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Intramolecular base-pairing pattern in RNA and DNA
Stem-loops are nucleic acid secondary structural elements which form via intramolecular base pairing in single-stranded DNA or RNA. They are also referred
Stem-loop
genetics, a kissing stem-loop, or kissing stem loop interaction, is formed in ribonucleic acid (RNA) when two bases between two hairpin loops pair. These intra-
Kissing_stem-loop
Components of human immunodeficiency virus
The 5'UTR structure consists of series of stem-loop structures connected by small linkers. These stem-loops (5' to 3') include the trans-activation region
Structure_and_genome_of_HIV
RNA family
The histone 3′ UTR stem-loop is an RNA element involved in nucleocytoplasmic transport of the histone mRNAs, and in the regulation of stability and of
Histone_3′_UTR_stem-loop
Nucleic acid sequence
stem of stem-loop A and are part of the loop for stem-loop B. Similarly, sets 3 and 4 are the stem for stem-loop B and are part of the loop for stem-loop
Inverted_repeat
Mechanism of termination of RNA transcription
transcript forms a stable secondary structure known as a hairpin loop or a stem-loop. This RNA hairpin is followed immediately downstream by multiple
Intrinsic_termination
Basepairing interactions within a single nucleic acid polymer or between two polymers
into stems and loops. The stem-loop structure (also often referred to as an "hairpin"), in which a base-paired helix ends in a short unpaired loop, is
Nucleic acid secondary structure
Nucleic_acid_secondary_structure
RNA family
for Stem-loop) which are connected by relatively short linkers. All four stem loops are important for genome packaging and each of the stem loops SL1
Retroviral psi packaging element
Retroviral_psi_packaging_element
RNA that facilitates the addition of amino acids to a new protein
gene. The D loop is a 4- to 6-bp stem ending in a loop that often contains dihydrouridine. The anticodon loop is a 5-bp stem whose loop contains the
Transfer_RNA
Protein-coding gene in humans
Histone RNA hairpin-binding protein or stem-loop binding protein (SLBP) is a protein that in humans is encoded by the SLBP gene. SLBP has been cloned
SLBP
RNA family
The Hepatitis C stem-loop IV is part of a putative RNA element found in the NS5B coding region. This element along with stem-loop VII, is important (but
Hepatitis_C_stem-loop_IV
Interactions between nucleic acid modules
structures suggest pRNA may also form pentameric rings. In the kissing stem-loop motif, a model based on Dengue virus methyltransferase, four monomers
Nucleic acid quaternary structure
Nucleic_acid_quaternary_structure
Second subphase of interphase
canonical histone transcripts possess a conserved 3` stem loop motif that selective binds to Stem Loop Binding Protein (SLBP). SLBP binding is required for
S_phase
RNA family
stem-loop VII is a regulatory element found in the coding region of the RNA-dependent RNA polymerase gene, NS5B. Similarly to stem-loop IV, the stem-loop
Hepatitis C virus stem-loop VII
Hepatitis_C_virus_stem-loop_VII
Sequence at the 3′ end of messenger RNA that does not code for product
the 5′ and the 3′ UTR are iron response elements (IREs). The IRE is a stem-loop structure within the untranslated regions of mRNAs that encode proteins
Three prime untranslated region
Three_prime_untranslated_region
Molecular machine that removes intron RNA from the primary transcript
interactions of U4/U6 stem loops I and II dissociate and the freed stem loop II region of U6 folds on itself to form an intramolecular stem loop and U4 is no longer
Spliceosome
Laboratory technique
the natural interaction of the MS2 bacteriophage coat protein with a stem-loop structure from the phage genome, which is used for biochemical purification
MS2_tagging
Family of viruses
cis-acting replication element (CRE) is required for replication. The stem-loop-structure that contains the CRE is independent of position, but changes
Picornavirus
Species of virus
stem-loop, H1 and H2, which is required for replication. When the dimer binds to this region, the replicases cleave the loop region of the stem-loop and
Porcine_circovirus
Biochemical changes to RNA
Stem loop structures can sometimes be found in introns. m6A residues located in these stem-loops weaken base-pairing interactions within the stem, thus
Epitranscriptome
Family of DNA sequences found in prokaryotic organisms
dyad symmetry, implying the formation of a secondary structure such as a stem-loop ('hairpin') in the RNA, while others are designed to be unstructured.
