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Journal articles on the topic 'RNA stem loop'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Yunus, Muhammad Amir, Xiaoyan Lin, Dalan Bailey, et al. "The Murine Norovirus Core Subgenomic RNA Promoter Consists of a Stable Stem-Loop That Can Direct Accurate Initiation of RNA Synthesis." Journal of Virology 89, no. 2 (2014): 1218–29. http://dx.doi.org/10.1128/jvi.02432-14.

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ABSTRACTAll members of theCaliciviridaefamily of viruses produce a subgenomic RNA during infection. The subgenomic RNA typically encodes only the major and minor capsid proteins, but in murine norovirus (MNV), the subgenomic RNA also encodes the VF1 protein, which functions to suppress host innate immune responses. To date, the mechanism of norovirus subgenomic RNA synthesis has not been characterized. We have previously described the presence of an evolutionarily conserved RNA stem-loop structure on the negative-sense RNA, the complementary sequence of which codes for the viral RNA-dependent

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2

Luo, Guangxiang, Shaojie Xin, and Zhaohui Cai. "Role of the 5′-Proximal Stem-Loop Structure of the 5′ Untranslated Region in Replication and Translation of Hepatitis C Virus RNA." Journal of Virology 77, no. 5 (2003): 3312–18. http://dx.doi.org/10.1128/jvi.77.5.3312-3318.2003.

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ABSTRACT Sequences of the untranslated regions at the 5′ and 3′ ends (5′UTR and 3′UTR) of the hepatitis C virus (HCV) RNA genome are highly conserved and contain cis-acting RNA elements for HCV RNA replication. The HCV 5′UTR consists of two distinct RNA elements, a short 5′-proximal stem-loop RNA element (nucleotides 1 to 43) and a longer element of internal ribosome entry site. To determine the sequence and structural requirements of the 5′-proximal stem-loop RNA element in HCV RNA replication and translation, a mutagenesis analysis was preformed by nucleotide deletions and substitutions. Eff

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3

Frank, D. N., H. Roiha, and C. Guthrie. "Architecture of the U5 small nuclear RNA." Molecular and Cellular Biology 14, no. 3 (1994): 2180–90. http://dx.doi.org/10.1128/mcb.14.3.2180.

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We have used comparative sequence analysis and deletion analysis to examine the secondary structure of the U5 small nuclear RNA (snRNA), an essential component of the pre-mRNA splicing apparatus. The secondary structure of Saccharomyces cerevisiae U5 snRNA was studied in detail, while sequences from six other fungal species were included in the phylogenetic analysis. Our results indicate that fungal U5 snRNAs, like their counterparts from other taxa, can be folded into a secondary structure characterized by a highly conserved stem-loop (stem-loop 1) that is flanked by a moderately conserved in

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4

Frank, D. N., H. Roiha, and C. Guthrie. "Architecture of the U5 small nuclear RNA." Molecular and Cellular Biology 14, no. 3 (1994): 2180–90. http://dx.doi.org/10.1128/mcb.14.3.2180-2190.1994.

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We have used comparative sequence analysis and deletion analysis to examine the secondary structure of the U5 small nuclear RNA (snRNA), an essential component of the pre-mRNA splicing apparatus. The secondary structure of Saccharomyces cerevisiae U5 snRNA was studied in detail, while sequences from six other fungal species were included in the phylogenetic analysis. Our results indicate that fungal U5 snRNAs, like their counterparts from other taxa, can be folded into a secondary structure characterized by a highly conserved stem-loop (stem-loop 1) that is flanked by a moderately conserved in

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5

Donahue, Christine P., Jake Ni, Eriks Rozners, Marcie A. Glicksman, and Michael S. Wolfe. "Identification of Tau Stem Loop RNA Stabilizers." Journal of Biomolecular Screening 12, no. 6 (2007): 789–99. http://dx.doi.org/10.1177/1087057107302676.

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Alternative splicing of tau exon 10 produces tau isoforms with either 3 (3R) or 4 (4R) repeated microtubule-binding domains. Increased ratios of 4R to 3R tau expression, above the physiological 1:1, leads to neurofibrillary tangles and causes neurodegenerative disease. An RNA stem loop structure plays a significant role in determining the ratio, with decreasing stability correlating with an increase in 4R tau mRNA expression. Recent studies have shown that aminoglycosides are able to bind and stabilize the tau stem loop in vitro, suggesting that other druglike small molecules could be identifi

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6

Shen, Ni, Louis Jetté, Chen Liang, Mark A. Wainberg, and Michael Laughrea. "Impact of Human Immunodeficiency Virus Type 1 RNA Dimerization on Viral Infectivity and of Stem-Loop B on RNA Dimerization and Reverse Transcription and Dissociation of Dimerization from Packaging." Journal of Virology 74, no. 12 (2000): 5729–35. http://dx.doi.org/10.1128/jvi.74.12.5729-5735.2000.

