates the Replication of RNA Viruses." Viruses 13, no. 3 (2021): 361. http://dx.doi.org/10.3390/v13030361.

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The RNA helicase A (RHA) is a member of DExH-box helicases and characterized by two double-stranded RNA binding domains at the N-terminus. RHA unwinds double-stranded RNA in vitro and is involved in RNA metabolisms in the cell. RHA is also hijacked by a variety of RNA viruses to facilitate virus replication. Herein, this review will provide an overview of the role of RHA in the replication of RNA viruses.

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3

SHIROGUCHI, Katsuyuki. "RNA Sequencing." Seibutsu Butsuri 53, no. 6 (2013): 290–94. http://dx.doi.org/10.2142/biophys.53.290.

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4

Afonin, Kirill A., Mathias Viard, Ioannis Kagiampakis, et al. "Triggering of RNA Interference with RNA–RNA, RNA–DNA, and DNA–RNA Nanoparticles." ACS Nano 9, no. 1 (2014): 251–59. http://dx.doi.org/10.1021/nn504508s.

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5

Kim, Hyunjong, and Juhee Ryu. "Mechanism of Circular RNAs and Their Potential as Novel Therapeutic Agents in Retinal Vascular Diseases." Yakhak Hoeji 67, no. 6 (2023): 325–34. http://dx.doi.org/10.17480/psk.2023.67.6.325.

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Maintaining and preserving visual function became critical in this aging society. The number of patients with retinal vascular disease such as retinopathy of prematurity, age-related macular degeneration, and diabetic retinopathy is gradually increasing due to increased life expectancy, advancements in the technology of delivering premature babies, and complications due to eating habits. To treat these retinal vascular diseases, surgical intervention such as laser photocoagulation and anti-vascular endothelial growth factor (VEGF) drugs can be considered. However, these treatment options are a

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6

Rajkowitsch, Lukas, Doris Chen, Sabine Stampfl, et al. "RNA Chaperones, RNA Annealers and RNA Helicases." RNA Biology 4, no. 3 (2007): 118–30. http://dx.doi.org/10.4161/rna.4.3.5445.

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7

Sengoku, T., O. Nureki, and S. Yokoyama. "Structural basis for RNA translocation by RNA helicase." Seibutsu Butsuri 43, supplement (2003): S98. http://dx.doi.org/10.2142/biophys.43.s98_2.

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8

Tang, Lin. "Mapping RNA–RNA interactions." Nature Methods 17, no. 8 (2020): 760. http://dx.doi.org/10.1038/s41592-020-0922-9.

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9

Ligoxygakis, P. "RNA that synthesizes RNA." Trends in Genetics 17, no. 7 (2001): 380. http://dx.doi.org/10.1016/s0168-9525(01)02391-5.

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10

Ogasawara, Shinzi, and Ai Yamada. "RNA Editing with Viral RNA-Dependent RNA Polymerase." ACS Synthetic Biology 11, no. 1 (2022): 46–52. http://dx.doi.org/10.1021/acssynbio.1c00332.

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11

Ahlquist, P. "RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing." Science 296, no. 5571 (2002): 1270–73. http://dx.doi.org/10.1126/science.1069132.

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12

Arnott, Struther, R. Chandrasekaran, R. P. Millane, and H. S. Park. "RNA-RNA, DNA-DNA, and DNA-RNA Polymorphism." Biophysical Journal 49, no. 1 (1986): 3–5. http://dx.doi.org/10.1016/s0006-3495(86)83568-8.

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13

Yano, A., and K. Harada. "2P142 Inhibition of RNA-protein interaction by RNA-RNA interaction." Seibutsu Butsuri 45, supplement (2005): S155. http://dx.doi.org/10.2142/biophys.45.s155_2.

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14

Taylor, J. P. "RNA That Gets RAN in Neurodegeneration." Science 339, no. 6125 (2013): 1282–83. http://dx.doi.org/10.1126/science.1236450.

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15

Stackebrandt, Erko, Werner Liesack, and Dagmar Witt. "Ribosomal RNA and rDNA sequence analyses." Gene 115, no. 1-2 (1992): 255–60. http://dx.doi.org/10.1016/0378-1119(92)90567-9.

