Synthesis and label free characterization of a bimolecular PNA homo quadruplex.

Background: G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed.
Methods: The bis-end-linked-(gggt) ₂ PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS).
Results: An unprecedented bimolecular PNA homo quadruplex is here reported. To achieve this goal, we developed a bifunctional linker that once functionalized with gggt PNA strands and annealed in K ⁺ buffer allowed the obtainment of a PNA homo quadruplex. The identification of the strong SERS band at ~1481cm ^-1 , attributable to vibrations involving the quadruplex diagnostic Hoogsteen type hydrogen bonds, confirmed the formation of the PNA homo quadruplex.
Conclusions: By tethering two G-rich PNA strands to the two ends of a suitable bifunctional linker it is possible to obtain bimolecular PNA homo quadruplexes after annealing in K ⁺ -containing buffers. The formation of such CD-unfriendly complexes can be monitored, even at low concentrations, by using the SERS technique.
General Significance: Given the importance of DNA G-quadruplexes in medicine and nanotechnology, the obtainment of G-quadruplex analogs provided with enhanced enzymatic stability, and their monitoring by highly sensitive label-free techniques are of the highest importance. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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