Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

Abstract

Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5′-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured glycosidic patterns has not emerged. This work presents MD simulation and free energetic analyses for simplified two-quartet [d(GG)]4 models and suggests that the four base pair step patterns show quite different relative stabilities: syn-anti > anti-anti > anti-syn > syn-syn. This suggests the following rule: when folding, anti-parallel G-quadruplexes tend to maximize the number of syn-anti steps and avoid the unfavorable anti-syn and syn-syn steps. This rule is consistent with most of the anti-parallel G-quadruplex structures in the Protein Databank (PDB). Structural polymorphisms of G-quadruplexes relate to these glycosidic conformational patterns and the lengths of the G-tracts. The folding topologies of G2- and G4-tracts are not very polymorphic because each strand tends to populate the stable syn-anti repeat. G3-tracts, on the other hand, cannot present this repeating pattern on each G-tract. This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes.

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

“…We suggest that the specific ion binding to the narrow grooves may be another structural and free energy factor which contributes to the basic rules determining stabilities of different G-DNA topologies [22,29,30,63]. We plan to further investigate this issue in the near future.…”

“…Moreover, additional diversity is brought by syn or anti orientation of the glycosidic torsion angle c of guanosines in the G-stem. The possible syn/ anti patterns are constrained by strand orientations and affected also by presence or absence of flanking nucleotides at the beginning/end of a sequence [29,30]. Thus far, six distinct folding topologies of telomeric G-quadruplex were reported [12e16,27].…”

“…Any Gquadruplex forming strand can in principle adopt altogether 26 distinct G-quadruplex topologies, differing in strand directionality and type of the loops [22,30]. Although not all of them are energetically feasible, at least five three-quartet (and in addition one two-quartet) topologies have already been observed for the human telomeric quadruplex (see above) as dominant equilibrium structures in various atomistic experiments [12e16, 27,29,35,36,49,63]. Further, the G-rich sequence can potentially form quadruplexes with incomplete number of tetrads, including structures with a slipped strand (actually, the two-quartet quadruplex PDB: 2KF8 [12] falls into this category).…”

The Determination of Quadruplex Structures

“…The simple molecular mechanics force field is still almost universally used, with the formalism being that the energetics of a molecule (V) is described in terms of the sum of a number of factors: The AMBER force field has been extensively parameterized for nucleic acids (see Pérez et al, 2007 for a recent update of backbone parameters) and is the most commonly used one for quadruplex simulations, usually performed within the AMBER11 package (http://ambermd.org). Molecular dynamics simulations of a number of quadruplex systems have now been successfully performed and in large part they are able to reproduce experimental findings, not least the relative energetics of G-quartet base stacking in quadruplexes (see for a recent example, Cang, Šponer & Cheatham, 2011). Use of simulation methods for the modeling of quadruplex complexes involving new ligands is becoming an increasing popular approach to rational quadruplex ligand discovery; it is important to ensure that force-field parameters are not used that are inappropriate for nucleic acids.…”

Flipping a G‐Tetrad in a Unimolecular Quadruplex Without Affecting Its Global Fold

“…In line with these differential thermal stabilities, molecular dynamics simulations and free energy analyses suggested that syn-anti and syn-syn are the most stable and most disfavored glycosidic conformational steps in antiparallel quadruplex structures, respectively. [13] It is therefore remarkable that an unusual all-syn G-tract forms in the thermodynamically most stable modified quadruplex, highlighting the contribution of connecting loops in determining the preferred conformation. Apparently, the particular loop regions in ODN(0) resist topological changes even upon enforcing syn$anti transitions.…”