CRISPR
Biomolecular structure of nucleic acids such as DNA and RNA
strands (internal loops) by unpaired nucleotides. Stem-loop or hairpin loop is the most common element of RNA secondary structure. Stem-loop is formed when
Nucleic_acid_structure
Protein family around which DNA winds to form nucleosomes
chromosomes in 4 different highly-conserved loci, lack introns and use a stem loop structure at the 3' end instead of a polyA tail. Genes encoding histone
Histone
Chemistry of reactions on 10^-15 second timescales
biological studies has also helped to elucidate the conformational dynamics of stem-loop RNA structures. Many publications have discussed the possibility of controlling
Femtochemistry
HIV-1 regulating protein
eight stem-loops. Rev initially binds to the purine-rich stem-loop IIB, then binds to a secondary site in stem-loop I. Within this purine-rich stem-loop, IIB
Rev_(HIV)
RNA processing within a biological cell
factors. Core histone mRNAs have a special stem-loop structure at 3-prime end that is recognized by a stem–loop binding protein and a downstream sequence
Post-transcriptional modification
Post-transcriptional_modification
RNA Structure
Structurally, the gamma-150 motif consists of four independent stem-loops. The first stem-loop (the stem-loop closest to the 5' end of the RNA) has significant covariation
Gamma-150_RNA_motif
Gene editing technique
Prime editing is a 'search-and-replace' genome editing technology in molecular biology by which the genome of living organisms may be modified. The technology
Prime_editing
DNA sequence
stem–loop in the Psi packaging element of many retroviruses. DIS is characterized by a conserved stem and palindromic loop that forms a kissing-loop complex
Long_terminal_repeat
RNA element found in Pospiviroids such as potato spindle tuber viroid (PSTVd)
The Pospiviroid RY motif stem loop is an RNA element found in Pospiviroids such as potato spindle tuber viroid (PSTVd). The RY nucleotide sequence motif
Pospiviroid RY motif stem loop
Pospiviroid_RY_motif_stem_loop
Genetic motif present in some viruses
The Coronavirus 3′ stem-loop II-like motif (also known as s2m) is a secondary structure motif identified in the 3′ untranslated region (3′UTR) of astrovirus
Coronavirus 3′ stem-loop II-like motif (s2m)
Coronavirus_3′_stem-loop_II-like_motif_(s2m)
Phenomenon during translation of mRNA
The majority of the structures shown are stem-loops, with the exception of the ALIL (apical loop-internal loop) pseudoknot structure. In these images,
Ribosomal_frameshift
RNA family
HIV gag stem loop 3 (GSL3) is a secondary structural component of the Retroviral Psi packaging element, also known as the psi recognition element. This
HIV_gag_stem_loop_3_(GSL3)
RNA family
HBV mRNAs. HBV PREalpha consists of a 30 nt stem-loop, with a 5 nt apical loop. The conserved stem-loop was predicted within the HBV PRE sequence and
Hepatitis_B_virus_PRE_alpha
Small nuclear RNA component of the spliceosome
short 5' stem-loop, much more extensive structures have been proposed for specific organisms such as in yeast. In addition to the 5' stem loop, all confirmed
U6_spliceosomal_RNA
RNA family
biology, the coronavirus frameshifting stimulation element is a conserved stem-loop of RNA found in coronaviruses that can promote ribosomal frameshifting
Coronavirus frameshifting stimulation element
Coronavirus_frameshifting_stimulation_element
RNA family
characteristic U-turn loop motif that shares a geometric conformation similar to that of tRNA anti-codon loops. All U2 snRNAs possess a terminal stem loop (IV) with
U2_spliceosomal_RNA
Repetitive DNA with distinct base composition
shown to adopt altered structures including triple-stranded DNA, Z-DNA, stem-loop, and other conformations under superhelical stress. Between the strand-biased
Satellite_DNA
Small non-coding ribonucleic acid molecule
regions of RNA transcripts that fold back on themselves to form short stem-loops (hairpins), whereas siRNAs derive from longer regions of double-stranded
MicroRNA
Three-dimensional shape of a nucleic acid polymer
interactions between separate RNA strands. Ribose zippers are often observed as Stem-loop interactions with very low sequence specificity. However, in the small
Nucleic acid tertiary structure
Nucleic_acid_tertiary_structure
RNA family
predicted secondary structure consists of a complex stem-loop region followed by a single stem-loop terminator region. An alternative and mutually exclusive
SAM_riboswitch_(S-box_leader)
Adjustment within a biological system
ligand may bind to the stem-loop and disrupt intermolecular bonding, resulting in the complementary Shine-Dalgarno stem-loop segment binding to the complementary
Autoregulation
Watson-Crick-Franklin base pairing between the nucleotides. Internal-loops differ from Stem-loops as they occur in middle of a stretch of double stranded RNA.
