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Supporting Information for: Robust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain

By Christopher A. Lavender, Feng Ding, Nikolay V. Dokholyan and Kevin M. Weeks


Sequences correspond to those used in prior structural studies (1-4). In HHR, where the crystallographic model includes two strands, the strands were connected with a 5'-AAAA-3 ' linker. The HCV-PK sequence was taken from genotype 1b (5). The HCV-PK model includes nucleotides 40-52, 111-139, and 285-354, comprising the base of domain II, the four-way junction at the base of domain III, and domain IV. During modeling, these three segments of the HCV IRES sequence were connected using two 5'-UUUU-3 ' linkers. Secondary and tertiary structure reference information. Sources for the secondary structures and tertiary contact information used to constrain DMD refinement are outlined in detail in Table S1. Base pairs in the secondary structures were constrained as described previously (6, 7). Tertiary contacts were imposed using the generic constraint system created in this work. In the case of the CrPV RNA, tertiary constraints were used to describe the pseudoknot identified using chemical modification techniques and mutational analysis (1, 8). For tRNA Asp, pair-wise tertiary contacts were inferred from covariation studies summarized by Gutell and colleagues (9). These contacts are consistent with the tertiary interactions originally compiled by Levitt (3)

Year: 2013
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