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Nucleic acid secondary structure
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two
Pseudoknot
RNA family
ALIL pseudoknot is an RNA element that induces frameshifting in bacteria. The expression of a minority of genes requires frameshifting to occur where the
ALIL_pseudoknot
RNA family
The prion pseudoknot is predicted RNA pseudoknot structure found in prion protein mRNA. It has been suggested that this element has a possible effect in
Prion_pseudoknot
RNA family
The Coronavirus 3′ UTR pseudoknot is an RNA structure found in the coronavirus genome. Coronaviruses contain 30 kb single-stranded positive-sense RNA genomes
Coronavirus_3′_UTR_pseudoknot
Nucleic acid sequence
of inverted repeats between several species, namely on archaea, see Pseudoknots are common structural motifs found in RNA. They are formed by two nested
Inverted_repeat
Genus of viruses
RNA molecules contains four hair-pin structures and a pseudoknot in the 3'UTR. The pseudoknot is unusual in that it contains a small stem-loop structure
Crinivirus
Basepairing interactions within a single nucleic acid polymer or between two polymers
marked as pairs of brackets. In a pseudoknot-free structure, this results in a neat stack of balanced brackets. Pseudoknots can be represented appear as different
Nucleic acid secondary structure
Nucleic_acid_secondary_structure
RNA family
virus pseudoknot is an RNA pseudoknot structure formed in one of the non-structural coding segments (NS) of influenza virus genome. Pseudoknots are commonly
Influenza_virus_pseudoknot
Genus of viruses
of some members of this genus contain four hair-pin structures and a pseudoknot in the 3'UTR. These secondary structures have been found to be important
Closterovirus
Graph layout on multiple half-planes
nucleic acid secondary structure, and two-page book embeddings represent pseudoknots. Other applications of book embeddings include abstract algebra and knot
Book_embedding
Biomolecular structure of nucleic acids such as DNA and RNA
second stem and loop. This causes formation of pseudoknots with two stems and two loops. Pseudoknots are functional elements in RNA structure having
Nucleic_acid_structure
RNA family
long range pseudoknot is a pseudoknot containing a long loop region, and may be a mechanism of translational control. A long range pseudoknot is thought
Long_range_pseudoknots
RNA family
four pseudoknots, one (pk1) upstream of the tag peptide CDS, and the other three pseudoknots (pk2 to pk4) downstream of the CDS. The pseudoknot regions
Transfer-messenger_RNA
Three-dimensional shape of a nucleic acid polymer
coaxial stacking motifs include the kissing loop interaction and the pseudoknot. The stability of these interactions can be predicted by an adaptation
Nucleic acid tertiary structure
Nucleic_acid_tertiary_structure
formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. The secondary structure of
NUPACK
RNA family
In plasmids, the regulatory region of repBA gene forms a pseudoknot. The repA gene, which encodes a protein likely to function as an initiator for replication
Regulatory region of repBA gene
Regulatory_region_of_repBA_gene
dependent on a pseudoknot located eight nucleotides downstream of the stop codon (UAG). Sequence conservation is found in the second pseudoknot loop. Secondary
Gag/pol translational readthrough site
Gag/pol_translational_readthrough_site
American molecular biologist and Nobel laureate
boundary (2003) of vertebrate telomerase RNA as well as analyzing the pseudoknot structure in human telomerase RNA (2005). In addition to working in Tetrahymena
Carol_W._Greider
RNA family
facilitating the pseudoknot. Several nucleotide positions are highly conserved, with many around the terminal loops involved in the pseudoknot interaction
Cyclic_di-GMP-II_riboswitch
Computational prediction of nucleic acid structure
dynamic programming and therefore are unable to efficiently identify pseudoknots. While the methods are similar, there are slight differences in the approaches
Nucleic acid structure prediction
Nucleic_acid_structure_prediction
Graph drawing with vertices on a line
secondary structure in which the crossings of the diagram represent pseudoknots in the structure. In an arc diagram, the vertices of a graph are arranged
Arc_diagram
RNA family
(R2Spy). Within this 5' protein binding site an RNA pseudoknot structure occurs. The pseudoknot is highly conserved between the five silk moth species
R2_RNA_element
Subfamily of viruses in the family Coronaviridae
frameshift caused by a slippery sequence (UUUAAAC) and a downstream RNA pseudoknot at the end of open reading frame ORF1a. The ribosomal frameshift allows