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ABSTRACT The kissing-loop domain (KLD) encompasses a stem-loop, named kissing-loop or dimerization initiation site (DIS) hairpin (nucleotides [nt] 248 to 270 in the human immunodeficiency virus type 1 strains HIV-1Lai and HIV-1Hxb2), seated on top of a 12-nt stem-internal loop called stem-loop B (nt 243 to 247 and 271 to 277). Destroying stem-loop B reduced genome dimerization by ∼50% and proviral DNA synthesis by ∼85% and left unchanged the dissociation temperature of dimeric genomic RNA. The most affected step of reverse transcription was plus-strand DNA transfer, which was reduced by ∼80%.

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7

Olsthoorn, R. C. L., A. Bruyere, A. Dzianott, and J. J. Bujarski. "RNA Recombination in Brome Mosaic Virus: Effects of Strand-Specific Stem-Loop Inserts." Journal of Virology 76, no. 24 (2002): 12654–62. http://dx.doi.org/10.1128/jvi.76.24.12654-12662.2002.

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ABSTRACT A model system of a single-stranded trisegment Brome mosaic bromovirus (BMV) was used to analyze the mechanism of homologous RNA recombination. Elements capable of forming strand-specific stem-loop structures were inserted at the modified 3′ noncoding regions of BMV RNA3 and RNA2 in either positive or negative orientations, and various combinations of parental RNAs were tested for patterns of the accumulating recombinant RNA3 components. The structured negative-strand stem-loops that were inserted in both RNA3 and RNA2 reduced the accumulation of RNA3-RNA2 recombinants to a much highe

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8

Walter, Brandon L., Todd B. Parsley, Ellie Ehrenfeld, and Bert L. Semler. "Distinct Poly(rC) Binding Protein KH Domain Determinants for Poliovirus Translation Initiation and Viral RNA Replication." Journal of Virology 76, no. 23 (2002): 12008–22. http://dx.doi.org/10.1128/jvi.76.23.12008-12022.2002.

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ABSTRACT The limited coding capacity of picornavirus genomic RNAs necessitates utilization of host cell factors in the completion of an infectious cycle. One host protein that plays a role in both translation initiation and viral RNA synthesis is poly(rC) binding protein 2 (PCBP2). For picornavirus RNAs containing type I internal ribosome entry site (IRES) elements, PCBP2 binds the major stem-loop structure (stem-loop IV) in the IRES and is essential for translation initiation. Additionally, the binding of PCBP2 to the 5′-terminal stem-loop structure (stem-loop I or cloverleaf) in concert with

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9

Lee, Haekyung, Hyukwoo Shin, Eckard Wimmer, and Aniko V. Paul. "cis-Acting RNA Signals in the NS5B C-Terminal Coding Sequence of the Hepatitis C Virus Genome." Journal of Virology 78, no. 20 (2004): 10865–77. http://dx.doi.org/10.1128/jvi.78.20.10865-10877.2004.

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ABSTRACT The cis-replicating RNA elements in the 5′ and 3′ nontranslated regions (NTRs) of the hepatitis C virus (HCV) genome have been thoroughly studied before. However, no cis-replicating elements have been identified in the coding sequences of the HCV polyprotein until very recently. The existence of highly conserved and stable stem-loop structures in the RNA polymerase NS5B coding sequence, however, has been previously predicted (A. Tuplin, J. Wood, D. J. Evans, A. H. Patel, and P. Simmonds, RNA 8:824-841, 2002). We have selected for our studies a 249-nt-long RNA segment in the C-terminal

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10

Evans, Donald, and Thomas Blumenthal. "trans Splicing of PolycistronicCaenorhabditis elegans Pre-mRNAs: Analysis of the SL2 RNA." Molecular and Cellular Biology 20, no. 18 (2000): 6659–67. http://dx.doi.org/10.1128/mcb.20.18.6659-6667.2000.

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ABSTRACT Genes in Caenorhabditis elegans operons are transcribed as polycistronic pre-mRNAs in which downstream gene products aretrans spliced to a specialized spliced leader, SL2. SL2 is donated by a 110-nucleotide RNA, SL2 RNA, present in the cell as an Sm-bound snRNP. SL2 RNA can be conceptually folded into a phylogenetically conserved three-stem-loop secondary structure. Here we report an in vivo mutational analysis of the SL2 RNA. Some sequences can be changed without consequence, while other changes result in a substantial loss of trans splicing. Interestingly, the spliced leader itself

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11

Kanai, Akio, Asako Sato, Jun Imoto, and Masaru Tomita. "Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein." Biochemical Journal 393, no. 1 (2005): 373–79. http://dx.doi.org/10.1042/bj20050608.

