Figure 3
From: Automatic workflow for the classification of local DNA conformations
Oxytricha nova guanine quadruplex. (a) A schematic diagram of a double-stranded (bimolecular) guanine quadruplex from Oxytricha nova telomeric sequence (G4T4G4)2. A solid line represents a sugar-phosphate backbone. O. nova G-quadruplex has four G-quartets formed from nucleotides in which syn and anti conformations of the glycosidic angle alternate along each strand [105]. Shaded rectangles indicate guanine residues in syn conformation (typically χ ~ 60°-70°), clear rectangles indicate guanine residues in anti conformation (typically χ ~ 250°-260°). (b) A crystal structure of a bimolecular O. nova G-quadruplex 1JPQ [104]. Overall topology is indicated by the orange ribbon. Bases are represented by green sticks, potassium ions stabilizing the whole structure are shown as yellow spheres. (c) A crystal structure of a complex of O. nova G-quadruplex with a drug acridine 3EUM [106]. Acridine affecting the conformation of a T4 loop in chain A is shown in blue. (d) Consensus conformational map of the O. nova G-quadruplex. By convention, chains are numbered in the 5′-to-3′ direction. Conformational classes of individual dinucleotide steps are indicated by red numbers, their size is proportional to the frequency of their occurrence in investigated structures. A description of individual conformations is given in Tables 1 and 3. The T5T6 step adopts either a canonical BI conformation 54 if the G4T5 step is also in a canonical BI conformation, or an A-to-B conformation 41 if the G4T5 step is in a conformation 32. (e) Consensus conformational map of the O. nova G-quadruplex complexed with a drug acridine. Individual conformations shown as red numbers are characterized in Tables 1 and 3.