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. 2005 Jun 13;33(10):3435–3446. doi: 10.1093/nar/gki664

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© The Author 2005. Published by Oxford University Press. All rights reserved

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Structural view of the transitions between different stacking patterns in the free RNA. (A) G32/G43 and A44/A33 stacking interactions as observed in the crystal structure of Kt-U4–15.5K complex. (B) A44/G32/G43 stacking interactions formed in the LES4 trajectory after ∼7 ns. (C) Rotation about the N9–C1′ bond in A33 and A44 as observed in the LES4 trajectory after ∼9 ns. (D) G32/G43/A33 stacking interactions formed in the LES1 trajectory. Guanines are blue, adenines red, oxygens pink, nitrogens cyan and the sugar–phosphate backbone gray.