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Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions.
Formation and stability
The formation of a stem-loop structure is dependent on the stability of the resulting helix and loop regions. The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability of this helix is determined by its length, the number of mismatches or bulges it contains (a small number are tolerable, especially in a long helix) and the base composition of the paired region. Pairings between guanine and cytosine have three hydrogen bonds and are more stable compared to adenine-uracil pairings, which have only two. In RNA, adenine-uracil pairings featuring two hydrogen bonds are equal to the adenine-thymine bond of the DNA. Base stacking interactions, which align the pi orbitals of the bases' aromatic rings in a favorable orientation, also promote helix formation.
The stability of the loop also influences the formation of the stem-loop structure. "Loops" that are less than three bases long are sterically impossible and do not form. Large loops with no secondary structure of their own (such as pseudoknot pairing) are also unstable. Optimal loop length tends to be about 4-8 bases long. One common loop with the sequence UNCG is known as the "tetraloop" and is particularly stable due to the base-stacking interactions of its component nucleotides.
Stem-loops occur in pre-microRNA structures and most famously in transfer RNA, which contain three true stem-loops and one stem that meet in a cloverleaf pattern. The anticodon that recognizes a codon during the translation process is located on one of the unpaired loops in the tRNA. Two nested stem-loop structures occur in RNA pseudoknots, where the loop of one structure forms part of the second stem.
Many ribozymes also feature stem-loop structures. The self-cleaving hammerhead ribozyme contains three stem-loops that meet in a central unpaired region where the cleavage site lies. The hammerhead ribozyme's basic secondary structure is required for self-cleavage activity.
Stem-loop structures are also important in prokaryotic rho-independent transcription termination. The hairpin loop forms in an mRNA strand during transcription and causes the RNA polymerase to become dissociated from the DNA template strand. This process is known as rho-independent or intrinsic termination, and the sequences involved are called terminator sequences.
- Svoboda, P., & Cara, A. (2006). Hairpin RNA: A secondary structure of primary importance. Cellular and Molecular Life Sciences CMLS, 63(7), 901-908.
- Meyer, Michelle; Deiorio-Haggar K; Anthony J (July 2013). "RNA structures regulating ribosomal protein biosynthesis in bacilli". RNA Biology. 7. 10: 1160–1164. doi:10.4161/rna.24151. PMC . PMID 23611891.
- Malys N, Nivinskas R (2009). "Non-canonical RNA arrangement in T4-even phages: accommodated ribosome binding site at the gene 26-25 intercistronic junction". Mol Microbiol. 73 (6): 1115–1127. doi:10.1111/j.1365-2958.2009.06840.x. PMID 19708923.
- Malys N, McCarthy JEG (2010). "Translation initiation: variations in the mechanism can be anticipated". Cellular and Molecular Life Sciences. 68 (6): 991–1003. doi:10.1007/s00018-010-0588-z. PMID 21076851.
You can either download the motif alignment or view it directly in your browser window. More...
You can download (or view in your browser) a text representation of a Rfam alignment in various formats:
- Gapped FASTA
- Ungapped FASTA
You can view or download motif alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".
There are 16 PDB entires which have been used to build the motif model.
The table of results below may be sorted by clicking on the column titles, or restored to the original order .
|Original order||PDB ID||PDB chain ID||PDB Residues|
|2||1c04||E||37 - 52|
|2||1j5e||A||243 - 273|
|2||1mms||C||37 - 52|
|2||1qa6||C||37 - 52|
|2||1s72||0||1189 - 1208|
|2||2avy||A||247 - 277|
|2||1u9s||A||102 - 120|
|2||1y69||0||2323 - 2350|
|2||2aw4||B||1086 - 1103|
|2||2j01||A||718 - 741|
|2||2a2e||A||150 - 170|
|2||2i82||E||1 - 21|
|2||1ffk||0||1698 - 1718|
|2||1giy||A||1133 - 1152|
|2||1mt4||A||2 - 23|
|2||3hhn||C||102 - 121|
There are 108 Rfam families which match this motif.
This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...
To annotate the family with a motif model, the seed sequence was first filtered using a 0.9 fraction identity cut-off. The filtered seed was then scanned using Infernal cmscan (v1.1) with a concatenated CM file containing each of the motifs. Significance of hits between a seed sequence and the CM was based on a gathering threshold that was individually set for each motif. Only motifs where more than two and at least 10% of seed sequences scored higher than the gathering threshold were included for the next stage of processing. These subsets of motifs were then rescanned against the entire (non-filtered) seed to generate matches.
