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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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
Protein-coding gene in the species Homo sapiens
activity exoribonuclease activity thiol-dependent deubiquitinase RNA stem-loop binding Cellular component cytoplasm nucleoplasm cytoskeleton nucleus
ZC3H12A
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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 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
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
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
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
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
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
Protein-coding gene in humans
2013). "Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs". Cell. 153 (4): 869–81. doi:10.1016/j.cell.2013.04
RC3H1
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
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 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
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 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 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
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
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
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
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
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 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
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)
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)
invented the first riboregulator in 1991. Lechner used a self pairing stem-loop which inhibited translation of a prokaryotic RNA, unless a complementary
Riboregulator
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
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
RNA family
wingless mRNA in flies. The structure consists of a stem, a bulge region, another stem and a loop. The published structure was determined and refined
Wingless localisation element 3 (WLE3)
Wingless_localisation_element_3_(WLE3)
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 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
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
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-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
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
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
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
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
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
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
RNA family
structure that contains a conserved guanosine residue at the end of a stem loop. Synthesis of DNA by the retron-encoded reverse transcriptase (RT) results
Retron
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
RNA family
motif consists primarily of two stem-loops, followed by a predicted rho-independent transcription termination stem-loop. As anti-hemB RNAs are generally
Anti-hemB_RNA_motif
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
structural level. The 5′ UTRs are predicted to contain three conserved stem-loops: SL1 is important for viral replication, most likely playing a role in
Coronavirus_5′_UTR
Protein-coding gene in the species Homo sapiens
human GPATCH2L (5'UTR) shows one stem-loop, inframe stop codon, start codon, and exon boundaries. In this stem-loop, g and g are not connected. However
GPATCH2L
ribozyme consists of six helical domains (Figure 1). Stem-loop I forms the substrate domain while stem-loop II-VI forms the catalytic domain. When these 2 domains
VS_ribozyme
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
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
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
Protein-coding gene in the species Homo sapiens
zinc finger protein is associated with U7 snRNP and interacts with the stem-loop binding protein in the histone pre-mRNP to stimulate 3'-end processing"
ZNF473
RNA family
contained within the stem-loop called "P2" in some gabT RNAs, and nearby to the "P1" stem-loop in those gabT RNAs that do not use a P2 stem-loop. This proximity
GabT_RNA_motif
RNA family
stem loop to be present at the 3' end of the roX RNA transcripts. Mutagenesis within this region that either altered the sequence or prevented stem loop
Drosophila_roX_RNA
RNA family
yellow dwarf virus has been predicted to contain 4 stem loop structures. Mutagenesis showed that stem loop 4 is essential for base pairing with 3'TE and only
Barley yellow dwarf virus 5'UTR
Barley_yellow_dwarf_virus_5'UTR
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
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)
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
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
Aspect of molecular biology
This long leader sequence has the potential to form an extensive complex stem-loop structure, which is an inhibitory element for expression of following
Ribosome_shunting
RNA family
stem loop structures have been predicted to surround the GCC initiation codon and are known as SL1 to SL3. Mutations that disrupted these stem-loop structures
ACAT1_mRNA
RNA family
C alternative reading frame stem-loop Hepatitis C virus 3'X element Hepatitis C virus stem-loop VII Hepatitis C stem-loop IV Hepatitis C You S, Stump
Hepatitis C virus cis-acting replication element
Hepatitis_C_virus_cis-acting_replication_element
Protein involved in processing RNA in animal cells
cofactors interacting with the microprocessor complex. The loop region of the pri-miRNA stem-loop is also a recognition element for regulatory proteins, which
Microprocessor_complex
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
Chinese American biochemist
human symplekin-Ssu72-CTD phosphopeptide complex, histone mRNA stem-loop, human stem-loop binding protein and 3’hExo ternary complex, human phosphofructokinase-1
Liang_Tong
FAM71E2. Conserved stem loop regions were found on both the 5' and 3' UTR in closely related orthologs. There were no conserved stem loops for distantly related
GARIN5B
Protein-coding gene in the species Homo sapiens
coactivators of poliovirus RNA via a sequence-specific interaction with stem-loop IV of the IRES and promote poliovirus RNA replication by binding to its
PCBP1
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
Protein-coding gene in the species Homo sapiens
a stem-loop formation for the 5' UTR region shows that there is a lack of conservation, meaning there is some precedence that these stems and loops are
MATCAP2
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
Enzyme in humans
translation termination. The 3' UTR of Sec-containing genes have a common stem-loop structure, the sec insertion sequence (SECIS), which is necessary for
Glutathione_peroxidase_3
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STEM LOOP
STEM LOOP
Boy/Male
American, British, English
Stem
Male
English
Short form of English Stewart, STEW means "steward."
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.
Male
Swedish
Swedish form of Old Norse Steinn, STEN means "stone."
Male
English
Variant spelling of English unisex Steph, STEF means "crown."
Boy/Male
Anglo Saxon
Stem.
Girl/Female
Assamese, Hindu, Indian, Kannada, Malayalam, Marathi, Sanskrit, Tamil, Telugu
Stem of Lotus
Boy/Male
Australian, Finnish, German, Slavic
Stem
Boy/Male
Hindu
Lotus stem
Boy/Male
Hindu, Indian, Sanskrit
Stem; Hollow Reed
Boy/Male
American, Anglo, British, English
Stem
Boy/Male
Scottish
Steward.
Biblical
same as Shem
Boy/Male
Tamil
Lotus stem
Boy/Male
Hindu, Indian
Stem of Lotus
Male
English
Short form of English Stephen, STE means "crown."
Girl/Female
Gujarati, Hindu, Indian, Kannada, Malayalam, Marathi, Sanskrit, Tamil, Telugu
Lotus Stem
Girl/Female
Hindu, Indian, Kannada, Malayalam, Marathi, Sanskrit, Tamil, Telugu
Stem of Lotus
Boy/Male
English
Austere
Girl/Female
Muslim
Name of a flower
STEM LOOP
STEM LOOP
STEM LOOP
STEM LOOP
STEM LOOP
STEM LOOP
STEM LOOP
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