Stem-loop

Intramolecular base pairs that form a hairpin structure (so called stem-loop ), occur in single-stranded RNA into DNA and more frequent. If it is a short loop, the terms are hairpin (English hairpin ) or hairpin (English hairpin loop) needed. These structures occur when two regions of the same molecule - form a double helix, which is concluded at the end by an unpaired loop - usually with a palindromic nucleotide sequence. The resulting " lollipop " structure is a key element in the construction of many RNA secondary structures.

Formation and stability

The formation of a hairpin structure depends on the stability of the resulting helical and loop regions. The first condition is a sequence that can fold back on itself to form a paired double helix. For the stability of this helix is its length, the number of dislocations and convexities ( a small number of sets, in particular in a long helix is not a problem ), and the base pairs in the paired portions responsible. Pairings of guanine with cytosine have three hydrogen bonds and are therefore more stable than the adenine - uracil pairs that form only two. It must be noted that in RNA uracil and guanine pairs with two hydrogen bonds are common and cheap. The formation of a helix is ​​also favored by interactions of the stacked bases that bring the π - bonds of the aromatic rings in a favorable orientation.

The stability of the loop also influences the formation of a hairpin structure. There are no loops with less than three bases. Large loops without its own secondary structure ( such as pseudoknot pairings ) are also unstable. The optimum loop length appears to be between 4 and 8 bases. The loop with the sequence UUCG tetraloop is called and is extremely stable due to the interactions of their nucleotides.

Occurrence in the RNA

Hairpin structures occur, for example, in pre- microRNA and tRNA. tRNAs consist of a cloverleaf-shaped arrangement of three real hairpin structures and a fourth helix. The anticodon that detects a codon during translation, located on one of the unpaired loop of tRNA. Two nested hairpin structures occur in pseudoknot, the loop of a portion of the second hairpin structure forms.

Many ribozymes also contain hairpin structures. In the hammerhead ribozyme, there are three hairpin structures that are related in a central unpaired portion where the cutting region is. The basic secondary structure of the hammerhead ribozyme is necessary for the cutting function.

Also in the termination of transcription in prokaryotes play hairpin structures play an important role. They form in a mRNA strand during transcription and ensure that the RNA polymerase is released from the DNA strand. This process is known as Rho- independent or intrinsic termination and the sequences involved are called terminator sequences.

Example

The following palindromic RNA sequence

CCUGCXXXXGCAGG ... ... can form the following hairpin structure:

C ... G ...      C G      U A      G C      C G     X X      X X credentials

  • Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004): Molecular Biology of the Gene. 5th edition Pearson Benjamin Cummings: CSHL Press. Chapter 6
  • RNA
Palindromic sequence Double helix (disambiguation) Transfer RNA#Anticodon Genetic code RNA-Polymerase Rho factor
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