WordNet

move in loops; "The bicycle looped around the tree"
anything with a round or oval shape (formed by a curve that is closed and does not intersect itself)
a flight maneuver; aircraft flies a complete circle in the vertical plane (同)loop-the-loop
an intrauterine device in the shape of a loop
a computer program that performs a series of instructions repeatedly until some specified condition is satisfied
an inner circle of advisors (especially under President Reagan); "hes no longer in the loop"
the basic pattern of the human fingerprint
make a loop in; "loop a rope" (同)intertwine
fasten or join with a loop; "He looped the watch through his belt"
fly loops, perform a loop; "the stunt pilot looped his plane"
a double pronged pin used to hold womens hair in place

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(糸・ひも・針金などで作った)『輪』・輪状のもの;(輪状の)湾曲部・(宙返り飛行・スケートなどで描く)輪・ループ (ある条件が成立するまで繰り返し実行される，プログラム中に記述された一連の命令のこと)・仲間、影響｝を受け合う間柄・同列の立場・「keep誰々in the loop」として、「keep誰々informed：情報を（人）に絶えず提供し続ける、報告を（人）に欠かさない、（人）に逐次連絡する、（人）に常に通知する」・避妊リング; (鉄道・電線などの)環状線(loop line)・…‘を'輪にする,輪で囲む・…‘を'輪で結ぶ,輪で締める《+『up』+『名,』+『名』+『up』》・輪になる,輪を描く
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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2017/08/27 16:18:56」(JST)

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An example of an RNA stem-loop

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.^[1]

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.

Structural contexts

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.

Hairpin loops are often elements found within the 5'UTR of prokaryotes. These structures are often bound by proteins or cause the attenuation of a transcript in order to regulate translation.^[2]

The mRNA stem-loop structure forming at the ribosome binding site may control an initiation of translation.^[3]^[4]

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.

References

^ 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. PMC 3849166 . PMID 23611891. doi:10.4161/rna.24151.
^ 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. PMID 19708923. doi:10.1111/j.1365-2958.2009.06840.x.
^ Malys N, McCarthy JEG (2010). "Translation initiation: variations in the mechanism can be anticipated". Cellular and Molecular Life Sciences. 68 (6): 991–1003. PMID 21076851. doi:10.1007/s00018-010-0588-z.

UpToDate Contents

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5. 腎でのマグネシウム処理における利尿剤の有効性 effect of diuretics on magnesium handling by the kidney

English Journal

Microfluidic biosensor for the detection of DNA by fluorescence enhancement and the following streptavidin detection by fluorescence quenching.

Wang J, Aki M, Onoshima D, Arinaga K, Kaji N, Tokeshi M, Fujita S, Yokoyama N, Baba Y.SourceDepartment of Applied Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, Japan; MEXT Innovative Research Center for Preventive Medical Engineering, Nagoya University, Nagoya, Japan; Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden. Electronic address: wjzyy988@gmail.com.
Biosensors & bioelectronics.Biosens Bioelectron.2014 Jan 15;51:280-5. doi: 10.1016/j.bios.2013.07.058. Epub 2013 Aug 6.
We reported an optical DNA/protein microfluidic sensor which consists of single stranded (ss) DNA-Cy3 probes on gold surface and simple line-shape microfluidic channel. These ssDNA-Cy3 probes with random sequence in bulk solution or on gold surface exhibits fluorescence enhancement after binding wit
PMID 23974159

A novel probe density controllable electrochemiluminescence biosensor for ultra-sensitive detection of Hg2+ based on DNA hybridization optimization with gold nanoparticles array patterned self-assembly platform.

Gao W, Zhang A, Chen Y, Chen Z, Chen Y, Lu F, Chen Z.SourceDepartment of Chemistry, Shantou University, Shantou, Guangdong 515063, China. whgao@stu.edu.cn
Biosensors & bioelectronics.Biosens Bioelectron.2013 Nov 15;49:139-45. doi: 10.1016/j.bios.2013.05.013. Epub 2013 May 15.
Biosensor based on DNA hybridization holds great potential to get higher sensitivity as the optimal DNA hybridization efficiency can be achieved by controlling the distribution and orientation of probe strands on the transducer surface. In this work, an innovative strategy is reported to tap the sen
PMID 23732860

The kissing-loop T-shaped structure translational enhancer of pea enation mosaic virus can bind simultaneously to ribosomes and a 5' proximal hairpin.

Gao F, Gulay SP, Kasprzak W, Dinman JD, Shapiro BA, Simon AE.SourceDepartment of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, USA.
Journal of virology.J Virol.2013 Nov;87(22):11987-2002. doi: 10.1128/JVI.02005-13. Epub 2013 Aug 28.
The Pea Enation Mosaic Virus (PEMV) 3' translational enhancer, known as the kissing-loop T-shaped structure (kl-TSS), binds to 40S subunits, 60S subunits, and 80S ribosomes, whereas the Turnip crinkle virus (TCV) TSS binds only to 60S subunits and 80S ribosomes. Using electrophoretic mobility gel sh
PMID 23986599

Japanese Journal

Short hairpin RNAs of designed sequences can be extracellularly produced by the marine bacterium Rhodovulum sulfidophilum

, , , ,
The Journal of General and Applied Microbiology 60(6), 222-226, 2014
… As a next step we attempted to produce another functional RNA, short hairpin RNAs (shRNAs) using this bacterial system. … Even if the shRNA has a long stem-loop structure which is thought to interfere with transcription in bacterial cells, the yield of the shRNA is almost the same as that of the streptavidin RNA aptamer. …
NAID 130004802274

Evaluation of Three RT-qPCR-Based miRNA Detection Methods Using Seven Rice miRNAs

, , [他],
Bioscience, Biotechnology, and Biochemistry 77(6), 1349-1353, 2013
… Three frequently-used reverse transcription-quantitative polymerase chain reaction (RT-qPCR)-based miRNA detection methods, stem-loop RT-qPCR, poly(A)-tailing RT-qPCR, and miQPCR, were evaluated using seven selected rice miRNAs. … The stem-loop amplification technique detected highly and moderately abundant miRNAs. … The poly(A)-tailing method detected both highly abundant and sparsely present miRNAs, but failed to detect miRNAs with a hairpin structure. …
NAID 130003361121

Promoter and Terminator Analysis of 40-kDa Outer Membrane Gene (hbp35) in Porphyromonas gingivalis 381

, ,
International Journal of Oral-Medical Sciences 10(2), 96-102, 2011
… Hairpin loop and stem parts analysis predicted two typical terminators downstream of hbp35. …
NAID 130001088326