Coronavirus
Pathogenic type of misfolded protein
polymerization Kuru (disease) Mad cow crisis Non-cellular life Prion pseudoknot Proteinopathy Subviral agents Tau protein "English pronunciation of prion"
Prion
Phenomenon that occurs during translation of a messenger RNA into proteins
the slippery sequence. The RNA structure (which can be a stem-loop or pseudoknot) is thought to pause the ribosome on the slippery site during translation
Ribosomal_frameshift
File format for biological sequence alignments
-------------- SS Secondary Structure For RNA [.,;<>(){}[]AaBb.-_] --supports pseudoknot and further structure markup (see WUSS documentation) For protein [HGIEBTSCX]
Stockholm_format
RNA family
segment 7 pre-mRNA can adopt two different types of RNA structure: a pseudoknot and a hairpin. This conformational switch is proposed to play a role in
Influenza A segment 7 splice site
Influenza_A_segment_7_splice_site
Viral disease
for stalling of the host 5′-3′ exonuclease XRN1. The UTR contains PKS3 pseudoknot structure, which serves as a molecular signal to stall the exonuclease
Yellow_fever
Protein involved in multiple prion diseases
helix (human PrPC numbering). PrP messenger RNA contains a pseudoknot structure (prion pseudoknot), which is thought to be involved in regulation of PrP protein
Major_prion_protein
sequence downstream is needed as well, since the upper loop region forms a pseudoknot (PK) with the single-stranded region directly downstream to its respective
Flavivirus_3'_UTR
expression of the repZ gene. repZ expression requires formation of a pseudoknot in the mRNA. repZ is repressed by a small antisense Inc RNA, which binds
Plasmid_copy_number
RNA family
33 to 58 nucleotides. PreQ1-III riboswitch has an atypically organized pseudoknot that does not appear to incorporate its downstream expression platform
PreQ1_riboswitch
Intramolecular base-pairing pattern in RNA and DNA
form, and large loops with no secondary structure of their own (such as pseudoknot pairing) are unstable. One common loop with the sequence UUCG is known
Stem-loop
BA (July 2010). "CyloFold: secondary structure prediction including pseudoknots". Nucleic Acids Research. 38 (Web Server issue): W368–W372. doi:10.1093/nar/gkq432
List of RNA structure prediction software
List_of_RNA_structure_prediction_software
Macromolecular machine that synthesizes proteins in cells
highly organized into various tertiary structural motifs, for example pseudoknots that exhibit coaxial stacking. The extra RNA in the larger ribosomes
Ribosome
RNA structure
noted, but also surprising differences, such as the absence of the two pseudoknot interactions in the twister ribozyme. The exact nature of the structural
Twister_sister_ribozyme
RNA family
consists of two stem-loop structures (SL-A and SL-B) together with a pseudoknot. Disruption of any of these elements impairs both viral replication and
Human parechovirus 1 (HPeV1) cis regulatory element (CRE)
Human_parechovirus_1_(HPeV1)_cis_regulatory_element_(CRE)
NcRNA found in eukaryotes
structure between vertebrates, ciliates and yeasts, but they share a 5' pseudoknot structure close to the template sequence; vertebrate telomerase RNAs also
Telomerase_RNA_component
RNA family
includes one pseudoknot, but one stem involved in this apparent pseudoknot exhibits only one example of covariation, so the existence of the pseudoknot is unclear
IMPDH_RNA_motif
3′ UTR pseudoknot). PK-SL2 has been confirmed in HCoV-229E and HCoV-NL63 by in vitro structure probing experiments. Downstream of this pseudoknot lies the
Coronavirus_3′_UTR
Non-coding RNA in hepatitis delta virus
crystallography and shows five helical segments connected by a double pseudoknot. In addition to the sense (genomic version), all HDV viruses also have
Hepatitis delta virus ribozyme
Hepatitis_delta_virus_ribozyme
depiction. The structural significance of the pairing interaction labeled "pseudoknot or alternate stem" is currently unknown. The P1 stem is unusually rich
PreQ1-III_riboswitch
also referred to as SL II and SL IV. Each xrRNA folds into a double pseudoknot (PK) centered around a three-way junction (3WJ), forming a protective
Exoribonuclease-resistant_RNA
Species of coronavirus causing SARS and COVID-19
frameshift caused by a slippery sequence (UUUAAAC) and a downstream RNA pseudoknot at the end of open reading frame ORF1a. The ribosomal frameshift allows
SARS-related_coronavirus
Queueing of ribosomes during protein synthesis
unknown. Also, the ribosome pauses if the pseudoknot is disrupted. 10% of the ribosome pauses at the pseudoknot and 4% of the ribosomes are terminated.