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Using a stem–loop RNA oligonucleotide (19-mer) containing an AUG sequence in the loop region as a probe, we screened the protein library from a hyperthermophilic archaeon, Pyrococcus furiosus, and found that a flavin-dependent thymidylate synthase, Pf-Thy1 (Pyrococcus furiosus thymidylate synthase 1), possessed RNA-binding activity. Recombinant Pf-Thy1 was able to bind to the stem–loop structure at a high temperature (75 °C) with an apparent dissociation constant of 0.6 μM. A similar stem–loop RNA structure was located around the translation start AUG codon of Pf-Thy1 RNA, and gel-shift analys

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12

Jacobson, M. R., M. Rhoadhouse, and T. Pederson. "U2 small nuclear RNA 3' end formation is directed by a critical internal structure distinct from the processing site." Molecular and Cellular Biology 13, no. 2 (1993): 1119–29. http://dx.doi.org/10.1128/mcb.13.2.1119.

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Mature U2 small nuclear RNA is generated by the removal of 11 to 12 nucleotides from the 3' end of the primary transcript. This pre-U2 RNA processing reaction takes place in the cytoplasm. In this study, the sequences and/or structures of pre-U2 RNA that are important for 3' processing have been examined in an in vitro system. The 7-methylguanosine cap, stem-loops I and II, the lariat branch site recognition sequence, the conserved Sm domain, and several other regions throughout the 5' end of U2 RNA have no apparent role in the 3' processing reaction. In fact, deletion of the entire first 104

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13

Jacobson, M. R., M. Rhoadhouse, and T. Pederson. "U2 small nuclear RNA 3' end formation is directed by a critical internal structure distinct from the processing site." Molecular and Cellular Biology 13, no. 2 (1993): 1119–29. http://dx.doi.org/10.1128/mcb.13.2.1119-1129.1993.

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Mature U2 small nuclear RNA is generated by the removal of 11 to 12 nucleotides from the 3' end of the primary transcript. This pre-U2 RNA processing reaction takes place in the cytoplasm. In this study, the sequences and/or structures of pre-U2 RNA that are important for 3' processing have been examined in an in vitro system. The 7-methylguanosine cap, stem-loops I and II, the lariat branch site recognition sequence, the conserved Sm domain, and several other regions throughout the 5' end of U2 RNA have no apparent role in the 3' processing reaction. In fact, deletion of the entire first 104

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14

Sarkar, K., D. A. Nguyen, and M. Gruebele. "Loop and stem dynamics during RNA hairpin folding and unfolding." RNA 16, no. 12 (2010): 2427–34. http://dx.doi.org/10.1261/rna.2253310.

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15

Headey, S. J., H. Huang, J. K. Claridge, et al. "NMR structure of stem-loop D from human rhinovirus-14." RNA 13, no. 3 (2007): 351–60. http://dx.doi.org/10.1261/rna.313707.

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16

Du, Hansen, Alexander V. Yakhnin, Subramanian Dharmaraj, and Paul Babitzke. "trp RNA-Binding Attenuation Protein-5′ Stem-Loop RNA Interaction Is Required for Proper Transcription Attenuation Control of the Bacillus subtilis trpEDCFBAOperon." Journal of Bacteriology 182, no. 7 (2000): 1819–27. http://dx.doi.org/10.1128/jb.182.7.1819-1827.2000.

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ABSTRACT The trp RNA-binding attenuation protein (TRAP) regulates expression of the Bacillus subtilis trpEDCFBAoperon by a novel transcription attenuation mechanism. Tryptophan-activated TRAP binds to the nascent trp leader transcript by interacting with 11 (G/U)AG repeats, 6 of which are present in an antiterminator structure. TRAP binding to these repeats prevents formation of the antiterminator, thereby promoting formation of an overlapping intrinsic terminator. A third stem-loop structure that forms at the extreme 5′ end of the trp leader transcript also plays a role in the transcription a

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17

Ishimaru, Daniella, Ewan P. Plant, Amy C. Sims, et al. "RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus." Nucleic Acids Research 41, no. 4 (2012): 2594–608. http://dx.doi.org/10.1093/nar/gks1361.

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Abstract Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the

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18

Shibata, Hirotaka S., Hiroaki Takaku, Masamichi Takagi, and Masayuki Nashimoto. "The T Loop Structure Is Dispensable for Substrate Recognition by tRNase ZL." Journal of Biological Chemistry 280, no. 23 (2005): 22326–34. http://dx.doi.org/10.1074/jbc.m502048200.

