Achievement

International group involving Marko Trajkovski and Janez Plavec has established rules that govern G-quadruplex assembly. The achievement represents an important step towards understanding and controlling of G-quadruplex formation, which is of great importance in controlling the processes of ageing, gene expression and also designing nanodevices. The results were published in Angewandte Chemie International Edition.
 
 

 
2’-deoxyguanosine, a nucleoside composed of a 2’-deoxyribose sugar and a purine base guanine, is one of the four constituents of DNA. Guanine adopts one of the two canonical conformations around glycosidic bond; anti exhibits guanine orientation away from the sugar, whereas syn conformation is characterized by position of guanine above the sugar moiety. Guanine rich DNA sequences can form G-quadruplexes – four stranded structures with stacks of basic structural elements called G-quartets with four H-bonded guanines. Dispositions of conformations of guanines in G-quadruplexes are intimately interrelated with 3D structure which in turn relates to function of G-quadruplexes in a cell. Discovery of novel G-quadruplex topology occurred through coincidental emergency or serendipity. The authors of this work demonstrated that a deductive system based on conformation of guanosines around glycosidic bond can be utilized to derive a novel G-quadruplex topology. An oligonucleotide sequence (d[G₃TG₃T₄G₃T₃G₃]) was synthesized with the purpose of designing a novel G-quadruplex structure with three types of loops. NMR in solution was used to verify that the synthesized sequence formed the predicted structure. In NOESY NMR spectrum correlations are seen for protons that are close to each other. Conformation of guanosine affects the intramolecular distance between H1’ and H8. NOESY spectra can be used to determine conformations of guanosines in a G-quadruplex. Furthermore correlations between H1’ of a certain nucleotide and H8 atom of consecutive nucleotide in an oligonucleotide sequence enable assignment of signals in NOESY spectrum which is a prerequisite for determination of 3D structure. Prediction and experimental verification of topology adopted by oligonucleotide d[G₃TG₃T₄G₃T₃G₃]  proves that proposed rational enables to drive folding of G-quadruplexes and thus control of their 3D structure.
 

Figure 1:  Schematic representation of topology of the G-quadruplex adopted by d[G₃TG₃T₄G₃T₃G₃] which was controlled through disposition of syn (shaded squares) and anti (black squares) conformations of guanine nucleotides and by the length and types of connecting loops (in blue, red and green). In NOESY spectrum (at mixing time 300 ms in H₂O at 278 K) there are five most intense signals corresponding to residues 1, 5, 12, 13 and 18 being in syn conformation. Sequential correlations are indicated with black lines.