Hairpin structure

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Example of an RNA hairpin structure.

Intramolecular base pairings that form a hairpin structure occur in single-stranded DNA and RNA . This is to secondary stem loop structures (English stem-loop ) with double-stranded stem and a short single-stranded loop trained also hairpin ( hairpin ) or hairpin loop ( hairpin loop ) mentioned. These occur when two sections of the same molecule - often with a palindromic nucleotide sequence - form a double-stranded region through complementary base pairs and enclose the unpaired intermediate section as a loop. The resulting “lollipop structure” is a key element in the construction of many RNA secondary structures .

Education and stability

The formation of a hairpin structure depends on the stability of the resulting helix and loop regions. The first requirement is a sequence that can fold back on itself to form a paired double helix . For the stability of this helix, its length, the number of base pairs and any dislocations or bulges in the paired area (which in particular make short helices unstable) are decisive . Pairings of guanine with cytosine have three hydrogen bonds and are therefore more stable than the adenine - uracil pairs, which only form two. In addition, guanine-uracil pairings with two hydrogen bonds are common and inexpensive in RNA . The formation of a helix is ​​also favored by the interactions of the stacked bases, which bring the π bonds of the aromatic rings into favorable alignment.

The stability of the loop also affects the formation of a hairpin structure. There are no loops with less than three bases. Large loops are also unstable if they do not carry additional secondary structures (such as pseudoknot pairings). The optimal loop length appears to be between 4 and 8 bases. The loop with the sequence UUCG is called a tetraloop and is particularly stable due to the interactions of its nucleotides.

Occurrence in the RNA

Hairpin structures occur, for example, in pre- microRNAs and tRNAs . tRNAs consist of a clover-leaf-shaped arrangement of three real hairpin structures and a stem area that combines both ends. The anticodon , with which a codon is recognized during translation , sits on one of the unpaired loops of the tRNA. In addition to nested loop formations, interlaced hairpin structures can also occur, for example in pseudo-knots .

Many ribozymes also include hairpin structures, such as B. the hairpin ribozyme, which was even named after this characteristic structural feature. The hammerhead ribozyme also contains hairpin structures that are connected in a central unpaired section where the cutting region is located. The basic secondary structure of the hammerhead ribozyme is necessary for the cutting function.

Hairpin structures also play an important role in the termination of transcription in prokaryotes . They form in an mRNA strand during transcription and ensure that the RNA polymerase is detached from the DNA strand. This process represents a Rho -independent or intrinsic termination, the sequences involved are called terminator sequences . They form the basis for a form of gene regulation known as attenuation .


The following RNA sequence


can shape the following hairpin structure:

   ... CG ...


  • JD Watson, TA Baker, SP Bell, A. Gann, M. Levine, R. Losick : Molecular Biology of the Gene. 5th edition. CSHL Press Pearson Benjamin Cummings, 2004, ISBN 0-8053-4635-X , Chapter 6.