Stem-loop
A non-spectroscopic optical biosensor for the detection of pathogenic Salmonella Typhimurium based on a stem-loop DNA probe and retro-reflective signaling
... using stem-loop DNA as a probe has attracted much attention because of the advantage of being able to clearly detect the on–off signal ...[16–18]. Stem-loop DNA probes consist of two regions; ...
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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 conserved ...
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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 subgroups of ...
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The requirement for a 5' stem-loop structure in brome mosaic virus replication supports a new model for viral positive-strand RNA initiation.
... Substitutions introduced at bases surrounding the ICR2 motif yielded levels of pRNA replication that differed, depending on the maintenance of a putative 5' stem-loop structure in the po[r] ...
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Analysis of Natural Variants of the Human Immunodeficiency Virus Type 1 gag-pol Frameshift Stem-Loop Structure
... In human immunodeficiency virus type 1 (HIV-1), the frameshift structure needed for translation of the Gag-Pol precursor polyprotein includes a slippery heptamer (UUU UUUA) region that allows ribosome repositioning in ⫺1 ...
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The Topology of Bulges in the Long Stem of the Flavivirus 3′ Stem-Loop Is a Major Determinant of RNA Replication Competence
... terminal stem-loop secondary structure (3 ⴕ SL) formed by the most downstream ⬃ 100 nucleotides (nt) of the viral ...long stem of the WN 3 ⴕ SL was essential for replication of mutant WN RNAs, and ...
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Interactions between the Dengue Virus Polymerase NS5 and Stem-Loop A
... 3= stem-loop is recognized by the thumb subdomain of RdRp, and the polymerase mutant that abolished the 3= stem-loop interaction also eliminated 5= SLA interactions ...3= ...
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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 stem-loop ...
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Mutational analysis of the J-K stem-loop region of the encephalomyocarditis virus IRES.
... of stem-loop structural ...terminal loop of J gave similar ...terminal loop of K had minimal impact on in vitro translation activity and IRES competitive ...
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The Murine Norovirus Core Subgenomic RNA Promoter Consists of a Stable Stem-Loop That Can Direct Accurate Initiation of RNA Synthesis
... RNA stem-loop structure on the negative-sense RNA, the complementary sequence of which codes for the viral RNA-dependent RNA polymerase ...conserved stem-loop is positioned 6 nucleotides 3= of ...
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Stem loop binding protein is a multifaceted cellular regulator of HIV 1 replication
... treatment. Identifying the mechanisms underlying this atypical response to infection may lead to therapeutic advances for treating HIV-1. Here, we developed a proteomic analysis to compare peripheral blood cell proteomes ...
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Role of Stem B, Loop B, and Nucleotides next to the Primer Binding Site and the Kissing-Loop Domain in Human Immunodeficiency Virus Type 1 Replication and Genomic-RNA Dimerization
... and stem I mutants), while ⌬SD, ⌬H3, and ⌬4AU had rather large yields (73 to ...a stem- loop as important as the KLD for genome encapsidation (9, ...242, stem B, loop B, or the klh ...
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A Hypervariable Region within the 3′ cis-Acting Element of the Murine Coronavirus Genome Is Nonessential for RNA Synthesis but Affects Pathogenesis
... The 3 ⴕ cis-acting element for mouse hepatitis virus (MHV) RNA synthesis resides entirely within the 301-nucleotide 3 ⴕ untranslated region (3 ⴕ UTR) of the viral genome and consists of three regions. Encompass- ing the ...
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Rep-Mediated Nicking of the Adeno-Associated Virus Origin Requires Two Biochemical Activities, DNA Helicase Activity and Transesterification
... potential stem-loop structure at the ...trs stem-loop in the extruded form no longer requires ...the stem-loop structure, prior to the ATP-independent Rep transesterification ...
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Expressional studies of microRNAs in Hepatitis B Patients of Quetta, Pakistan
... Hepatitis B (HB) is a severe and widespread infectious liver disease affecting millions of people throughout the globe and caused by hepatitis B virus (HBV). Persistent HBV infections results severe pathologies which ...
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Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity
... the stem- loop and frameshift efficiency in ...site stem-loop was modified in order to dissect the relative contributions of local and overall RNA thermodynamic stability to HIV-1 frameshift ...
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Untranslated regions of mRNAs
... An alternative mechanism for translation initiation, which occurs independently of the 5 cap, was discovered for the first time in picornaviruses [28]: a sequence element in the 5 UTR acts as an internal ribosome entry ...
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Molecular characterization of the sequences of the 16S 23S rDNA internal spacer region (ISR) from isolates of Taylorella asinigenitalis
... sus sequences of the antiterminators of boxB a stem-loop structure with no apparent sequence conservation at nucleotide position 486–500 and boxA a conserved sequence, TGTTCTTTAACA, at n[r] ...
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Structural Elements in the 5′-Untranslated Region of Giardiavirus Transcript Essential for Internal Ribosome Entry Site-Mediated Translation Initiation
... predicted stem- loop U4a (nt U204 to A219) with a short (4-bp) stem and a large (8-nt) loop ...the stem-loop, other than C216 to C218, were significantly modified by chemicals ...
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The UCUAAAC promoter motif is not required for high-frequency leader recombination in bovine coronavirus defective interfering RNA.
... FIG. 1. Structure of the bovine coronavirus DI RNA and enzymatic structure probing of its 59-end sequence on plus-strand RNA synthesized in vitro. (A) Structural relationship between the BCV genome and BCV DI RNA. The DI ...
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