Conserved stem-loop structure
A Phylogenetically Conserved Stem-Loop Structure at the 5′ Border of the Internal Ribosome Entry Site of Hepatitis C Virus Is Required for Cap-Independent Viral Translation
... terminal loop and internal bulge loops (highlighted in ...the structure. The highly conserved nature of these loop sequences among flaviviruses that infect very different host species and ...
10
A stem loop structure in the wingless transcript defines a consensus motif for apical RNA transport
... highly conserved stem-loop ...predicted structure conservation, however, mutagenesis shows significant leeway for both sequence and structure variation in the predicted ...
11
The UCUAAAC promoter motif is not required for high-frequency leader recombination in bovine coronavirus defective interfering RNA.
... the structure of the BCV leader one that would suggest accessibility as a template for polymerase strand switching? Mechanisms directing strand switching by RNA-dependent RNA polymerases are in general poorly ...
10
Phenotypic Characterization of Three Phylogenetically Conserved Stem-Loop Motifs in the Mengovirus 3′ Untranslated Region
... well-defined structure elements within the required por- tions of their 3⬘ UTRs to help guide the polymerase in the initiation of minus-strand ...also conserved and of low Pnum in 12 independent folds with ...
10
A twist in the tail: SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication.
... phylogenetically conserved and exhibit low levels of synonymous site sequence variation between divergent HCV genotypes, implying likely functional constraints on the evolution of these sequences out with their ...
14
Efficient and Specific Initiation of Subgenomic RNA Synthesis by Cucumber Mosaic Virus Replicase In Vitro Requires an Upstream RNA Stem-Loop
... a stem-loop at nt ⫺28 to ⫺5 upstream of the ⫹1C is respon- sible for the efficient and accurate initiation of subgenomic RNA ...This stem-loop structure is conserved in all ...
9
Identification and characterization of a hepatitis delta virus RNA transcriptional promoter.
... highly conserved structure, represents a RNA-RNA ...secondary structure predicted that the promoter contains two bulge regions in a stem-loop structure which encompasses a ...
10
A twist in the tail : SHAPE mapping of long range interactions and structural rearrangements of RNA elements involved in HCV replication
... phylogenetically conserved and exhibit low levels of synonymous site sequence variation between divergent HCV genotypes, implying likely functional constraints on the evolution of these sequences out with their ...
15
Stem-Loop IV in the 5′ Untranslated Region Is a cis-Acting Element in Bovine Coronavirus Defective Interfering RNA Replication
... as stem-loops I to IV, which may function as cis-acting elements in genomic RNA ...that stem-loop IV, a bulged stem-loop mapping at nt 186 through 215, (i) is phylogenetically ...
13
Hepatitis C Virus Internal Ribosome Entry Site (IRES) Stem Loop IIId Contains a Phylogenetically Conserved GGG Triplet Essential for Translation and IRES Folding
... IIId stem loop sequences of HCV compared to those of GBV-B and related pestiviruses shows distinct differences ...asymmetric loop whereas BVDV and CSFV actually contain two IIId loops (IIId and ...
8
Structure of the 5′ Nontranslated Region of the Coxsackievirus B3 Genome: Chemical Modification and Comparative Sequence Analysis
... basal stem nearly every base is accessible, including most of the proposed pairs that separate the ...internal loop sequences do, however, present the intriguing possibility for loop E motifs ...The ...
19
Role of the 3′ tRNA-Like Structure in Tobacco Mosaic Virus Minus-Strand RNA Synthesis by the Viral RNA-Dependent RNA Polymerase In Vitro
... tRNA-like structure (TLS) containing a 3⬘ pseudoknotted domain (D1) which mimics a tRNA acceptor branch terminating in an unpaired CCA sequence and a do- main (D2) which resembles a tRNA anticodon branch (19, ...
10
Comparative analysis of the structure and function of adenovirus virus-associated RNAs.
... Secondary structure analysis indicated that all seven RNAs conform to the model in which VA RNA possesses three main structural regions, a terminal stem, an apical stem-loop, and a centr[r] ...
13
Molecular characterization of the sequences of the 16S 23S rDNA internal spacer region (ISR) from isolates of Taylorella asinigenitalis
... highly conserved sequence close to the 3' end of the mature 16S rRNA that is complementary to the Shine-Dal- garno sequence on mRNA [14,15], was identified in the sequences of the amplicons of ...
6
Selective Interactions of Polyanions with Basic Surfaces on Human Immunodeficiency Virus Type 1 gp120
... V3 loop charge on the overall electrostatic potential of the conserved coreceptor binding surface, we carried out modeling, as described in reference 45, based on the HXBc2 crystal structure of the ...
13
Identification of transactivation-response sequences in the long terminal repeat of bovine immunodeficiency-like virus.
... Deletion analysis of the long terminal repeat indicated that sequences containing the proximal stem-loop structure located between +4 and +31 are required for virus-specific transactivat[r] ...
5
The sequence and structure of the 3' arm of the first stem-loop of the human immunodeficiency virus type 2 trans-activation responsive region mediate Tat-2 transactivation.
... proximal stem-loop structure of TAR-2 RNA and that this element is crucial to the Tat-2 ...9 stem portion of the proximal hairpin but did not detect any binding to the distal ...
8
Exploratory analysis of pathogen resistance responsible genetic elements in two eudicots from whole genome sequence
... A search of the genome was performed using BLAST. This search retrieved mature- miRNA target sites from similarity to targets in other organisms. Genes responsible for coding products are still subject to the normal ...
56
An RNA stem-loop structure directs hepatitis B virus genomic RNA encapsidation.
... These studies reveal that i in the lower stem, base pairing but not specific primary sequence is required for function; ii there is no requirement for base pairing in the lower portion o[r] ...
10
Genetic variation in vivo and proposed functional domains of the 5' noncoding region of poliovirus RNA.
... The variation seen in stem-loop G was concentrated mainly in the loop, and only few strains had nucleotide substitutions in the stem; none of these would prevent the proposed base pairin[r] ...
7