Internal_loop
RNA element
The G-CSF factor stem-loop destabilising element (SLDE) is an RNA element secreted by fibroblasts and endothelial cells in response to the inflammatory
G-CSF factor stem-loop destabilising element
G-CSF_factor_stem-loop_destabilising_element
Proteins that substitute in eukaryotes
variation among species; (3) canonical histone genes lack introns and use a stem loop structure at the 3' end of their mRNA, whereas histone variant genes may
Histone_variants
RNA element
contains three stem-loop structures that are essential for replication. Hepatitis C alternative reading frame stem-loop Hepatitis C stem-loop IV Hepatitis
Hepatitis_C_virus_3'X_element
RNA family
hairy gene. HLE contains two stem-loops. HLE is essential for the mediation of apical localisation and the two stem-loop structures act to allow the recognition
Hairy RNA localisation element (HLE)
Hairy_RNA_localisation_element_(HLE)
RNA family
complementary sequences is found within a stem-loop, which forms a target for RNAI. Binding of RNAI to this stem-loop inhibits pseudoknot formation and translation
Regulatory region of repBA gene
Regulatory_region_of_repBA_gene
transcription factor Nrf2. It contains a stem-loop structure upstream of a ribosome binding site. This stem loop inhibits ribosome binding and translation
Nrf2 internal ribosome entry site (IRES)
Nrf2_internal_ribosome_entry_site_(IRES)
Human protein-coding gene
blood cells. It is suspected that the mature mRNA of C19orf67 forms a stem loop on the 3' UTR that spans from 1,296bp to 1,350bp of the transcript. In
C19orf67
RNA family
The Alfalfa mosaic virus RNA 1 5′ UTR stem-loop represents a putative stem-loop structure found in the 5′ UTR in RNA 1 of alfalfa mosaic virus. RNA 1
Alfalfa mosaic virus RNA 1 5′ UTR stem-loop
Alfalfa_mosaic_virus_RNA_1_5′_UTR_stem-loop
Non-coding RNA involved in alternative splicing
U2 snRNA). U11 snRNA has a stem-loop structure with a 5' end as splice site sequence (5' ss) and contains four stem loops structures (I-IV). A structural
U11_spliceosomal_RNA
Non-coding RNA
local intra-repeat stem-loop structures. Later work using in vitro biochemical structure probing proposed several inter-repeat stem-loop structures. A recent
XIST
Species of viroid
stunt viroid. Present within the viroidal RNA is the Pospiviroid RY motif stem loop common to its genus. The natural hosts are potatoes (Solanum tuberosum)
Potato_spindle_tuber_viroid
virus coat protein binding (CPB) RNA Alfalfa mosaic virus RNA 1 5′ UTR stem-loop Alpha operon ribosome binding site Antizyme RNA frameshifting stimulation
List of cis-regulatory RNA elements
List_of_cis-regulatory_RNA_elements
Protein-coding gene in the species Homo sapiens
multiple stem loops in its 5' and 3' untranslated regions (UTR) . In the 3' UTR, miRNA has-miR-499-5p binds to a nucleotide region predicted as a stem loop. The
DEPDC1B
Protein-coding gene in the species Homo sapiens
mRNA has been shown to contain three stem-loop structures that influence gene expression. These three-stem loop structures are known as M1, M2, and M3
DNA_polymerase_beta
Protein complexes that mix with other proteins to form spliceosome
in splicing at all, as U7 snRNP is responsible for processing the 3′ stem-loop of histone pre-mRNA. The two essential components of snRNPs are protein
SnRNP
Type of common three-dimensional structure in chain-like biological molecules
structural motifs which is thought to have biological significance. Stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded
Structural_motif
Non-modified oligonucleotides (DNA molecules)
fashion, linked by a pentathymidine stretch forming double-stranded DNA stem-loop molecules. The two polypurine domains interact by intramolecular reverse-Hoogsteen
Polypurine reverse-Hoogsteen hairpin
Polypurine_reverse-Hoogsteen_hairpin
Species of the genus Orthohepadnavirus
Wijmenga S (November 2002). "The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulges"
Hepatitis_B_virus
Protein-coding gene in the species Homo sapiens
