Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch.

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Furniss S, Grover N

Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch.

RNA. 2011 Apr;17(4):710-7. doi: 10.1261/rna.2263211. Epub 2011 Mar 2.

PubMed ID

21367973 [ View in PubMed

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Abstract

Riboswitches are functional mRNA that control gene expression. Thiamine pyrophosphate (TPP) binds to thi-box riboswitch RNA and allosterically inhibits genes that code for proteins involved in the biosynthesis and transport of thiamine. Thiamine binding to the pyrimidine sensor helix and pyrophosphate binding to the pyrophosphate sensor helix cause changes in RNA conformation that regulate gene expression. Here we examine the thermodynamic properties of the internal loop of the pyrophosphate binding domain by comparing the wild-type construct (RNA WT) with six modified 2 x 2 bulged RNA and one 2 x 2 bulged DNA. The wild-type construct retains five conserved bases of the pyrophosphate sensor domain, two of which are in the 2 x 2 bulge (C65 and G66). The RNA WT construct was among the most stable (DeltaG degrees (3)(7) = -7.7 kcal/mol) in 1 M KCl at pH 7.5. Breaking the A*G mismatch of the bulge decreases the stability of the construct ~0.5-1 kcal/mol, but does not affect magnesium binding to the RNA WT. Guanine at position 48 is important for RNA-Mg(2)+ interactions of the TPP-binding riboswitch at pH 7.5. In the presence of 9.5 mM magnesium at pH 5.5, the bulged RNA constructs gained an average of 1.1 kcal/mol relative to 1 M salt. Formation of a single A+*C mismatch base pair contributes about 0.5 kcal/mol at pH 5.5, whereas two tandem A+*C mismatch base pairs together contribute about 2 kcal/mol.

DrugBank Data that Cites this Article

Drug Targets

Drug	Target	Kind	Organism	Pharmacological Action	Actions
Cocarboxylase	RNA	Nucleotide	Humans	Yes	Binder	Details