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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
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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.
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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.
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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
229:" and is particularly stable due to the base-stacking interactions of its component nucleotides. Therefore, such loops can form on the microsecond time scale.
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Malys N, Nivinskas R (2009). "Non-canonical RNA arrangement in T4-even phages: accommodated ribosome binding site at the gene 26-25 intercistronic junction".
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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
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Svoboda, P., & Cara, A. (2006). Hairpin RNA: A secondary structure of primary importance. Cellular and
Molecular Life Sciences, 63(7), 901-908.
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pairing) are also unstable. Optimal loop length tends to be about 4-8 bases long. One common loop with the sequence UUCG is known as the "
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of prokaryotes. These structures are often bound by proteins or cause the attenuation of a transcript in order to regulate translation.
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The stability of the loop also influences the formation of the stem-loop structure. "Loops" that are fewer than three bases long are
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pairings, which have only two. In RNA, adenine-uracil pairings featuring two hydrogen bonds are equal to the adenine-
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173:(mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions.
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Ma H, Proctor D, Bevilacqua P, Gruebele M (2006). "Exploring the energy landscape of a small RNA hairpin".
169:. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for
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process is located on one of the unpaired loops in the tRNA. Two nested stem-loop structures occur in RNA
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impossible and do not form. Large loops with no secondary structure of their own (such as
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514:"Translation initiation: variations in the mechanism can be anticipated"
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It occurs when two regions of the same strand, usually complementary in
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422:"RNA structures regulating ribosomal protein biosynthesis in bacilli"
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rings in a favorable orientation, also promote helix formation.
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bond of the DNA. Base stacking interactions, which align the
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Meyer, Michelle; Deiorio-Haggar K; Anthony J (July 2013).
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also feature stem-loop structures. The self-cleaving
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62:. Unsourced material may be challenged and removed.
271:Hairpin loops are often elements found within the
27:Intramolecular base-pairing pattern in RNA and DNA
149:is a pattern that can occur in single-stranded
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405:: CS1 maint: multiple names: authors list (
278:The mRNA stem-loop structure forming at the
300:strand during transcription and causes the
289:Stem-loop structures are also important in
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294:rho-independent transcription termination
122:Learn how and when to remove this message
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518:Cellular and Molecular Life Sciences
60:adding citations to reliable sources
153:. The structure is also known as a
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483:10.1111/j.1365-2958.2009.06840.x
241:structures and most famously in
194:and are more stable compared to
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296:. The hairpin loop forms in an
47:needs additional citations for
512:Malys N, McCarthy JEG (2010).
138:An example of an RNA stem-loop
1:
282:may control an initiation of
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756:Nucleic acid double helix
530:10.1007/s00018-010-0588-z
237:Stem-loops occur in pre-
177:Formation and stability
596:Biomolecular structure
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280:ribosome binding site
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329:Palindromic sequence
167:secondary structures
56:improve this article
726:Protein engineering
266:hammerhead ribozyme
233:Structural contexts
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438:10.4161/rna.24151
385:10.1021/ja0553856
324:Kissing stem-loop
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16:(Redirected from
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751:Structural motif
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477:(6): 1115–1127.
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432:(7): 1160–1164.
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379:(5): 1523–1530.
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334:Repeat sequences
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524:(6): 991–1003.
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192:hydrogen bonds
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685:Determination
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73: –
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67:Find sources:
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45:This article
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736:Nucleic acid
657:Nucleic acid
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243:transfer RNA
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147:base pairing
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54:Please help
49:verification
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18:Hairpin loop
426:RNA Biology
291:prokaryotic
284:translation
255:pseudoknots
251:translation
249:during the
190:have three
71:"Stem-loop"
771:Categories
731:Proteasome
690:Prediction
680:Quaternary
637:Prediction
627:Quaternary
350:References
223:pseudoknot
219:sterically
163:nucleotide
82:newspapers
670:Secondary
617:Secondary
262:ribozymes
227:tetraloop
143:Stem-loop
709:See also
675:Tertiary
622:Tertiary
556:31720000
548:21076851
539:11115079
491:19708923
456:23611891
393:16448122
308:See also
239:microRNA
212:aromatic
208:pi bonds
188:cytosine
112:May 2010
716:Protein
665:Primary
612:Primary
604:Protein
499:8187771
447:3849166
204:thymine
196:adenine
184:guanine
155:hairpin
96:scholar
695:Design
642:Design
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200:uracil
98:
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552:S2CID
495:S2CID
428:. 7.
344:5'UTR
273:5'UTR
260:Many
247:codon
103:JSTOR
89:books
544:PMID
487:PMID
452:PMID
407:link
389:PMID
298:mRNA
186:and
75:news
782:DNA
777:RNA
746:RNA
741:DNA
534:PMC
526:doi
479:doi
442:PMC
434:doi
381:doi
377:128
157:or
151:RNA
58:by
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