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Single unusual DNA

Final Report Summary - SINGLE UNUSUAL DNA (Single unusual DNA)

Nucleic acid sequences containing guanine tracts are able to adopt non-canonical four-stranded nucleic acid structures called G-quadruplexes (G4s). These structures are based on the stacking of two or more G-tetrads; each tetrad is a planar association of four guanines held together by eight hydrogen bonds. The four G-tracts forming the core delimit four negatively charged grooves linked together by three types of loops. Unlike the canonical duplex, these degrees of freedom confer a high level of plasticity to this family of globularly shaped nucleic acid structures. Under near physiological conditions, G4s easily form within milliseconds and can be thermally stable with melting temperatures typically above 50°C. Polymorphism, robustness and fast folding are altogether intrinsic features of these structures that suggest biological functions. Genome scale bioinformatics analysis showed a significant enrichment of these sequences in various key elements of the human genome such as telomeres, oncogenes and introns.

DNA has been used in the design of nanomaterials due to the ability of complementary strands to hybridize in a controllable fashion. In addition, chemical synthesis of DNA is straightforward. G-quadruplex structures are also being used in supramolecular chemistry and nanotechnology, acting as basic units of formation for nanostructures. A number of groups have constructed different DNA nanodevices based on switching between structures induced by changes in environmental factors.

In our project, our work encompassed projects related to the design of quadruplex sequences that may be used for single molecule experiments. Specifically:
- We have demonstrated a new type of duplex-quadruplex assembly, which allowed the unprecedented formation of a trimolecular quadruplex. The principle of our design is that G-quadruplex formation requires the presence of a G4-compatible cation such as sodium, whereas duplexes do not. Therefore, we used short duplexes as guide strands to preposition the G-rich tracts into close spatial proximity, and then we induced the formation of a defined G-quadruplex structure by adding Na+. This work led to a publication in the prestigious journal, Angew Chem Int Ed (2012, 51:11002-11005), which has been highlighted as a new finding by Faculty of 1000 (http://f1000.com/prime/717964317).
- We have studied the impact of modified sugar-phosphate backbone on quadruplex formation. We decided to explore the role of the sugar using two strategies: the first was to remove the sugar and the second was to expand five-membered rings to six-membered ones. These work were published in two very important journals (Chem. Eur. J., 2013, 19: 14719–14725; Chem. Sci., 2013, 4: 3693–3698.). Our work demonstrated that the sugar is very important for the properties of G-quadruplex.
- We have investigated the impact of the role of hydroxyl group on structure and stability of tetramolecular G-quadruplexes. We have found important position-specific effects that were unexpected. Structural studies are currently being performed in the Host laboratory; this work will be submitted soon.
- We have showed that one may combine a G-quadruplex with a C-quadruplex on the same strand. This work was presented in Angew Chem Int Ed (2013, 2013, 52: 7742–7746). We demonstrated that by using a long single strand, one can obtain a highly compact structure with two different quadruplexes. As these two tetraplexes have different sequence and condition requirements (pH or potassium) we could convert this device into a DNA logic gate. Such system is also of interest for single molecule studies, as one can control which tetraplex is formed by controlling the incubation buffer.

Our bulk experiments will allow others and us to know the exact properties of tetraplex, and supply the information for choosing stable quadruplex motifs that will induce a large change in length upon dissociation. Furthermore, as mentioned above, our paper shown in Angew Chem Int Ed (2012, 51:11002-11005) was recommended to readers by the Faculty of 1000 website, which is the prestigious web reference for biological and medical researchers.