Dimeric quadruplexes

Keniry M A, Owen E, Shafer R. (1997) The contribution of thymine-thymine interactions to the stability of folded dimeric quadruplexes. Nucleic Acids Res. 25 4389 392... 

Structure of the 93del dimeric quadruplex. (a) Ribbon and (b) schematic view of the structure, (c) Structure of the 93del dimeric quadruplex with one subunit shown in surface view, thereby emphasizing the recognition feature between the two subunits... 

Fig. 4. Possible homo-dimers of psPtDNA (A) antiparallel duplex, (B) parallel duplex, (C) quadruplex. Adapted from Ref. (28).

It is worth to mention that this definition is not always consistent with the nature of the macromolecular assembly when applying to nucleic acids. For example, from all different types of quadruplex nucleic acids only quadruplex monomers are covered by lUPAC definition of tertiary structure being a single chain of DNA or RNA. However, also the quadruplexes with higher molecularity of the formed structures (dimers, tetramers) belong to this important tertiary structure family. 

The smallest unimolecular G-quadruplex belongs to the family d(G2NnG2NnG2NnG2), and forms two stacked G-tetrads. The solution structure of such a G-quadruplex in which the first loops are diagonal has been solved. ° A similar structure of a guanosine- and adenosine-rich sequence, but which forms a dimeric structure with two G-tetrads has also been solved by NMR. ° In determining the solution structure of a DNA 3-way junction, van Buuren et... 

The simplest quadruplex-based higher order structure is a double-quadruplex, in which two tetramolecular quadruplexes associate to form an octaplex. One may distinguish two types of dimers (a) those based on simple stacking of terminal quartets and (b) those involving interlocked base quartets. 

One way to identify these elusive intermediates is mass spectrometry. Electrospray allows the isolation of species of various molecular weights, (Figure 7) (Rosu et al., in preparation). These dimeric and trimeric species might be intermediates leading to the formation of the tetrameric structure. However, we cannot exclude yet that they represent dead ends in the pathway towards quadruplexes their progressive disappearance at long incubation times do not unambiguously demonstrate they are true intermediates. 

Figure 7 ESI-MS studies of tetramolecular quadruplexes. The TG5T oligonucleotide was incubated in 0.15 M pH 7.0 ammonium acetate buffer for various amounts of time, then analysed by electrospray mass spectrometry (negative mode). From the initial peak corresponding to the TG5T single-strand (SS), one can see the gradual conversion to a quadruplex (G4), as well as the presence of dimeric (Di) and trimeric (Tri) species...

The d(G3AG2T3G3AT) forms a dimeric G-quadruplex (Figure 6) with several new structural elements.There is a V-shaped loop connecting two corners... 

E. Skripkin and D.J. Patel, V-shaped scaffold A new architectural motif identified in an A.(G.G.G.G) pentad-containing dimeric DNA quadruplex involving stacked G anti).G anti).G anti).G syn) tetrads, J. Mol. Biol., 2001, 311, 1063-1079. 

A.T. Phan, Y.S. Modi and D.J. Patel, Two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) sequence interconverts between asymmetric dimeric G-quadruplexes in solution, J. Mol. Biol., 2004, 338, 93-102. 

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