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. 2013 Nov 25;42(4):2687–2696. doi: 10.1093/nar/gkt1213

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© The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Folding analysis of the extended sequence of the SAM-I riboswitch using Kinetic MC simulations. (A) Normalized regional Q-value as a function of time for free folding. (B) Normalized regional Q-value as a function of time for the chain growing at a transcription rate of ≈ 50 nt/s. (C) Probability (color coded) to find AT formed at the time when the complete chain is fully grown as a function of the transcription rate and . (D) Normalized regional Q-value as a function of time for the chain growing at a transcription rate of ≈ 50 nt/s. Here the multiloop is stabilized by to mimic the effect of the ligand.

Inline graphic — Folding analysis of the extended sequence of the SAM-I riboswitch using Kinetic MC simulations. (A) Normalized regional Q-value as a function of time for free folding. (B) Normalized regional Q-value as a function of time for the chain growing at a transcription rate of ≈ 50 nt/s. (C) Probability (color coded) to find AT formed at the time when the complete chain is fully grown as a function of the transcription rate and . (D) Normalized regional Q-value as a function of time for the chain growing at a transcription rate of ≈ 50 nt/s. Here the multiloop is stabilized by to mimic the effect of the ligand.