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Cooperative and directional folding of the preQ1 riboswitch aptamer domain.

Feng, Jun ; Walter, Nils G ; Brooks, Charles L Feng, Jun (correspondence author) ; Feng, Jun (record owner)

Journal of the American Chemical Society, March 30, 2011, Vol.133(12), pp.4196-4199 [Peer Reviewed Journal]

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  • Title:
    Cooperative and directional folding of the preQ1 riboswitch aptamer domain.
  • Author: Feng, Jun ; Walter, Nils G ; Brooks, Charles L
  • Feng, Jun (correspondence author) ; Feng, Jun (record owner)
  • Subjects: Aptamers, Nucleotide–Chemistry ; Bacillus Subtilis–Genetics ; Kinetics–Genetics ; Nucleic Acid Conformation–Chemistry ; Nucleoside Q–Genetics ; Riboswitch–Genetics ; Aptamers, Nucleotide ; Riboswitch ; Nucleoside Q
  • Is Part Of: Journal of the American Chemical Society, March 30, 2011, Vol.133(12), pp.4196-4199
  • Description: Riboswitches are cis-acting RNA fragments that regulate gene expression by sensing cellular levels of the associated small metabolites. In bacteria, the class I preQ(1) riboswitch allows the fine-tuning of queuosine biosynthesis in response to the intracellular concentration of the queuosine anabolic intermediate preQ(1). When binding preQ(1), the aptamer domain undergoes a significant degree of secondary and tertiary structural rearrangement and folds into an H-type pseudoknot. Conformational "switching" of the riboswitch aptamer domain upon recognizing its cognate metabolite plays a key role in the regulatory mechanism of the preQ(1) riboswitch. We investigate the folding mechanism of the preQ(1) riboswitch aptamer domain using all-atom Go̅-model simulations. The folding pathway of such a single domain is found to be cooperative and sequentially coordinated, as the folding proceeds in the 5' → 3' direction. This kinetically efficient folding mechanism suggests a fast ligand-binding response in competition with RNA elongation.
  • Language: English
  • Identifier: E-ISSN: 1520-5126 ; DOI: 10.1021/ja110411m

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