loop that consequently cannot be paired or transcribed. The trapped material, most notably, includes the 6th exon that codes in TBXT. In a stem-loop structure
T-box_transcription_factor_T
RNA family
Hepatitis C alternative reading frame stem-loop is a conserved secondary structure motif identified in the RNA genome of the hepatitis C virus (HCV) which
Hepatitis C alternative reading frame stem-loop
Hepatitis_C_alternative_reading_frame_stem-loop
The formation of these stem-loops, especially xrRNA1, is vital to ensure resistance against XRN1 activity. The Y-shaped stem-loop is also termed SL II and
Flavivirus_3'_UTR
Byproduct in PCR formed by primer annealing to itself
of the 5' tail it anneals to the 3' end of the primer. The result is a stem-loop primer that excludes annealing involving shorter overlaps, but permits
Primer_dimer
RNA family
pre-microRNA that produces mature microRNAs from both strands of the TAR stem-loop. These miRNAs are thought to prevent infected cells from undergoing apoptosis
Trans-activation response element
Trans-activation_response_element
RNA sequence directing the translation of UGA codons as selenocysteines
sequence) is an RNA element around 60 nucleotides in length that adopts a stem-loop structure. This structural motif (pattern of nucleotides) directs the
SECIS_element
Protein-coding gene in the species Homo sapiens
termination. The 3' UTR of selenocysteine-containing genes have a common stem-loop structure, the sec insertion sequence (SECIS), that is necessary for the
TXNRD1
RNA family
which the Sm ring is assembled. Stem-loop I binds to the U1-70K protein, stem-loop II binds to the U1 A protein, stem-loops III and IV bind to the core RNP
U1_spliceosomal_RNA
DNA or RNA sequence that matches its complement when read backwards
nucleotides. Dyad symmetry Inverted repeat Repeat sequences Satellite DNA Stem-loop Larionov S, Loskutov A, Ryadchenko E (February 2008). "Chromosome evolution
Palindromic_sequence
Protein-coding gene in the species Homo sapiens
sequence had a total of 7 step loops with a single site for potential miRNA binding. In contrast, the 5’ UTR had only 2 stem loops and contained no other notable
C6orf136
the RRE, stem IA, that binds Rev in a specific manner, but with a 5-fold weaker affinity than stem IIB. Recent crystal structure of RRE stem-loop II shows
HIV_Rev_response_element
Genus of viruses
5'UTR, a large stem loop (SLA) and a short stem loop (SLB). SLA folds into a Y-shaped structure with a side stem loop and a small top loop. SLA is likely
Orthoflavivirus
RNA family
step loop structures. Calreticulin (CAL), which is known to bind calcium in most eukaryotic cells, is able to specifically bind to the first stem loop of
Rubella virus 3′ cis-acting element
Rubella_virus_3′_cis-acting_element
RNA family
minimal HBV PREbeta structure consists of a 23 nt stem-loop, with a 9 nt apical loop. The conserved stem-loop was predicted within the HBV PRE sequence and
Hepatitis_B_virus_PRE_beta
RNA component of the ribosome, essential for protein synthesis in all living organisms
within these sequences commonly forms stem-loop configurations. The length and position of these rRNA stem-loops allow them to create three-dimensional
Ribosomal_RNA
Class of RNA molecules
3′ trimming to form a 3′ stem-loop structure, as well as hypermethylation of the 5′ cap to form trimethylguanosine. The 3′ stem structure is necessary for
Small_nuclear_RNA
Protein-coding gene in the species Homo sapiens
5' UTR indicate that one stem loop upstream of the start of transcription is conserved in all Primates. Within the stem loop, EWSR1-FLI1 binding site
C6orf118
Burkholderia RNA motif) is a conserved stem-loop RNA structure present in many species in the genus Burkholderia. MAEB stem-loops typically occur in blocks of repeats
MAEB_RNA_motif
the process of degradation to develop the double helix structure in RNA stem-loops. Occasionally, copurification of rRNA with degradosome is appreciated
Degradosome
Non-coding RNA component of the spliceosome