Ribosomal_pause
RNA family
The Upstream pseudoknot (UPSK) domain is an RNA element found in the turnip yellow mosaic virus, beet virus Q, barley stripe mosaic virus and tobacco mosaic
UPSK_RNA
aureus via trans-acting mechanisms. Its secondary structure contains a pseudoknot formed between two highly conserved unpaired sequences. RsaD, E H and
Rsa_RNA
Structural element
requires +1 translational frameshifting. This frameshift is stimulated by a pseudoknot present 3' of the frameshift site in the antizyme mRNA. The frameshifting
Antizyme RNA frameshifting stimulation element
Antizyme_RNA_frameshifting_stimulation_element
American computational chemist killed in 2015 train wreck
developed an algorithm capable of efficiently handling certain types of pseudoknots, a class of structure that is more computationally intensive to analyze
Robert_Dirks
RNA family
of replication (OriR) for the initiation of (-) strand RNA synthesis. Pseudoknots have also been predicted in this structure. Enterovirus 5′ cloverleaf
Enteroviral_3′_UTR_element
Species of virus
four-way helical Holliday junction that is integrated within a predicted pseudoknot. The conformation of this core domain constrains the open reading frame's
Hepatitis_C_virus
Family of viruses
reading frame (ORF) due to the presence of secondary structures such as pseudoknots. Paramyxoviridae also undergo transcriptional stuttering to produce the
Paramyxoviridae
3D conformation of a biological sequence, like DNA, RNA, proteins
or combinations of them can be further classified, e.g. tetraloops, pseudoknots and stem loops. There are many secondary structure elements of functional
Biomolecular_structure
RNA family
structure of the riboswitch has been solved (PDB 6FZ0). It contains a pseudoknot. SAM-I riboswitch SAM-II riboswitch SAM-III riboswitch SAM-IV riboswitch
SAM-V_riboswitch
Open reading frame
The frameshift occurs at a slippery sequence which is followed by a pseudoknot RNA secondary structure. This has been measured at between 20-50% efficiency
ORF1ab
RNA family
Betaproteobacteria-1 RNAs likely function in trans as sRNAs. The motif has three pseudoknots in a moderate size of roughly 120 nucleotides on average. Weinberg Z
Betaproteobacteria-1 RNA motif
Betaproteobacteria-1_RNA_motif
Methodology to reveal RNA structure by Ruth Nussinov
"flowers"). If chords drawn intersect, this corresponds to pseudoknots in the tRNA structure. Pseudoknots imply twists in the RNA or tRNA structure (the RNA or
Nussinov_plots
RNA family
held together by a pseudoknot formed between the loop on the end of stem P2 and the J3/4 joining region. The formation of the pseudoknot is facilitated by
SAM_riboswitch_(S-box_leader)
Base pairs in molecular genetics
interactions between the secondary structures. This leads to the formation of pseudoknots, ribose zippers, kissing hairpin loops, or co-axial pseudocontinuous
Non-canonical_base_pairing
Bioinformatics software for RNA structure analysis and prediction
8 to 2.0 format RNAPKplex Predict RNA secondary structures including pseudoknots RNAplex Find targets of a query RNA RNAplfold Calculate average pair
ViennaRNA_Package
Conserved RNA structure
Fusobacteriota. 6A RNAs likely function in trans as sRNAs, and contain a pseudoknot. The 6A RNA motif was named after 6 A (adenosine) nucleotides that are
6A_RNA_motif
InterPro Family
"Human interferon-gamma mRNA autoregulates its translation through a pseudoknot that activates the interferon-inducible protein kinase PKR". Cell. 108
Interferon_gamma
Regulartory element in coronaviruses
(s2m), as well as the 5′- and 3′ UTR pseudoknot. Coronavirus 5′ UTR Coronavirus 3′ UTR Coronavirus 3′ UTR pseudoknot Coronavirus 3′ stem-loop II-like motif
Coronavirus_packaging_signal
Fluoride-binding RNA structure
helical stems adjoined by a helical loop with the capacity to become a pseudoknot. The bound fluoride ligand is found to be located within the center of
Fluoride_riboswitch
