16 research outputs found

    Structural Dynamics of Human Telomeric G-Quadruplex Loops Studied by Molecular Dynamics Simulations

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    <div><p>Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel) G-quadruplex. A series of molecular dynamics (MD) simulations were carried out to investigate the structural dynamics of TTA loops. We found that (1) the TA base pair formed in TTA loops are very stable, the occupied of all hydrogen bonds are more than 0.95. (2) The TA base pair makes the adjacent G-quartet more stable than others. (3) For the edgewise loop and the diagonal loop, most loop bases are stacking with others, only few bases have considerable freedom. (4) The stabilities of these stacking structures are distinct. Part of the loops, especially TA base pairs, and bases stacking with the G-quartet, maintain certain stable conformations in the simulation, but other parts, like TT and TA stacking structures, are not stable enough. For the first time, spontaneous conformational switches of TTA edgewise loops were observed in our long time MD simulations. (5) For double chain reversal loop, it is really hard to maintain a stable conformation in the long time simulation under present force fields (parm99 and parmbsc0), as it has multiple conformations with similar free energies.</p></div

    TTA loops conformations discussed in this work.

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    <p>Thymine in blue, adenine in green and guanine in yellow. Hydrogen bonds are drawn in gray dash lines, and all bonds connected with hydrogen are hidden.</p

    Details of hydrogen bonds between loop bases and between loop base and quartet base.

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    <p>Results under parm99 force field are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071380#pone.0071380.s005" target="_blank">Table S2</a>.</p>a<p>This hydrogen bond formed after 250 ns in the simulation, so just last 700 ns of the trajectory was used to count the hydrogen bond.</p

    Structural dynamics of hybrid_bsc0 loops.

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    <p>(a), distance and angle between two thymine bases T and T of double chain reversal loop. (b), The RMSD of TTA loop in [3+1] hybrid structure, and the NMR experimental structure was chosen as reference. (c), angle between T and T and angle between T and A.</p

    Illustration of the G-quartet base-triads.

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    <p>(a), G-quartet base-triads. All four bases have similar Z-axis but distinct X-axis and Y-axis. (b), Calculating for Z by rotating the Z by /2 about the <i>rt</i> axis, and is the angle between two Z-axes Z and Z.</p

    List of simulations involved in this work.

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    a<p>In these two structures, loop bases are deleted and just G-quartets left.</p

    The probability distribution of the RMSD of G-quartets in anti_bsc0 and hybrid_bsc0 models (solid lines), and in anti_stem and hybrid_stem (dash lines).

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    <p>The probability distribution of the RMSD of G-quartets in anti_bsc0 and hybrid_bsc0 models (solid lines), and in anti_stem and hybrid_stem (dash lines).</p

    Scheme of two hTel G-quadruplex structures involved in this work.

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    <p><i>Syn</i> and <i>anti</i> glycosidic bond orientations are drawn in white and gray. From layer 1 to layer 3 are three G-quartets named from the orient of the first strand of G-quadruplexes.</p

    Structural dynamics of anti_bsc0 loops.

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    <p>(a), distance and angle between two thymine bases T and T of the upper diagonal loop. The small fluctuation reflects that these two thymine bases stacked with each other in the trajectory. (b), distance and angle between A and upper G-quartet, in the first 250 ns, A stacked with the G-quartet, but then this stacking structure was destroyed. (c), angle between T and T and angle between T and A.</p

    Structural dynamics of anti-parallel and hybrid type hTel G-quadruplex on different time scales assessed by pairwise RMSD matrices.

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    <p>Structural dynamics of anti-parallel and hybrid type hTel G-quadruplex on different time scales assessed by pairwise RMSD matrices.</p
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