Conclusions

In this study the G-quadruplex folding properties of the DNA sequence (G4CT)3G4 that occurs wide-spread in bacterial genomes was characterized. The G-rich sequence was recently identified as a potential quadruplex-forming sequence associated with loci involved in antigenic variation in the human pathogen Treponema pallidum (231). Structural characterizations were carried out employing a combination of CD spectroscopy, EPR spectroscopy, analytical ultracentrifugation, and EMSA. We demonstrate that d[(G4CT)3G4] displays unique features among the many G-quadruplex-forming sequences studied so far: Primarily a remarkable continuous and complete transition from an antiparallel, monomolecular G-quadruplex structure into a tetrameric, parallel conformation is observed upon increasing K⁺-concentrations. Furthermore the oligonucleotide d[(G4CT)3G4] shows a so far unprecedented selectivity for K⁺ with even high concentrations of Na⁺ unable to induce pronounced G-quadruplex formation.

Furthermore we investigate effects of cation selectivity, quadruplex loop composition and length as well as G-tract length on quadruplex conversion. d[(G4CT)3G4] was the only sequence of the studied G-rich oligonucleotides to adopt exclusively the anti-parallel fold at low K⁺ and at the same time completely converting into the all-parallel topology with increasing concentrations of stabilizing cations. We found that while Na⁺ and Li⁺ alone did not stabilize either of the two conformations, addition of either cation to increase ionic strength was sufficient to switch the conformations once initial K⁺ was available. This definitive requirement for the presence of K⁺ in order to fold quadruplexes even in the presence of high concentrations of other cations is remarkable and so-far not reported for any other DNA sequence. Further analysis of the sequence requirements of the structural transition showed that thymidines in the loops seemed to be necessary for quadruplex interconversion. All 2 nt loop sequences with at least a single thymine could adopt multiple topologies whereas sequences lacking thymidines always showed a parallel quadruplex conformation. The variation of loop length determined that loop sizes of 2 to 3 nt promoted conformational switching. Furthermore, tract variations showed that a shortened G-tract of 3 guanines showed the parallel conformation but increasing G-G-tract length to 5 guanines

conformational polymorphism, Na⁺ alone was in most cases unable to induce pronounced quadruplex formation. Hence we were able to identify several additional sequences that display a so-far unknown, remarkable selectivity for K⁺.

Several open questions remain regarding a potential role of the studied sequence in cellular processes. Although it seems likely that in Treponema pallidum the motif is involved in genetic recombination events that result in antigenic variation in other species (66,138) the sequence is often associated with intracellular proteins where antigenic variation processes are very unlikely to play a role. Alternatively, an involvement in regulation of gene expression could be discussed.

Whether the peculiar structural transitions of the sequence motif upon K⁺ variation contributes to some mechanism that responds to conditional changes of the bacterial environment is at this point very speculative. However it is intriguing to note that in Salmonella the motif is found associated with two genes coding for K⁺-transport proteins. To gain insight in the putative function of (G4CT)3G4 as transcriptional or translational regulator gene expression studies in dependence on intracellular K⁺-concentrations are necessary.

Apart from potential roles in cellular processes, the investigated quadruplex sequence might be utilized as building block in DNA nanotechnology applications (244). Due to their cation specific stabilization G-quadruplex structures quadruplex folding in a K⁺ dependent manner can be implemented in the construction of nucleic acid based K⁺ sensors. Construction of such sensor elements have been reported for DNA as well as RNA G-quadruplexes as output signal intrinsic quadruplex fluorescence, attachment of fluorescent labels, incubation with fluorescent G-quadruplex binders as well as colorimetric effects have been used (255-259). A general challenge for such sensors is the selectivity for K⁺ in comparison to other monovalent cations especially Na⁺ especially with regard to usein biological samples. Furthermore the response range is often narrow. Set-ups focusing either on monomolecular quadruplex folding or quadruplex interconversion may be followed up. For lower concentrations of K⁺ a set up exploiting only the anti-parallel conformation could be envisioned, e.g. by the attachment of FRET labels that would only be in close proximity in the monomolecularly folded structure, but be spaced further apart in the tetrameric structure or in the unfolded oligo. Although d[(G4CT)3G4] shows the definite requirement of the presence of K⁺ for quadruplex folding, interconversion was also shown to be enhanced by other monovalent cations. This can have a detrimental effect on the overall selectivity. However, the possibility of switching between drastically different conformations and being able to control the molecularity of well-defined complexes makes quadruplexes such as the investigated sequence well-suited for building functional DNA nanoobjects. Especially, a tetrameric, parallel arrangement of G-quadruplex folding sequences is of interest, as it would allow the formation of so-called G-wires (245). DNA can self-assemble into DNA nanostructures or can easily be coupled to nanomaterials such as gold nanoparticles or quantum dots (81,248).

Switchability of the DNA building block in such an assembly could be used to regulate the

functional properties of a material, or reactive moieties attached to the DNA oligonucleotide could be brought into close proximity to each other by tetramerization. With regard to technical applications it would also be interesting to further elucidate the exact structure of the monomolecular antiparallel conformer in solution, e.g. by 2D NMR. In addition structural characterizations of the respective RNA G-quadruplex may be carried out to support further biological functions.