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- W3011888654 endingPage "3463" @default.
- W3011888654 startingPage "3447" @default.
- W3011888654 abstract "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." @default.
- W3011888654 created "2020-03-23" @default.
- W3011888654 creator A5016773569 @default.
- W3011888654 creator A5026399646 @default.
- W3011888654 creator A5028187203 @default.
- W3011888654 creator A5041529029 @default.
- W3011888654 creator A5050850407 @default.
- W3011888654 creator A5069555359 @default.
- W3011888654 date "2020-03-12" @default.
- W3011888654 modified "2023-10-16" @default.
- W3011888654 title "Stability of Two-Quartet G-Quadruplexes and Their Dimers in Atomistic Simulations" @default.
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