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16

Günzl, Arthur, Thomas Bruderer, Gabriele Laufer, et al. "RNA Polymerase I Transcribes Procyclin Genes and Variant Surface Glycoprotein Gene Expression Sites in Trypanosoma brucei." Eukaryotic Cell 2, no. 3 (2003): 542–51. http://dx.doi.org/10.1128/ec.2.3.542-551.2003.

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ABSTRACT In eukaryotes, RNA polymerase (pol) I exclusively transcribes the large rRNA gene unit (rDNA) and mRNA is synthesized by RNA pol II. The African trypanosome, Trypanosoma brucei, represents an exception to this rule. In this organism, transcription of genes encoding the variant surface glycoprotein (VSG) and the procyclins is resistant to α-amanitin, indicating that it is mediated by RNA pol I, while other protein-coding genes are transcribed by RNA pol II. To obtain firm proof for this concept, we generated a T. brucei cell line which exclusively expresses protein C epitope-tagged RNA

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17

Zhang, X., D. Wu, L. Chen, et al. "RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction." RNA 20, no. 7 (2014): 989–93. http://dx.doi.org/10.1261/rna.044776.114.

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18

Alkan, Can, Emre Karakoç, Joseph H. Nadeau, S. Cenk Sahinalp, and Kaizhong Zhang. "RNA–RNA Interaction Prediction and Antisense RNA Target Search." Journal of Computational Biology 13, no. 2 (2006): 267–82. http://dx.doi.org/10.1089/cmb.2006.13.267.

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19

Newburn, Laura R., and K. Andrew White. "Trans-Acting RNA–RNA Interactions in Segmented RNA Viruses." Viruses 11, no. 8 (2019): 751. http://dx.doi.org/10.3390/v11080751.

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RNA viruses represent a large and important group of pathogens that infect a broad range of hosts. Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle. These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA. Genera that possess these genome types include, respectively, Orbivirus (e.g., Bluetongue virus), Dianthovirus (e.g., Red clover necrotic mosaic virus) and Alphainfluenzavirus (e.g., Inf

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20

Cazenave, C., and O. C. Uhlenbeck. "RNA template-directed RNA synthesis by T7 RNA polymerase." Proceedings of the National Academy of Sciences 91, no. 15 (1994): 6972–76. http://dx.doi.org/10.1073/pnas.91.15.6972.

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21

McGinness, Kathleen E., and Gerald F. Joyce. "RNA-Catalyzed RNA Ligation on an External RNA Template." Chemistry & Biology 9, no. 3 (2002): 297–307. http://dx.doi.org/10.1016/s1074-5521(02)00110-2.

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22

Predki, Paul F., L. Mike Nayak, Morris B. C. Gottlieb, and Lynne Regan. "Dissecting RNA-protein interactions: RNA-RNA recognition by Rop." Cell 80, no. 1 (1995): 41–50. http://dx.doi.org/10.1016/0092-8674(95)90449-2.

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23

HONDA, Tomoyuki, and Keizo TOMONAGA. "Possible roles of endogenous RNA virus elements in RNA virus infection." Uirusu 66, no. 1 (2016): 39–46. http://dx.doi.org/10.2222/jsv.66.39.

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24

Xue, Yuanchao. "Architecture of RNA–RNA interactions." Current Opinion in Genetics & Development 72 (February 2022): 138–44. http://dx.doi.org/10.1016/j.gde.2021.11.007.

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25

Röthlisberger, Pascal, Christian Berk, and Jonathan Hall. "RNA Chemistry for RNA Biology." CHIMIA International Journal for Chemistry 73, no. 5 (2019): 368–73. http://dx.doi.org/10.2533/chimia.2019.368.

