functional rna secondary structure
Characterization of an Essential RNA Secondary Structure in the 3′ Untranslated Region of the Murine Coronavirus Genome
... targeted RNA recombination (20, 22, 31, 40, ...via RNA-RNA recombina- tion between a synthetic donor RNA and the genome of a recipient virus that can be selected ...targeted RNA ...
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RNA motif discovery: a computational overview
... ondary structure based local patterns from a set of related RNA ...their structure and thereby directly influence the production of proteins encoded by the mRNA on which they ...selected RNA, ...
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Secondary Structural Elements within the 3′ Untranslated Region of Mouse Hepatitis Virus Strain JHM Genomic RNA
... genomic RNA participate in DI RNA ...stem-loop structure spanning nt 302 to 234 within the 3⬘ UTR of MHV (7, ...similar structure also exists in BCoV. Functional studies suggested that ...
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Reconstructing phylogeny from RNA secondary structure via simulated evolution
... their functional activity depends upon their specific three-dimensional structures 6,11,23 ; these structures, in turn, are primarily determined by pairings between bases in different parts of the ...
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Translation of the Flavivirus Kunjin NS3 Gene in cis but Not Its RNA Sequence or Secondary Structure Is Essential for Efficient RNA Packaging
... viral RNA to be encap- sidated, the NS3 helicase and RNA 5 ⬘ -triphosphatase activities are required to release the nascent positive-stranded RNA from the RC and cap the RNA at its 5 ⬘ ...
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Functional analysis of the Tat trans activator of human immunodeficiency virus type 2.
... This RNA secondary structure displays an additional loop within the predicted TAR recognition sequence, and it has been suggested that a requirement for recognition of two such structure[r] ...
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Importance of the Positive-Strand RNA Secondary Structure of a Murine Coronavirus Defective Interfering RNA Internal Replication Signal in Positive-Strand RNA Synthesis
... single-strand RNA bacteriophage Qb contains two internal viral polymerase rec- ognition sites for negative-strand RNA synthesis; each internal recognition site is separated from its functional ...
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Functional Characterization of the Dimer Linkage Structure RNA of Moloney Murine Sarcoma Virus
... DLS RNA and that this interaction is medi- ated through the presence of the ...of RNA dimerization as a dynamic ...genomic RNA proposed by several investi- gators (5, ...of RNA conformers that ...
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Identification of a cis-Acting Replication Element within the Poliovirus Coding Region
... positive-stranded RNA virus, requires translation of the infecting genome followed by virus-encoded VPg and 3D polymerase-primed synthesis of a negative-stranded ...template. RNA sequences involved in the ...
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Thermal adaptation of the phage G4 and molecular evolution of RNA secondary structure
... The study of evolutionary responses to temperature has served as an important model for understanding the process of adaptation to novel environments [3], in part because the evolutionary and mechanistic causes of ...
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Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection
... The influenza A virus (IAV) poses a serious threat to human health. Despite significant progress in surveil- lance and control measures, including the development of antiviral drugs, vaccines and diagnostics, IAV con- ...
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Secondary Structure of the 3′ Terminus of Hepatitis C Virus Minus-Strand RNA
... minimal RNA frag- ment required for efficient replication of the (⫺) strand spans nt ⫺239 to ⫺1 (43), which corresponds to the domain I iden- tified in the present ...stable structure at the 3⬘ end of the ...
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Effects of dynamic ultra-high pressure homogenization on the structure and functional properties of casein
... the structure and functional properties of casein were systematically ...the functional properties of casein changed with dynamic UHPH treatment, and the treatment at 150 MPa could significantly ...
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Research on folding diversity in statistical learning methods for RNA secondary structure prediction
... of RNA secondary structure is currently a hot ...of RNA secondary ...an RNA secondary structure prediction framework is proposed, namely “Cluster - Training - ...
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A 371-nucleotide region between the herpes simplex virus type 1 (HSV-1) LAT promoter and the 2-kilobase LAT is not essential for efficient spontaneous reactivation of latent HSV-1.
... We then found that although deletion of the ICP34.5 gene, which overlaps LAT nt 6200 to 7100, reduces spontaneous reactivation (19), wild-type reactivation can be restored by insertion of the ICP34.5 gene at a distant ...
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GTfold: Enabling parallel RNA secondary structure prediction on multi core desktops
... We also demonstrate that GTfold’s reduced running time does not come at the expense of prediction accuracy, rel- ative to UNAfold and RNAfold, as measured against ribo- somal structures obtained by comparative sequence ...
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Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain
... RT were too distant to be of any relevance for this particular analysis. HIV-1 RT p66 residues K353 to T365 comprise a loop within the connection domain. This loop is structurally located in the exact region where the E. ...
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SL1 revisited: functional analysis of the structure and conformation of HIV 1 genome RNA
... stable structure, com- puter predictions have indicated the shapes of SL1 within the models are all rather ...viral RNA including SHAPE assay (selective 2 ′ -hydroxyl acylation analyzed by primer extension) ...
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CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
... Given that various CRISPRO features such as conserva- tion and disorder scores were correlated with CRISPR scores, we sought to test if the collection of features and annotations used in CRISPRO could be used to predict ...
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Structure and Functional Relevance of a Transcription-Regulating Sequence Involved in Coronavirus Discontinuous RNA Synthesis
... genomic RNA transcription generates 5 ⴕ - and 3 ⴕ -cotermi- nal subgenomic ...minus-sense RNA that is modulated by transcription-regulating sequences located at the 3 ⴕ end of the leader (TRS-L) and also ...
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