G-quartet motif

Figure 13.18 A ribbon structure of a folic acid derivative self-assembles into a disc-like tetramer based on a G-quartet motif showing liquid crystalline behaviour on the addition of a metal ion such as Na+.

Figure 10.15 Examples of G-quartet DNA aptamers from secondary (a) and tertiary (b) structural perspectives. The planar G quartet found in many DNA aptamers is also illustrated in detail (c). Solid bars (a) indicate regions of G quartet motifs. The M+ ion in (c) is typically Na+ or K. G-quartets produce stacks wherein backbones can be parallel or anti-parallel with respect to each other. Stacked G-quartets are also identified in special regions of eukaryotic chromosomes called telomeres.

Sreenivasachary and Lehn have described a hydrazone DCL in which selection is driven by the formation of a stable gel (Scheme 1.7) [7]. Hydrazide-functional-ized guanosine and serine building blocks were reacted with two different aldehyde building blocks in sodium acetate buffer at pH 6 to form a library of four interconverting hydrazones (12-15). Hydrazone 13, which is capable of forming a stable gel based on the G-quartet motif, was amplified in the mixture here, the distribution of components in the library was determined not by the relative stabilities of the individual hydrazones, but rather by the formation of the insoluble fibers that create a stable gel. 

Figure 5.8 Self-assembled dimer of 5.25 with Na+ binding by a guanosine tetramer motif (G-quartet) and Cl- binding by amide functionalities. Remaining space if filled by water molecules. (Reproduced with permission from [22] 2003 American Chemical Society).

J. Kondo, W. Adachi, S. Umeda, T. Sunami and A. Takenaka, Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats. Nucleic Acids Res., 2004, 32, 2541-2549. 

Single-stranded DNA aptamers identified were found to bind thrombin with a value of 25-200 nM. The central core (15-17 residues in length) was found to assume a G-quartet structure, a very common structural motif in both DNA and RNA aptamers (Figure 10.15). DNA aptamers that bind other proteins have since been found to have several... 

Correspondingly G in the third strand binds to G in the duplex [21,22,23], The second motif often requires high divalent cation concentrations, and the third strand being G-rich, is prone to form self-associated structures involving G-quartets [24]. This is particularly pronounced when the third strand is a triplexforming oligonucleotide (TFO) [25,26]. Another competing structure, a G-A parallel duplex, can also interfere with triplex formation [27]. 

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