while protein Prp24 re-anneals U4 and U6. The crystal structure of a 5′ stem-loop of U4 in complex with a binding protein has been solved. The U4 snRNA
U4_spliceosomal_RNA
Biological process of gene regulation
transcripts from such genes are first processed to form the characteristic stem-loop structure of pre-miRNA in the nucleus, then exported to the cytoplasm
RNA_interference
Class of drugs
the bulge, lower stem, or loop region of the TAR RNA. One of the compounds discovered, 2,4,5,6-tetraaminoquinozaline, binds to the loop region of TAR, downregulates
RNA-targeting small molecule drugs
RNA-targeting_small_molecule_drugs
Nucleic acid secondary structure
containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first
Pseudoknot
Vaccine to prevent poliomyelitis
mutation located in the virus's internal ribosome entry site, which alters stem-loop structures and reduces the ability of poliovirus to translate its RNA
Polio_vaccine
RNA family
complex with another spliceosomal RNA U4atac via two stem loop regions. These interacting stem loops have been shown to be required for in vivo splicing
U6atac_minor_spliceosomal_RNA
RNA family
response element or iron-responsive element (IRE) is a short conserved stem-loop which is bound by iron response proteins (IRPs, also named IRE-BP or IRBP)
Iron_response_element
RNA family
complex with another spliceosomal RNA U6atac via two stem loop regions. These interacting stem loops have been shown to be required for in vivo splicing
U4atac_minor_spliceosomal_RNA
of this rpoS mRNA. The 5′ UTR of the rpoS mRNA forms a self-inhibitory stem loop that shields the shine-dalgarno sequence and therefore inhibits translation
RpoS_mRNA_5′UTR
Protein
as compared to the Y-27632 agent. The diagram to the right depicts the stem-loop formation of the 5' untranslated region of RNF227. The BED4.02, ZFX.01
RNF227
Chemical compound
structural motif is the TΨC stem loop which incorporates Ψ55. Ψ is commonly found in the D stem and anticodon stem and loop of tRNAs from each domain.
Pseudouridine
an alternate conformation (PK-SL1) where the loop region of the second hairpin interacts with the stem of the first hairpin (see Coronavirus 3′ UTR pseudoknot)
Coronavirus_3′_UTR
Process of copying a segment of DNA into RNA
by incorporating RNA stem loops, such as MS2, into a gene, these become incorporated into newly synthesized RNA. The stem loops can then be detected using
Transcription_(biology)
Protein-coding gene in humans
termination of RNA polymerase II transcription mRNA 3'-end processing by stem-loop binding and cleavage mRNA processing mRNA export from nucleus mRNA polyadenylation
CPSF3
Protein-coding gene in the species Homo sapiens
translation termination. The 3' UTR of selenoprotein genes have a common stem-loop structure, the sec insertion sequence (SECIS), which is necessary for
SEPP1
RNA family
simple stem-loop secondary structures, although the earlier pan motif often consists of two stem-loops that are similar to each other. The stem-loops in the
Zeta-pan_RNA_motif
Measurement of genetic variations
located in between. This design allows the probe to take on a hairpin, or stem-loop, structure in its natural, isolated state. Attached to one end of the
SNP_genotyping
guanosine of an RNA molecule. The resultant DNA/RNA chimera possesses two stem-loops joined by a branch similar to the branches found in RNA splicing intermediates
Multicopy_single-stranded_DNA
Family of viruses
sites between the two RNA molecules have been identified as a "kissing stem-loop". Although virions of different retroviruses do not have the same morphology
Retrovirus
Genetic transcription mechanism in prokaryotes
motif (ARM) family of RNA binding proteins, binds to a 15-nucleotide (nt) stem-loop called BOXB. (We will capitalize the names of sites in RNA and italicize
Antitermination
STEM LOOP
STEM LOOP
Boy/Male
Hindu, Indian
Stem of Lotus
Biblical
same as Shem
Girl/Female
Gujarati, Hindu, Indian, Kannada, Malayalam, Marathi, Sanskrit, Tamil, Telugu
Lotus Stem
Boy/Male
Australian, Finnish, German, Slavic
Stem
Boy/Male
Anglo Saxon
Stem.
