Biological significance and structure

All bases in a double-strand DNA helix appear as Watson-Crick base pairs. Normally there are two hydrogen bonds between A:T (DNA) base pairs and three hydrogen bonds between G:C base pairs.

In addition to these "canonical" base pairings, however, there are so called non-canonical base pairs, including the quite rare G:G and A:A base pairs. Two separate types of pairing can be distinguished: the Hoogsteen and "shallow groove" pairings.

The superstructures studied to date are nearly all stabilised using Hoogsteen hydrogen bonds. Even the best known, the triple helix, is traced back to Hoogsteen base pairs. In a triple helix, polypurines form base triplets in combination with two polypyrimidines, with one of each base pair on the Hoogsteen side and one on the Watson-Crick side.

Superstructures play an important role as cellular effector motives. Such motives are found in eukaryotes, for example, at the end of the linear chromosomes. These motives, also known as telomeres, represent protective superstructures made up of repetitive sequence motives. At the centre of these are so called G-quadruplexes (also known as G-quartets or G-tetrads). It was already postulated in the early 60s that such planar structures existed.

They are stabilised through a combination of Hoogsteen and Watson-Crick base pairs, similar to those found in d(CpGpCp) triplets. Each base forms a hydrogen bond to the neighbouring two bases. The interior of such as G-quadruplexes forms a cavity which is also able to form complexes out of certain cations via the four O-atoms of such a guanosine. Cations have a crucial function in the stabilisation of G-quartets. Potassium ions are particularly stabilising, whereas lithium ions function as powerful structure breakers. Based on numerous studies, it is assumed that the reversible formation of superstructures can also function as a sort of molecular switch in the cell.

As various working groups have shown, special proteins, such as topoisomerase I and RAP1, favour the transition of double-strand, helical DNA into G-quadruplex structures. In turn, certain helicases, such as the Sgs1 helicase present in yeast, are able to recognise the G-quadruplex structures and unfold them quite effectively.

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