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tRNA 3′-processing endoribonucleases (tRNase Z, or 3′-tRNase; EC 3.1.26.11) are enzymes that remove 3′-trailers from pre-tRNAs. An about 12-base-pair stem, a T loop-like structure, and a 3′-trailer were considered to be the minimum requirements for recognition by the long form (tRNase ZL) of tRNase Z; tRNase ZL can recognize and cleave a micro-pre-tRNA or a hooker/target RNA complex that resembles a micro-pre-tRNA. We examined four hook RNAs containing systematically weakened T stems for directing target RNA cleavage by tRNase ZL. As expected, the cleavage efficiency decreased with the decreas

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19

Harrich, David, C. William Hooker, and Emma Parry. "The Human Immunodeficiency Virus Type 1 TAR RNA Upper Stem-Loop Plays Distinct Roles in Reverse Transcription and RNA Packaging." Journal of Virology 74, no. 12 (2000): 5639–46. http://dx.doi.org/10.1128/jvi.74.12.5639-5646.2000.

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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) RNA genome is flanked by a repeated sequence (R) that is required for HIV-1 replication. The first 57 nucleotides of R form a stable stem-loop structure called the transactivation response element (TAR) that can interact with the virally encoded transcription activator protein, Tat, to promote high levels of gene expression. Recently, we demonstrated that TAR is also important for efficient HIV-1 reverse transcription, since HIV-1 mutated in the upper stem-loop of TAR showed a reduced ability both to initiate and to complete reverse tran

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20

Haneef, I., Simon J. Talbot, and Peter G. Stockley. "Modeling loop structures in proteins and nucleic acids: an RNA stem-loop." Journal of Molecular Graphics 7, no. 4 (1989): 186–95. http://dx.doi.org/10.1016/0263-7855(89)80001-3.

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21

Chen, M. H., M. J. Roossinck, and C. C. Kao. "Efficient and Specific Initiation of Subgenomic RNA Synthesis by Cucumber Mosaic Virus Replicase In Vitro Requires an Upstream RNA Stem-Loop." Journal of Virology 74, no. 23 (2000): 11201–9. http://dx.doi.org/10.1128/jvi.74.23.11201-11209.2000.

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ABSTRACT We defined the minimal core promoter sequences responsible for efficient and accurate initiation of cucumber mosaic virus (CMV) subgenomic RNA4. The necessary sequence maps to positions −28 to +15 relative to the initiation cytidylate used to initiate RNA synthesis in vivo. Positions −28 to −5 contain a 9-bp stem and a 6-nucleotide purine-rich loop. Considerable changes in the stem and the loop are tolerated for RNA synthesis, including replacement with a different stem-loop. In a template competition assay, the stem-loop and the initiation cytidylate are sufficient to interact with t

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22

Xi, Xiangmei, Yan Sun, Christine B. Karim, Vladimir M. Grigoryants, and Charles P. Scholes. "HIV-1 Nucleocapsid Protein NCp7 and Its RNA Stem Loop 3 Partner: Rotational Dynamics of Spin-Labeled RNA Stem Loop 3†." Biochemistry 47, no. 38 (2008): 10099–110. http://dx.doi.org/10.1021/bi800602e.

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23

Huang, Cheng-Yen, Yih-Leh Huang, Menghsiao Meng, Yau-Heiu Hsu, and Ching-Hsiu Tsai. "Sequences at the 3′ Untranslated Region of Bamboo Mosaic Potexvirus RNA Interact with the Viral RNA-Dependent RNA Polymerase." Journal of Virology 75, no. 6 (2001): 2818–24. http://dx.doi.org/10.1128/jvi.75.6.2818-2824.2001.

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ABSTRACT The 3′ untranslated region (UTR) of bamboo mosaic potexvirus (BaMV) genomic RNA was found to fold into a series of stem-loop structures including a pseudoknot structure. These structures were demonstrated to be important for viral RNA replication and were believed to be recognized by the replicase (C.-P. Cheng and C.-H. Tsai, J. Mol. Biol. 288:555–565, 1999). Electrophoretic mobility shift and competition assays have now been used to demonstrate that theEscherichia coli-expressed RNA-dependent RNA polymerase domain (Δ893) derived from BaMV open reading frame 1 could specifically bind

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24

Heinrich, Stephanie, Corinne L. Sidler, Claus M. Azzalin, and Karsten Weis. "Stem–loop RNA labeling can affect nuclear and cytoplasmic mRNA processing." RNA 23, no. 2 (2016): 134–41. http://dx.doi.org/10.1261/rna.057786.116.

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25

Jambor, H., S. Mueller, S. L. Bullock, and A. Ephrussi. "A stem-loop structure directs oskar mRNA to microtubule minus ends." RNA 20, no. 4 (2014): 429–39. http://dx.doi.org/10.1261/rna.041566.113.

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26

Colletti, Kelly S., Kate E. Smallenburg, Yiyang Xu, and Gregory S. Pari. "Human Cytomegalovirus UL84 Interacts with an RNA Stem-Loop Sequence Found within the RNA/DNA Hybrid Region of oriLyt." Journal of Virology 81, no. 13 (2007): 7077–85. http://dx.doi.org/10.1128/jvi.00058-07.