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Advances in the chemical synthesis of RNA have opened new possibilities to address current questions in RNA biology. Access to site-specifically modified oligoribonucleotides is often a pre-requisite for RNA chemical-biology projects. Driven by the enormous research efforts for development of oligonucleotide therapeutics, a wide range of chemical modifications have been developed to modulate the intrinsic properties of nucleic acids in order to fit their use as therapeutics or research tools. The RNA synthesis platform, supported by the NCCR RNA & Disease, aims to provide access to a large

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26

GUTHRIE, CHRISTINE. "Catalytic RNA and RNA Splicing." American Zoologist 29, no. 2 (1989): 557–67. http://dx.doi.org/10.1093/icb/29.2.557.

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27

Fu, Xiang-Dong. "RNA helicases regulate RNA condensates." Cell Research 30, no. 4 (2020): 281–82. http://dx.doi.org/10.1038/s41422-020-0296-7.

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28

Newman, Andy. "RNA enzymes for RNA splicing." Nature 413, no. 6857 (2001): 695–96. http://dx.doi.org/10.1038/35099665.

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29

Abe, Hiroshi. "Nanostructured RNA for RNA Intereference." YAKUGAKU ZASSHI 133, no. 3 (2013): 373–78. http://dx.doi.org/10.1248/yakushi.12-00239-4.

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30

Khemici, Vanessa, and Patrick Linder. "RNA helicases in RNA decay." Biochemical Society Transactions 46, no. 1 (2018): 163–72. http://dx.doi.org/10.1042/bst20170052.

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RNA molecules have the tendency to fold into complex structures or to associate with complementary RNAs that exoribonucleases have difficulties processing or degrading. Therefore, degradosomes in bacteria and organelles as well as exosomes in eukaryotes have teamed-up with RNA helicases. Whereas bacterial degradosomes are associated with RNA helicases from the DEAD-box family, the exosomes and mitochondrial degradosome use the help of Ski2-like and Suv3 RNA helicases.

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31

Meyer, Irmtraud M. "Predicting novel RNA–RNA interactions." Current Opinion in Structural Biology 18, no. 3 (2008): 387–93. http://dx.doi.org/10.1016/j.sbi.2008.03.006.

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32

Westhof, Eric, Benoît Masquida, and Luc Jaeger. "RNA tectonics: towards RNA design." Folding and Design 1, no. 4 (1996): R78—R88. http://dx.doi.org/10.1016/s1359-0278(96)00037-5.

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33

Peng, LiNa, YuJiao Li, Lan Zhang, and WenQiang Yu. "Moving RNA moves RNA forward." Science China Life Sciences 56, no. 10 (2013): 914–20. http://dx.doi.org/10.1007/s11427-013-4545-6.

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34

Li, Thomas J. X., and Christian M. Reidys. "Combinatorics of RNA–RNA interaction." Journal of Mathematical Biology 64, no. 3 (2011): 529–56. http://dx.doi.org/10.1007/s00285-011-0423-7.

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35

Muckstein, U., H. Tafer, J. Hackermuller, S. H. Bernhart, P. F. Stadler, and I. L. Hofacker. "Thermodynamics of RNA-RNA binding." Bioinformatics 22, no. 10 (2006): 1177–82. http://dx.doi.org/10.1093/bioinformatics/btl024.

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36

SCHMIDT, FRANCIS J., BONGRAE CHO, and HUGH B. NICHOLAS. "RNA Libraries and RNA Recognitiona." Annals of the New York Academy of Sciences 782, no. 1 (1996): 526–33. http://dx.doi.org/10.1111/j.1749-6632.1996.tb40590.x.

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37

Menzel, Peter, Stefan E. Seemann, and Jan Gorodkin. "RILogo: visualizing RNA–RNA interactions." Bioinformatics 28, no. 19 (2012): 2523–26. http://dx.doi.org/10.1093/bioinformatics/bts461.

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38

Kok, Chee Choy, and Peter C. McMinn. "Picornavirus RNA-dependent RNA polymerase." International Journal of Biochemistry & Cell Biology 41, no. 3 (2009): 498–502. http://dx.doi.org/10.1016/j.biocel.2008.03.019.

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39

Mitra, Manu. "Review of RNA sequence of pX330-U6." International Journal of Forensic Research 3, no. 1 (2021): 67–74. https://doi.org/10.1234/opast.1234.

