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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 4. — Folding analysis based on Kinetic MC simulations. (A) Fraction of base pairs formed in each helix (normalized regional Q-value) as a function of the total number of formed base pairs for free folding of the adenine and SAM-I riboswitch secondary structures. (B) Folding of each helix over the chain growth rate for the SAM-I and adenine riboswitches. Folding events are characterized by the number of base pairs formed in the whole structure when a normalized regional Q-value of 0.5 is reached (mid Q-value, Figure 3B).