Part of ribosome biogenesis
alternate structures is a series of three hairpins, the other includes a pseudoknot. This structure causes translational regulation of the S15 protein. Only
Ribosomal_S15_leader
conserved region can pair with the 5’ UTR of the HAC1 mRNA forming a pseudoknot, which stalls the translation. The unconventional splicing is performed
BZIP_intron_saccharomycetales
Genetic motif present in some viruses
element, the coronavirus packaging signal and the coronavirus 3′ UTR pseudoknot. Functionally during host invasion by viral RNA, it appears that s2m first
Coronavirus 3′ stem-loop II-like motif (s2m)
Coronavirus_3′_stem-loop_II-like_motif_(s2m)
RNA family
conserved internal loop, with a three-nucleotide segment predicted to form a pseudoknot by base-pairing with a portion of the Shine-Dalgarno sequence of the adjacent
NAD-II_riboswitch
RNA structure that catalyzes its own cleavage at a specific site
base-paired stems: P1, P2, and P3, which are all connected by loops. A pseudoknot interaction exists between the loop of P1 and the junction connecting
Pistol_ribozyme
Order of positive-sense, single-stranded RNA viruses
sequence located upstream of the ORF1a stop codon and a putative RNA pseudoknot structure.[citation needed] Many proteins have been identified on the
Nidovirales
American biophysicist
CA; Feigon, J (4 March 2005). "Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function". Molecular
Juli_Feigon
Class of ribonucleic acid that is not translated into proteins
at nucleotide 70 that is in a loop region two bases 5' of a conserved pseudoknot. However, many other mutations within RNase MRP also cause CHH. The antisense
Non-coding_RNA
RNA family
ORFs, although the biological role of the ORFs is unknown. Third, the pseudoknot structure has a moderate complexity that is typical of riboswitches. Finally
Downstream-peptide_motif
RNA family
with a downstream region to form a pseudoknot structure; the region varies according to the virus but pseudoknot formation is known to stimulate frameshifting
Coronavirus frameshifting stimulation element
Coronavirus_frameshifting_stimulation_element
Nucleic acid structure prediction algorithm
not account for the three-dimensional shape of RNA, nor predict RNA pseudoknots. Furthermore, in its basic form, it does not account for a minimum stem
Nussinov_algorithm
RNA family
However, there is also evidence that the frameshift signal may exist as a pseudoknot structure or as an intramolecular RNA triplex. Regardless of the exact
HIV ribosomal frameshift signal
HIV_ribosomal_frameshift_signal
structure of many RNAs. RNA kissing interactions, also called loop-loop pseudoknots, occur when the unpaired nucleotides in one hairpin loop, base pair with
Kissing_stem-loop
Topics referred to by the same term
prodromal period of the Creutzfeldt–Jakob disease Prion pseudoknot, a predicted RNA pseudoknot structure found in prion protein mRNA Prion (journal), a
Prion_(disambiguation)
2008). "Genetic Interactions between an Essential 3′ cis -Acting RNA Pseudoknot, Replicase Gene Products, and the Extreme 3′ End of the Mouse Coronavirus
Cis-acting replication element
Cis-acting_replication_element
frameshift is restricted to one (in some cases two) nucleotides with a pseudoknot or choke points on both sides of the sequence. A polymerase that exhibits
Polymerase_stuttering
Open reading frame found in the genome of the SARS-CoV-2 coronavirus
which extends beyond ORF10 itself, overlaps with the coronavirus 3' UTR pseudoknot region, a secondary structure known to be involved in genome replication
ORF10
Species of virus
hallmarks, such the 7 nucleotide long “slippery sequence” or downstream pseudoknot that is seen in other members of Birnaviridae. It is hypothesized the
Drosophila_X_virus
RNA family
highly conserved unpaired sequences which have the ability to form a pseudoknot. Northern blot experiments show that RsaOG is expressed in several S.