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ABSTRACT Human cytomegalovirus (HCMV) lytic DNA replication is initiated at the complex cis-acting oriLyt region, which spans nearly 3 kb. DNA synthesis requires six core proteins together with UL84 and IE2. Previously, two essential regions were identified within oriLyt. Essential region I (nucleotides [nt] 92209 to 92573) can be replaced with the constitutively active simian virus 40 promoter, which in turn eliminates the requirement for IE2 in the origin-dependent transient-replication assay. Essential region II (nt 92979 to 93513) contains two elements of interest: an RNA/DNA hybrid domain

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27

Hsue, Bilan, Toinette Hartshorne, and Paul S. Masters. "Characterization of an Essential RNA Secondary Structure in the 3′ Untranslated Region of the Murine Coronavirus Genome." Journal of Virology 74, no. 15 (2000): 6911–21. http://dx.doi.org/10.1128/jvi.74.15.6911-6921.2000.

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ABSTRACT We have previously identified a functionally essential bulged stem-loop in the 3′ untranslated region of the positive-stranded RNA genome of mouse hepatitis virus. This 68-nucleotide structure is composed of six stem segments interrupted by five bulges, and its structure, but not its primary sequence, is entirely conserved in the related bovine coronavirus. The functional importance of individual stem segments of this stem-loop was characterized by genetic analysis using targeted RNA recombination. We also examined the effects of stem segment mutations on the replication of mouse hepa

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Vlot, A. Corina, and John F. Bol. "The 5′ Untranslated Region of Alfalfa Mosaic Virus RNA 1 Is Involved in Negative-Strand RNA Synthesis." Journal of Virology 77, no. 20 (2003): 11284–89. http://dx.doi.org/10.1128/jvi.77.20.11284-11289.2003.

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ABSTRACT The three genomic RNAs of alfalfa mosaic virus each contain a unique 5′ untranslated region (5′ UTR). Replacement of the 5′ UTR of RNA 1 by that of RNA 2 or 3 yielded infectious replicons. The sequence of a putative 5′ stem-loop structure in RNA 1 was found to be required for negative-strand RNA synthesis. A similar putative 5′ stem-loop structure is present in RNA 2 but not in RNA 3.

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Lin, Jen-Wen, Hsiao-Ning Chiu, I.-Hsuan Chen, Tzu-Chi Chen, Yau-Heiu Hsu, and Ching-Hsiu Tsai. "Structural and Functional Analysis of the cis-Acting Elements Required for Plus-Strand RNA Synthesis of Bamboo Mosaic Virus." Journal of Virology 79, no. 14 (2005): 9046–53. http://dx.doi.org/10.1128/jvi.79.14.9046-9053.2005.

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ABSTRACT Bamboo mosaic virus (BaMV) has a single-stranded positive-sense RNA genome. The secondary structure of the 3′-terminal sequence of the minus-strand RNA has been predicted by MFOLD and confirmed by enzymatic structural probing to consist of a large, stable stem-loop and a small, unstable stem-loop. To identify the promoter for plus-strand RNA synthesis in this region, transcripts of 39, 77, and 173 nucleotides (Ba-39, Ba-77, and Ba-173, respectively) derived from the 3′ terminus of the minus-strand RNA were examined by an in vitro RNA-dependent RNA polymerase assay for the ability to d

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Pollack, J. R., and D. Ganem. "An RNA stem-loop structure directs hepatitis B virus genomic RNA encapsidation." Journal of Virology 67, no. 6 (1993): 3254–63. http://dx.doi.org/10.1128/jvi.67.6.3254-3263.1993.

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Friebe, Peter, Julien Boudet, Jean-Pierre Simorre, and Ralf Bartenschlager. "Kissing-Loop Interaction in the 3′ End of the Hepatitis C Virus Genome Essential for RNA Replication." Journal of Virology 79, no. 1 (2005): 380–92. http://dx.doi.org/10.1128/jvi.79.1.380-392.2005.

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ABSTRACT The hepatitis C virus (HCV) is a positive-strand RNA virus belonging to the Flaviviridae. Its genome carries at either end highly conserved nontranslated regions (NTRs) containing cis-acting RNA elements that are crucial for replication. In this study, we identified a novel RNA element within the NS5B coding sequence that is indispensable for replication. By using secondary structure prediction and nuclear magnetic resonance spectroscopy, we found that this RNA element, designated 5BSL3.2 by analogy to a recent report (S. You, D. D. Stump, A. D. Branch, and C. M. Rice, J. Virol. 78:13

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Koh, Hye Ran, Amirhossein Ghanbariniaki, and Sua Myong. "RNA stem structure governs coupling of dicing and gene silencing in RNA interference." Proceedings of the National Academy of Sciences 114, no. 48 (2017): E10349—E10358. http://dx.doi.org/10.1073/pnas.1710298114.

