Stability of Two-Quartet G‑Quadruplexes and Their Dimers in Atomistic Simulations

G-quadruplexes (GQs) are four-stranded
noncanonical DNA and RNA
architectures that can be formed by guanine-rich sequences. The stability
of GQs increases with the number of G-quartets, and three G-quartets
generally form stable GQs. However, the stability of two-quartet GQs
is an open issue. To understand the intrinsic stability of two-quartet
GQ stems, we have carried out a series of unbiased molecular dynamics
(MD) simulations (505 μs in total) of two- and four-quartet
DNA and RNA GQs, with attention paid mainly to parallel-stranded arrangements.
We used AMBER DNA parmOL15 and RNA parmOL3 force fields and tested
different ion and water models. Two-quartet parallel-stranded DNA
GQs unfolded in all the simulations, while the equivalent RNA GQ was
stable in most of the simulations. GQs composed of two stacked units
of two-quartet GQs were stable for both DNA and RNA. The simulations
suggest that a minimum of three quartets are needed to form an intrinsically
stable all-anti parallel-stranded DNA GQ. Parallel
two-quartet DNA GQ may exist if substantially stabilized by another
molecule or structural element, including multimerization. On the
other hand, we predict that isolated RNA two-quartet parallel GQs
may form, albeit being weakly stable. We also show that ionic parameters
and water models should be chosen with caution because some parameter
combinations can cause spurious instability of GQ stems. Some in-so-far
unnoticed limitations of force-field description of multiple ions
inside the GQs are discussed, which compromise the capability of simulations
to fully capture the effect of increase in the number of quartets
on the GQ stability.