Classification of G-Quadruplex DNA on the Basis of the Quadruplex Twist Angle and Planarity of G-Quartets

Abstract

The present work is devoted to the analysis of the G-quadruplex DNA structure using the bioinformatics method. The interest towards quadruplex DNAs is determined by their involvement in the functioning of telomeres and onco-promoters as well as by the possibility to create on their basis aptamers and nanostructures. Here, we present an algorithm for a general analysis of the polymorphism of the G-quadruplex structure from the data bank PDB using original parameters. 74 structures were grouped according to the following parameters: the number of DNA strands, the number of G-quartets, and the location and orientation of the connecting loops. Two quantitative parameters were used to describe the quadruplex structure: the twist angle between two adjacent quartets (analogous to that for the complementary pair in the duplex DNA) and the quartet planarity (an original parameter). The distribution patterns of these values are specific for each group of quadruplex structures and are dependent upon the type of connecting loops used (diagonal, lateral or propeller). The tetramolecular loopless parallel quadruplex was used as a comparison template. The lateral loops introduce the strongest distortion into the structure of quadruplexes: the values of the twist angles are the lowest and are not typical for the other quadruplex groups. The loops of the diagonal type introduce much weaker deformation into quadruplexes; the structures with propeller loops are characterized by the optimum geometry of G-quartets. Hence, the correlation between the twist angle and the tension in the structure of quadruplex DNA is revealed.

Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX

“…The G-quartets are spaced by 3.4 Å (S7 Table), leading to optimal π-π base stacking interactions. The average intramolecular helical twist between G-quartets within each GQ monomer is 29 ± 4˚for T1 and 28 ± 1˚for T7 (S8 Table), consistent with values reported for parallel GQs [39,41] and calculated for the parallel Tel22-NMM structure (29 ± 1˚) [30]. The two monomers are twisted with respect to each other by 116 ± 1˚, 117 ± 2˚(S9 Table), and 120 ± 3˚, for T1, T7 and Tel22, respectively.…”

Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex–Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

“…Successful stabilization from the cations has reportedly maintained an average interquartet distance of 3.3 Å between the bipyramidal antiprism that is formed. 83 Zheng and co-workers 85 have shown that single-strand G-rich sequence can fold into a G-quadruplex with very low K + -ion concentration (0.01–01 mM), indicating strong binding of K + . To look into this feature, distance calculations were performed to define some parameters of the K + cations relative to the surrounding G4 DNA.…”

Technological prospects of developing DNA-modified biosensors based on carbon nanotubes

“…In the absence of thrombin, 15 TBA aptamers are in an equilibrium between two states: a complex with the nanotube and a quadruplex structure (which is a four stranded DNA helix that acts to stabilize aptamer molecules; for the DNA aptamer in question, it was previously described by R.V. Reshetnikov and one of the authors of this work in [10]). Basically, the equilib rium is shifted towards the DNA-nanotube complex, but when the aptamer is able form a complex with thrombin, the conformation equilibrium becomes shifted towards the quadruplex structure, which has much smaller contacts with the nanotube.…”