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PremicroRNAs (premiRNAs) possess secondary structures consisting of a loop and a stem with multiple mismatches. Despite the well-characterized RNAi pathway, how the structural features of premiRNA contribute to dicing and subsequent gene-silencing efficiency remains unclear. Using single-molecule FISH, we demonstrate that cytoplasmic mRNA, but not nuclear mRNA, is reduced during RNAi. The dicing rate and silencing efficiency both increase in a correlated manner as a function of the loop length. In contrast, mismatches in the stem drastically diminish the silencing efficiency without impacting

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Gamarnik, Andrea V., and Raul Andino. "Interactions of Viral Protein 3CD and Poly(rC) Binding Protein with the 5′ Untranslated Region of the Poliovirus Genome." Journal of Virology 74, no. 5 (2000): 2219–26. http://dx.doi.org/10.1128/jvi.74.5.2219-2226.2000.

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ABSTRACT The poly(rC) binding protein (PCBP) is a cellular protein required for poliovirus replication. PCBP specifically interacts with two domains of the poliovirus 5′ untranslated region (5′UTR), the 5′ cloverleaf structure, and the stem-loop IV of the internal ribosome entry site (IRES). Using footprinting analysis and site-directed mutagenesis, we have mapped the RNA binding site for this cellular protein within the stem-loop IV domain. A C-rich sequence in a loop at the top of this large domain is required for PCBP binding and is crucial for viral translation. PCBP binds to stem-loop IV

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Hoffman, D. W., Z. Du, J. A. Holland, M. R. Hansen, Y. Wang, and D. P. Giedroc. "Pseudoknot Structures in Retroviral and Bacteriophage Messenger RNA: a Family of Structurally Related RNA Pseudoknots." Microscopy and Microanalysis 3, S2 (1997): 95–96. http://dx.doi.org/10.1017/s1431927600007364.

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Nuclear magnetic resonance (NMR) spectroscopy was used to determine the three-dimensional structure of an RNA pseudoknot with a sequence corresponding to the 5' end region of the gene 32 messenger RNA of bacteriophage T2. NMR results show that the pseudoknot contains two coaxial A-form helical stems connected by two loops. One of the loops consists of a single nucleotide, which spans the major groove of the seven base pair helical stem 2. The second loop consists of 7 nucleotides, and spans the minor groove of stem 1. A three-dimensional model of the pseudoknot that is consistent with the NMR

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35

Clever, Jared L., Daniel A. Eckstein, and Tristram G. Parslow. "Genetic Dissociation of the Encapsidation and Reverse Transcription Functions in the 5′ R Region of Human Immunodeficiency Virus Type 1." Journal of Virology 73, no. 1 (1999): 101–9. http://dx.doi.org/10.1128/jvi.73.1.101-109.1999.

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ABSTRACT The efficient packaging of genomic RNA into virions of human immunodeficiency virus type 1 (HIV-1) is directed bycis-acting encapsidation signals, which have been mapped to particular RNA stem-loop structures near the 5′ end of the genome. Earlier studies have shown that three such stem-loops, located adjacent to the major 5′ splice donor, are required for optimal packaging; more recent reports further suggest a requirement for the TAR and poly(A) hairpins of the 5′ R region. In the present study, we have compared the phenotypes that result from mutating these latter elements in the H

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36

Raman, Sharmila, and David A. Brian. "Stem-Loop IV in the 5′ Untranslated Region Is a cis-Acting Element in Bovine Coronavirus Defective Interfering RNA Replication." Journal of Virology 79, no. 19 (2005): 12434–46. http://dx.doi.org/10.1128/jvi.79.19.12434-12446.2005.

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ABSTRACT The 210-nucleotide (nt) 5′ untranslated region (UTR) in the positive-strand bovine coronavirus (BCoV) genome is predicted to contain four higher-order structures identified as stem-loops I to IV, which may function as cis-acting elements in genomic RNA replication. Here, we describe evidence that stem-loop IV, a bulged stem-loop mapping at nt 186 through 215, (i) is phylogenetically conserved among group 2 coronaviruses and may have a homolog in groups 1 and 3, (ii) exists as a higher-order structure on the basis of enzyme probing, (iii) is required as a higher-order element for repli

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Churkin, Alexander, Franziska Totzeck, Rami Zakh, et al. "A Mathematical Analysis of RNA Structural Motifs in Viruses." Mathematics 9, no. 6 (2021): 585. http://dx.doi.org/10.3390/math9060585.