Number of Hits: the number of sequences in the family seed that score above the gathering threshold from motif.
Fraction of Hits: the fraction of sequences in the family seed that score above the gathering threshold from motif.
Sum of Bits: the sum of the bit scores of matches between the motif and the family seed sequence.
Image: plot illustrating where on the consensus secondary structure matches occur between seed sequences and the motif model.
|Original order||Family Accession||Family Description||Number of Hits||Fraction of Hits||Sum of Bits||Image|
|3||RF00004||U2 spliceosomal RNA||30||0.144||392.1|
|3||RF00007||U12 minor spliceosomal RNA||31||0.500||372.3|
|3||RF00009||Nuclear RNase P||30||0.259||386.0|
|3||RF00010||Bacterial RNase P class A||376||0.821||5926.2|
|3||RF00018||CsrB/RsmB RNA family||8||0.211||80.8|
|3||RF00024||Vertebrate telomerase RNA||4||0.108||47.5|
|3||RF00029||Group II catalytic intron||13||0.141||139.3|
|3||RF00043||R1162-like plasmid antisense RNA||4||0.500||47.1|
|3||RF00050||FMN riboswitch (RFN element)||14||0.097||154.6|
|3||RF00096||U8 small nucleolar RNA||11||0.200||123.8|
|3||RF00156||Small nucleolar RNA SNORA70||9||0.209||96.8|
|3||RF00166||PrrB/RsmZ RNA family||35||0.946||493.9|
|3||RF00177||Bacterial small subunit ribosomal RNA||99||1.000||2802.4|
|3||RF00209||Pestivirus internal ribosome entry site (IRES)||2||0.080||20.4|
|3||RF00224||FGF-2 internal ribosome entry site (IRES)||4||0.667||41.9|
|3||RF00263||Small nucleolar RNA SNORA68||5||0.192||59.3|
|3||RF00291||Small nucleolar RNA snoR639/H1||5||0.556||55.8|
|3||RF00357||Small nucleolar RNA R44/J54/Z268 family||2||0.069||20.0|
|3||RF00373||Archaeal RNase P||9||0.129||147.4|
|3||RF00386||Enterovirus 5' cloverleaf cis-acting replication element||68||0.425||724.3|
|3||RF00403||Small nucleolar RNA SNORA41||2||0.065||23.7|
|3||RF00495||Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES)||7||0.500||74.9|
|3||RF00513||Tryptophan operon leader||3||0.136||36.0|
|3||RF00514||Histidine operon leader||9||0.273||96.5|
|3||RF00515||PyrR binding site||5||0.122||83.6|
|3||RF00548||U11 spliceosomal RNA||7||0.097||77.0|
|3||RF00558||Ribosomal protein L20 leader||11||0.256||135.9|
|3||RF00602||Small Cajal body specific RNA 21||6||0.250||99.9|
|3||RF00603||Small nucleolar RNA SNORD23||2||0.133||21.5|
|3||RF00604||Small nucleolar RNA SNORD88||2||0.057||23.1|
|3||RF00617||flavivirus capsid hairpin cHP||11||0.186||123.1|
|3||RF00629||Pseudomonas sRNA P24||7||0.500||101.1|
|3||RF00630||Pseudomonas sRNA P26||10||0.370||108.3|
|3||RF00634||S-adenosyl methionine (SAM) riboswitch,||3||0.075||34.9|
|3||RF01071||Ornate Large Extremophilic RNA||5||0.250||58.5|
|3||RF01089||Pseudoknot of the regulatory region of the repBA gene||2||0.286||20.2|
|3||RF01268||Small Cajal body-specific RNA 2||3||0.150||31.2|
|3||RF01330||CRISPR RNA direct repeat element||6||1.000||78.3|
|3||RF01390||isrG Hfq binding RNA||5||1.000||51.7|
|3||RF01401||rseX Hfq binding RNA||7||0.583||79.8|
|3||RF01529||Cauldobacter sRNA CC3552||2||1.000||24.7|
|3||RF01675||Pseudomonas sRNA CrcZ||17||0.895||191.9|
|3||RF01708||L17 ribosomal protein downstream element||6||0.115||71.2|
|3||RF01796||Fumarate/nitrate reductase regulator sRNA||3||0.188||34.0|
|3||RF01808||MicX Vibrio cholerae sRNA||5||0.500||61.9|
|3||RF01849||Alphaproteobacteria transfer-messenger RNA||11||0.099||140.2|