RsaOG
Toxin
ring structure, which is innervated by a third sulfide bond creating a pseudoknot. This comprises an extraordinarily stable protein structure, which is
Cl6a
RNA sequences similar in structure to tRNA, found in plant virus genomes
have a similar tertiary structure to tRNA; they frequently contain a pseudoknot close to the 3' end. The presence of tRNA-like structures has been demonstrated
Transfer_RNA-like_structures
Genus of viruses
complex". Although evidence has been presented for an existence of a pseudoknot structure in this RNA, it does not appear to be well conserved across
Orthoflavivirus
Family of viroids
their branched secondary structure (21, 45, 65), which is stabilized by a pseudoknot (10; S. Gago, M. De la Peňa & R. Flores, unpublished results) (Figure
Avsunviroidae
Bacterial RNA structure
nucleotides are required for optimal binding to the ligand and might form a pseudoknot with the terminal loop within the main stem-loop structure. Occlusion
SAM–SAH_riboswitch
Species of virus
organized in a branched formation. This branched formation is stabilized by a pseudoknot between two kissing loops. This branched structure makes these viroids
Peach_latent_mosaic_viroid
Laboratory technique
oligonucleotides, which tend to adopt complex conformations such as stem-loops and pseudoknots. NMR is also useful for probing the binding of nucleic acid molecules
Nuclear magnetic resonance spectroscopy
Nuclear_magnetic_resonance_spectroscopy
RNA family
binding to the nested pseudoknot region. The mechanism of repression is thought to involve a conformational switch in the pseudoknot region and ribosome
Alpha operon ribosome binding site
Alpha_operon_ribosome_binding_site
Protein family
to the 16S ribosomal RNA. In addition, the S4 domain binds a complex pseudoknot and represses translation. More specifically, this protein domain delivers
S4_protein_domain
RNA family
regulatory elements are a family of regulatory RNAs. This family represents a pseudoknot containing stem-loop structure found in the 5' UTR of interferon-gamma
Interferon gamma 5' UTR regulatory element
Interferon_gamma_5'_UTR_regulatory_element
Set of three congruent geometrical helices with the same axis
Blois CA, Feigon J (March 2005). "Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function". Molecular
Triple_helix
Temperature-dependent RNA structure
the case of a region found in CspA mRNA which is thought to contain a pseudoknot, as well as multiple hairpins. Synthetic RNA thermometers have been designed
RNA_thermometer
RNAs could regulate polyamine metabolism. The ldcC motif might have a pseudoknot in its secondary structure, but it is unclear. Weinberg Z, Lünse CE, Corbino
LdcC_RNA_motif
Dichroism with circularly polarized light
and helical geometry. Similarly, RNA structures, including stem-loops, pseudoknots, and G-quadruplexes, produce unique CD spectra that reflect their specific
Circular_dichroism
Region of non-coding DNA that regulates the transcription of neighboring genes
PMID 20114053. Giedroc DP, Cornish PV (February 2009). "Frameshifting RNA pseudoknots: structure and mechanism". Virus Research. 139 (2): 193–208. doi:10.1016/j
Cis-regulatory_element
RNA family
contains a pseudoknot. This acts as a molecular switch controlling translation of repZ and repY. Asano K, Mizobuchi K (May 1998). "An RNA pseudoknot as the
Regulatory region of repZ gene
Regulatory_region_of_repZ_gene
as a growth suppressor in tumour cells, and activates p53. A conserved pseudoknot in exon 3 was shown to be essential for p53 pathway upregulation. A pituitary
MEG3
PSEUDOKNOT
PSEUDOKNOT
PSEUDOKNOT
PSEUDOKNOT
Boy/Male
Hindu, Indian, Marathi, Sanskrit
The Sole Lord; The Supreme Being
Boy/Male
American, Anglo, Australian, British, English, Portuguese
Bright Guardian; Of the Tiber; River
Boy/Male
British, English
From the White Hollow
Girl/Female
Hindu
Prosperity
Girl/Female
Tamil
Is associated to Lord Vishnu
Girl/Female
English
Famous.
Boy/Male
Tamil
Spiritual, Name of An ancient king
Boy/Male
Tamil
Rajatanshu | ராஜாதாஂஷà¯
Boy/Male
Muslim
Migrator
Female
French
French form of Italian Arabella, ARABELLE means "answered prayer."
PSEUDOKNOT
PSEUDOKNOT
PSEUDOKNOT
PSEUDOKNOT
PSEUDOKNOT