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RNA stem-loop structures play an important role in almost every step of the viral replication cycle. In this contribution, a mathematical analysis is performed on a large dataset of RNA secondary structure elements in the coding regions of viruses by using topological indices that capture the Laplacian eigenvalues of the associated RNA graph representations and thereby enable structural classification, supplemented by folding energy and mutational robustness. The application of such an analysis for viral RNA structural motifs is described, being able to extract structural categories such as st

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Dominski, Zbigniew, Judith A. Erkmann, John A. Greenland, and William F. Marzluff. "Mutations in the RNA Binding Domain of Stem-Loop Binding Protein Define Separable Requirements for RNA Binding and for Histone Pre-mRNA Processing." Molecular and Cellular Biology 21, no. 6 (2001): 2008–17. http://dx.doi.org/10.1128/mcb.21.6.2008-2017.2001.

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ABSTRACT Expression of replication-dependent histone genes at the posttranscriptional level is controlled by stem-loop binding protein (SLBP). One function of SLBP is to bind the stem-loop structure in the 3′ untranslated region of histone pre-mRNAs and facilitate 3′ end processing. Interaction of SLBP with the stem-loop is mediated by the centrally located RNA binding domain (RBD). Here we identify several highly conserved amino acids in the RBD mutation of which results in complete or substantial loss of SLBP binding activity. We also identify residues in the RBD which do not contribute to b

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Chen, Yu, Jessica Fender, Jason D. Legassie, Michael B. Jarstfer, Tracy M. Bryan, and Gabriele Varani. "Structure of stem-loop IV of Tetrahymena telomerase RNA." EMBO Journal 25, no. 13 (2006): 3156–66. http://dx.doi.org/10.1038/sj.emboj.7601195.

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Gorodkin, J. "Discovering common stem-loop motifs in unaligned RNA sequences." Nucleic Acids Research 29, no. 10 (2001): 2135–44. http://dx.doi.org/10.1093/nar/29.10.2135.

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Singh, R., S. Gupta, and R. Reddy. "Capping of mammalian U6 small nuclear RNA in vitro is directed by a conserved stem-loop and AUAUAC sequence: conversion of a noncapped RNA into a capped RNA." Molecular and Cellular Biology 10, no. 3 (1990): 939–46. http://dx.doi.org/10.1128/mcb.10.3.939.

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The cap structure of U6 small nuclear RNA (snRNA) is gamma-monomethyl phosphate and is distinct from other known RNA cap structures (R. Singh and R. Reddy, Proc. Natl. Acad. Sci. USA 86:8280-8283, 1989). Here we show that the information for capping the U6 snRNA in vitro is within the initial 25 nucleotides of the U6 RNA. The capping determinant in mammalian U6 snRNA is a bipartite element--a phylogenetically conserved stem-loop structure and an AUAUAC sequence, or a part thereof, following this stem-loop. Wild-type capping efficiency was obtained when the AUAUAC motif immediately followed the

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42

Singh, R., S. Gupta, and R. Reddy. "Capping of mammalian U6 small nuclear RNA in vitro is directed by a conserved stem-loop and AUAUAC sequence: conversion of a noncapped RNA into a capped RNA." Molecular and Cellular Biology 10, no. 3 (1990): 939–46. http://dx.doi.org/10.1128/mcb.10.3.939-946.1990.

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The cap structure of U6 small nuclear RNA (snRNA) is gamma-monomethyl phosphate and is distinct from other known RNA cap structures (R. Singh and R. Reddy, Proc. Natl. Acad. Sci. USA 86:8280-8283, 1989). Here we show that the information for capping the U6 snRNA in vitro is within the initial 25 nucleotides of the U6 RNA. The capping determinant in mammalian U6 snRNA is a bipartite element--a phylogenetically conserved stem-loop structure and an AUAUAC sequence, or a part thereof, following this stem-loop. Wild-type capping efficiency was obtained when the AUAUAC motif immediately followed the

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Toczyski, D. P., and J. A. Steitz. "The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1." Molecular and Cellular Biology 13, no. 1 (1993): 703–10. http://dx.doi.org/10.1128/mcb.13.1.703.

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EAP (EBER-associated protein) is an abundant, 15-kDa cellular RNA-binding protein which associates with certain herpesvirus small RNAs. We have raised polyclonal anti-EAP antibodies against a glutathione S-transferase-EAP fusion protein. Analysis of the RNA precipitated by these antibodies from Epstein-Barr virus (EBV)- or herpesvirus papio (HVP)-infected cells shows that > 95% of EBER 1 (EBV-encoded RNA 1) and the majority of HVP 1 (an HVP small RNA homologous to EBER 1) are associated with EAP. RNase protection experiments performed on native EBER 1 particles with affinity-purified anti-E

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Toczyski, D. P., and J. A. Steitz. "The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1." Molecular and Cellular Biology 13, no. 1 (1993): 703–10. http://dx.doi.org/10.1128/mcb.13.1.703-710.1993.