Male
English
Short form of English Stephen, STE means "crown."
Boy/Male
American, Anglo, British, English
Stem
Male
Hebrew
(ש×Öµ×) Hebrew name SHEM means "conspicuous position, name, renown, sigma." In the bible, this is the name of a son of Noah.
Boy/Male
American, British, English
Stem
Boy/Male
Tamil
Lotus stem
Boy/Male
Hindu
Lotus stem
Male
English
Variant spelling of English unisex Steph, STEF means "crown."
Girl/Female
Assamese, Hindu, Indian, Kannada, Malayalam, Marathi, Sanskrit, Tamil, Telugu
Stem of Lotus
Male
Swedish
Swedish form of Old Norse Steinn, STEN means "stone."
Girl/Female
Muslim
Name of a flower
Boy/Male
Hindu, Indian, Sanskrit
Stem; Hollow Reed
Boy/Male
English
Austere
Boy/Male
Scottish
Steward.
Male
English
Short form of English Stewart, STEW means "steward."
Girl/Female
Hindu, Indian, Kannada, Malayalam, Marathi, Sanskrit, Tamil, Telugu
Stem of Lotus
STEM LOOP
STEM LOOP
Girl/Female
American, Australian, Chinese, Christian, German
Just; Fairness; Upright; Fair
Surname or Lastname
English
English : variant spelling of Broomfield.
Surname or Lastname
English
English : variant spelling of Pearsall or Purcell.
Boy/Male
Hindu, Indian
Warrior; Eatrior
Male
French
Older form of French Yves, IVES means "yew tree."
Boy/Male
English
From Simon's Estate
Surname or Lastname
English
English : variant spelling of Waites.
Girl/Female
Hindu
Fire
Girl/Female
Muslim/Islamic
Lotus Water lily
Boy/Male
American, Australian, British, English
In Charge of Royal Linens
STEM LOOP
STEM LOOP
STEM LOOP
STEM LOOP
STEM LOOP
v. i.
To emit steam or vapor.
v. t.
To oppose or cut with, or as with, the stem of a vessel; to resist, or make progress against; to stop or check the flow of, as a current.
v. i.
Alt. of Steem
a.
Embracing the stem with its base; amplexicaul; as a leaf or petiole.
v. t.
To boil slowly, or with the simmering or moderate heat; to seethe; to cook in a little liquid, over a gentle fire, without boiling; as, to stew meat; to stew oysters; to stew apples.
n.
Anything resembling a stem or stalk; as, the stem of a tobacco pipe; the stem of a watch case, or that part to which the ring, by which it is suspended, is attached.
n.
Alt. of Steem
v. i.
To generate steam; as, the boiler steams well.
v. t.
To expose to the action of steam; to apply steam to for softening, dressing, or preparing; as, to steam wood; to steamcloth; to steam food, etc.
v. t.
To remove the stem or stems from; as, to stem cherries; to remove the stem and its appendages (ribs and veins) from; as, to stem tobacco leaves.
n. & v.
See 1st and 2nd Stem.
v. i.
To move or travel by the agency of steam.
a.
Wound by mechanism connected with the stem; as, a stem-winding watch.
v. i.
The space passed over by one movement of the foot in walking or running; as, one step is generally about three feet, but may be more or less. Used also figuratively of any kind of progress; as, he improved step by step, or by steps.
n.
See Stee.
n.
A stem-winding watch.
v. t.
To fix the foot of (a mast) in its step; to erect.
n.
A short article in a newspaper; a paragraph; as, an item concerning the weather.
n.
A little branch which connects a fruit, flower, or leaf with a main branch; a peduncle, pedicel, or petiole; as, the stem of an apple or a cherry.
v. i.
A small space or distance; as, it is but a step.