|3||RF01850||Betaproteobacteria transfer-messenger RNA||2||0.286||22.8|
|3||RF01852||Selenocysteine transfer RNA||9||0.083||106.3|
|3||RF01959||Archaeal small subunit ribosomal RNA||86||1.000||4568.1|
|3||RF01960||Eukaryotic small subunit ribosomal RNA||36||0.396||526.2|
|3||RF02033||HNH endonuclease-associated RNA and ORF (HEARO) RNA||12||0.109||145.4|
|3||RF02053||Enterobacterial sRNA STnc430||5||0.714||55.8|
|3||RF02055||Enterobacterial sRNA STnc380||4||0.800||50.8|
|3||RF02057||Salmonella enterica sRNA STnc40||2||0.118||23.8|
|3||RF02065||Enterobacterial sRNA STnc340||3||0.750||34.8|
|3||RF02074||Enterobacterial sRNA STnc240||8||0.533||89.3|
|3||RF02103||Deleted in lymphocytic leukemia 1 conserved region 1||3||0.115||35.4|
|3||RF02118||FMR1 antisense RNA 1 conserved region 2||9||0.360||112.2|
|3||RF02189||ST7 overlapping transcript 4 conserved region 3||2||0.100||22.8|
|3||RF02219||ZNRD1 antisense RNA 1 conserved region 2||2||0.059||22.0|
|3||RF02230||Proteobacterial sRNA sX11||2||0.200||20.2|
|3||RF02249||Six3os1 conserved region 4||2||0.286||20.4|
|3||RF02276||Hammerhead ribozyme (type II)||3||0.125||34.3|
|3||RF02278||Betaproteobacteria toxic small RNA||7||0.137||87.0|
|3||RF02342||Alphaproteobacterial sRNA ar7||6||0.207||68.7|
|3||RF02343||Alphaproteobacterial sRNA ar9||16||0.571||166.8|
|3||RF02351||Proteobacteria sRNA psRNA14||2||0.667||23.7|
|3||RF02354||Bradyrhizobiaceae sRNA BjrC80||7||0.467||83.6|
|3||RF02356||Alphaproteobacterial sRNA BjrC1505||3||0.120||35.7|
|3||RF02357||RNaseP truncated form||7||0.778||92.6|
|3||RF02379||Cia-dependent small RNA csRNA1||8||0.167||97.7|
|3||RF02423||Burkholderia sRNA Bp1_Cand871_SIPHT||14||0.933||170.8|
|3||RF02471||Actinobacteria sRNA Ms_IGR-5||6||0.286||66.5|
|3||RF02502||Rhizobiales sRNA Atu_C8||3||0.111||31.2|
|3||RF02524||Streptococcus sRNA sagA||3||0.500||37.0|
|3||RF02540||Archaeal large subunit ribosomal RNA||83||0.912||3404.2|
|3||RF02541||Bacterial large subunit ribosomal RNA||102||1.000||3700.8|
|3||RF02542||Microsporidia small subunit ribosomal RNA||43||0.935||832.7|
|3||RF02543||Eukaryotic large subunit ribosomal RNA||80||0.909||2165.6|
|3||RF02630||Hfq-regulated sRNA 12||2||1.000||28.6|
|3||RF02684||Type-P5 twister ribozyme||4||0.267||47.2|
This section shows the database cross-references that we have for this Rfam motif.
Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB J Math Biol. 2008;56:215-52. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. PUBMED:17694311
Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB Nucleic Acids Res. 2009;37:4898-918. Classification and energetics of the base-phosphate interactions in RNA. PUBMED:19528080
Gutell RR, Cannone JJ, Konings D, Gautheret D J Mol Biol. 2000;300:791-803. Predicting U-turns in ribosomal RNA with comparative sequence analysis. PUBMED:10891269
Quigley GJ, Rich A Science. 1976;194:796-806. Structural domains of transfer RNA molecules. PUBMED:790568
External database links
|External sites:|| 1: http://rna.bgsu.edu/FR3D/MotifLibrary/Hairpins/LIB70006_HL_cWW_tSH_U_turn.html
Curation and motif details
This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.
|Seed source||Published; PMID:19528080|
cmbuild -F U-CM U-SEED
cmcalibrate --mpi --seed 1 U-CM
|Covariance model||Download the Infernal CM for the motif here|