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RNA sequencing can be used for studying various factors such as mRNA including single cell gene expression. For more than 10 years RNA sequencing has become vital means for wide analysis of gene expression and differential splicing of mRNAs. Gene manipulation has become more important and sophisticated to study the gene structure of RNA especially when it comes to deadly viruses. In this review paper RNA sequence of pX330-U6 is elaborated based on plasmid structure, its RNA sequence is illustrated from 10 to 8500 bases.

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40

Hammond, T. M., and N. P. Keller. "RNA Silencing inAspergillus nidulansIs Independent of RNA-Dependent RNA Polymerases." Genetics 169, no. 2 (2004): 607–17. http://dx.doi.org/10.1534/genetics.104.035964.

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41

Skeparnias, Ilias, and Jinwei Zhang. "Cooperativity and Interdependency between RNA Structure and RNA–RNA Interactions." Non-Coding RNA 7, no. 4 (2021): 81. http://dx.doi.org/10.3390/ncrna7040081.

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Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. Herein, we discuss different modalities of RNA–RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure. We dissect recently structurally elucidated RNA–RNA complexes including RNA triplexes, riboswitches, ribozy

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42

Snider, Daltry L., and Stacy M. Horner. "RNA modification of an RNA modifier prevents self-RNA sensing." PLOS Biology 19, no. 7 (2021): e3001342. http://dx.doi.org/10.1371/journal.pbio.3001342.

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43

Koh, Hye Ran, Li Xing, Lawrence Kleiman, and Sua Myong. "Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing." Nucleic Acids Research 42, no. 13 (2014): 8556–64. http://dx.doi.org/10.1093/nar/gku523.

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44

Shioda, Norifumi. "RNA toxicity and RAN translation in repeat expansion disorders." Folia Pharmacologica Japonica 150, no. 3 (2017): 165. http://dx.doi.org/10.1254/fpj.150.165.

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45

KIKUCHI, Yo. "Current RNA World." Journal of the Japan Veterinary Medical Association 52, no. 1 (1999): 1–5. http://dx.doi.org/10.12935/jvma1951.52.1.

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46

Sharathkumar, S., T. K. Chethankumar, Jain Rajath, and T. Ram Ashish. "Identification and Validation of miRNA in the Field of Agriculture Data." Journal of Data Mining and Management 4, no. 3 (2019): 9–16. https://doi.org/10.5281/zenodo.3459422.

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<em>India is a developing country and statistics shows there is a lot of disease-causing insects or organisms that affects the growth and yield of plants. We can overcome from these kinds of problems by using the modern genetic technique, i.e., genetic modification of plant cells. To reduce the losses caused by the organisms and the harmful insects for the farmers on the rural area and bring it to the light, so that the people who actually need help should get a helping hand. There is a misconception on genetic modification that it can affects on the genetic functions in the human body but if

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47

Grass, Lena M., Jan Wollenhaupt, Tatjana Barthel, et al. "Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility." Proceedings of the National Academy of Sciences 118, no. 30 (2021): e2100370118. http://dx.doi.org/10.1073/pnas.2100370118.

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Many bacteria harbor RNA-dependent nucleoside-triphosphatases of the DEAH/RHA family, whose molecular mechanisms and cellular functions are poorly understood. Here, we show that the Escherichia coli DEAH/RHA protein, HrpA, is an ATP-dependent 3 to 5′ RNA helicase and that the RNA helicase activity of HrpA influences bacterial survival under antibiotics treatment. Limited proteolysis, crystal structure analysis, and functional assays showed that HrpA contains an N-terminal DEAH/RHA helicase cassette preceded by a unique N-terminal domain and followed by a large C-terminal region that modulates

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48

付, 洪. "Multifunction of LncRNA RMRP RNA." Biophysics 08, no. 02 (2020): 19–27. http://dx.doi.org/10.12677/biphy.2020.82002.

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49

Turner, Richard. "RNA." Nature 418, no. 6894 (2002): 213. http://dx.doi.org/10.1038/418213a.

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50

Darnell, James E. "RNA." Scientific American 253, no. 4 (1985): 68–78. http://dx.doi.org/10.1038/scientificamerican1085-68.

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