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EAP (EBER-associated protein) is an abundant, 15-kDa cellular RNA-binding protein which associates with certain herpesvirus small RNAs. We have raised polyclonal anti-EAP antibodies against a glutathione S-transferase-EAP fusion protein. Analysis of the RNA precipitated by these antibodies from Epstein-Barr virus (EBV)- or herpesvirus papio (HVP)-infected cells shows that > 95% of EBER 1 (EBV-encoded RNA 1) and the majority of HVP 1 (an HVP small RNA homologous to EBER 1) are associated with EAP. RNase protection experiments performed on native EBER 1 particles with affinity-purified anti-E

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Mayo, Christopher B., C. Jason Wong, Prisma E. Lopez, Jeffrey W. Lary, and James L. Cole. "Activation of PKR by short stem–loop RNAs containing single-stranded arms." RNA 22, no. 7 (2016): 1065–75. http://dx.doi.org/10.1261/rna.053348.115.

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Byun, Yanga, and Kyungsook Han. "An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type." Journal of Bioinformatics and Computational Biology 14, no. 03 (2016): 1650009. http://dx.doi.org/10.1142/s0219720016500098.

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An RNA pseudoknot is a tertiary structural element in which bases of a loop pair with complementary bases are outside the loop. A drawing of RNA secondary structures is a tree, but a drawing of RNA pseudoknots is a graph that has an inner cycle within a pseudoknot and possibly outer cycles formed between the pseudoknot and other structural elements. Visualizing a large-scale RNA structure with pseudoknots as a planar drawing is challenging because a planar drawing of an RNA structure requires both pseudoknots and an entire structure enclosing the pseudoknots to be embedded into a plane without

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Tuplin, A., D. J. Evans, and P. Simmonds. "Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods." Journal of General Virology 85, no. 10 (2004): 3037–47. http://dx.doi.org/10.1099/vir.0.80141-0.

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There is accumulating evidence from bioinformatic studies that hepatitis C virus (HCV) possesses extensive RNA secondary structure in the core and NS5B-encoding regions of the genome. Recent functional studies have defined one such stem–loop structure in the NS5B region as an essential cis-acting replication element (CRE). A program was developed (structur_dist) that analyses multiple rna-folding patterns predicted by mfold to determine the evolutionary conservation of predicted stem–loop structures and, by a new method, to analyse frequencies of covariant sites in predicted RNA folding betwee

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Shokeen, Sonia, Smita Patel, Tony J. Greenfield, Cassandra Brinkman, and Keith E. Weaver. "Translational Regulation by an Intramolecular Stem-Loop Is Required for Intermolecular RNA Regulation of the par Addiction Module." Journal of Bacteriology 190, no. 18 (2008): 6076–83. http://dx.doi.org/10.1128/jb.00660-08.

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ABSTRACT The par stability determinant of Enterococcus faecalis plasmid pAD1 is the only antisense RNA-regulated addiction module identified to date in gram-positive bacteria. par encodes two small, convergently transcribed RNAs, designated RNA I and RNA II, that function as the toxin (Fst)-encoding and antitoxin components, respectively. Previous work showed that structures at the 5′ end of RNA I are important in regulating its translation. The work presented here reveals that a stem-loop sequestering the Fst ribosome binding site is required for translational repression but a helix sequester

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Raman, Sharmila, Peter Bouma, Gwyn D. Williams, and David A. Brian. "Stem-Loop III in the 5′ Untranslated Region Is a cis-Acting Element in Bovine Coronavirus Defective Interfering RNA Replication." Journal of Virology 77, no. 12 (2003): 6720–30. http://dx.doi.org/10.1128/jvi.77.12.6720-6730.2003.

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ABSTRACT Higher-order structures in the 5′ untranslated region (UTR) of plus-strand RNA viruses are known in many cases to function as cis-acting elements in RNA translation, replication, or transcription. Here we describe evidence supporting the structure and a cis-acting function in defective interfering (DI) RNA replication of stem-loop III, the third of four predicted higher-order structures mapping within the 210-nucleotide (nt) 5′ UTR of the 32-kb bovine coronavirus (BCoV) genome. Stem-loop III maps at nt 97 through 116, has a calculated free energy of −9.1 kcal/mol in the positive stran

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Beerens, Nancy, and Eric J. Snijder. "RNA signals in the 3′ terminus of the genome of Equine arteritis virus are required for viral RNA synthesis." Journal of General Virology 87, no. 7 (2006): 1977–83. http://dx.doi.org/10.1099/vir.0.81750-0.

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RNA virus genomes contain cis-acting sequences and structural elements involved in virus replication. Both full-length and subgenomic negative-strand RNA synthesis are initiated at the 3′ terminus of the positive-strand genomic RNA of Equine arteritis virus (EAV). To investigate the molecular mechanism of EAV RNA synthesis, the RNA secondary structure of the 3′-proximal region of the genome was analysed by chemical and enzymic probing. Based on the RNA secondary structure model derived from this analysis, several deletions were engineered in a full-length cDNA copy of the viral genome. Two RNA

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