PMC

Various modulated versions of the HDV ribozyme. The inactive and active states are indicated by “off” and “on”, respectively. The substrate is shown in green, and the portion of the ribozyme responsible for the modulation in blue. a The SOFA module []. BL and BS indicate blocker and biosensor, respectively. b The G-quartzyme []. c The theophylline aptamer attached by a communication module []

Various modulations of the activity of the hairpin ribozyme. The inactive and active states are indicated by “off” and “on”, respectively. The substrate is shown in green, and the portion of the ribozyme responsible for the modulation in blue. a The adenosine-dependant hairpin ribozyme []. b The FMN aptamer attached by a communication module []. c The SOFA module []. BL and BS indicate blocker and biosensor, respectively. d The oligonucleotide modulation []. The trans-acting oligonucleotide is represented by the dotted line

Various modulation strategies for the hammerhead ribozyme based on complementary sequences. The inactive and active states are indicated by “off” and “on”, respectively. The substrate is shown in green and the portion of the ribozyme responsible for the modulation in blue. The trans-acting oligonucleotides are represented by the dotted lines. a The SOFA module []. BL and BS indicate blocker and biosensor, respectively. b Three-strand ribozyme strategy []. c Blocker release strategy []. d Stem II stabilization strategy []

Structure of the glmS ribozyme. The ribozyme and substrate are denoted by Rz and S, respectively. The cleavage site is indicated by an arrow. a Secondary structure of a trans-acting version of the glmS ribozyme according to the notation of Leontis and Westhof []. The harmonized nomenclature using roman numbers for the stems is indicated as well as the previous one in parentheses. b Crystal structure of the glmS ribozyme from Thermoanaerobacter tengcongensis []. The colors of the various domains are the same in panels A and B

Structure of the VS ribozyme. The ribozyme and substrate are denoted by Rz and S, respectively. The cleavage site is indicated by an arrow. a Secondary structure of a trans-acting version of the VS ribozyme according to the notation of Leontis and Westhof []. A shortened version can be obtained by removing the non-essential shaded region at the bottom. The tertiary interactions forming the kissing loop between loops I and V are illustrated by the thin curved lines. The dotted line represents the junction that has been removed in order to generate a trans-acting version. b Structure of the VS ribozyme obtained by SAXS []. The colors of the various domains are the same in panels A and B

Structure and folding pathway of the hammerhead ribozyme. The ribozyme and substrate are denoted by Rz and S, respectively. The cleavage site is indicated by an arrow. a Secondary structure of a trans-acting version of the hammerhead ribozyme [] according to the notation of Leontis and Westhof []. The corresponding minimal version is obtained by removing the shaded region at the top. The tertiary interactions between the loop of stem II and the bulge of stem I are illustrated by the thin curved lines. b Crystal structure of the Schistosome version of hammerhead ribozyme []. The colors of the various domains are the same in panels A and B. c Hammerhead ribozyme’s folding pathway. The substrate is shown in green, and the products in red

Structure and folding pathway of the hairpin ribozyme. The ribozyme and substrate are denoted by Rz and S, respectively. The cleavage site is indicated by an arrow. a Secondary structure of a four-way junction trans-acting version of the hairpin ribozyme [] according to the notation of Leontis and Westhof []. The corresponding minimal two-way version is obtained by removing the shaded region at the top. The tertiary interactions between the internal loops A and B are illustrated by the thin curved lines. The harmonized nomenclature using roman numbers for the stems is indicated as well as the previous one in parenthesis. b Crystal structure of the four-way junction version []). The colors of the various domains are the same in panels A and B. c Hairpin ribozyme’s folding pathway. The substrate is shown in green and the products in red

Structure and folding pathway of HDV ribozyme. The ribozyme and substrate are denoted by Rz and S, respectively. The cleavage site is indicated by an arrow. a Secondary structure of a shortened trans-acting version of the wild-type antigenomic HDV ribozyme according to the notation of Leontis and Westhof []. The harmonized nomenclature using roman numbering for the stems is indicated as well as the previous one in parenthesis. The dotted line represents the junction that has been removed in order to generate a trans-acting version. b Crystal structure of the genomic version of HDV ribozyme []. The colors of the various domains are the same in both panels A and B. c Proposed folding pathway of HDV ribozyme according to Reymond et al. []. The substrate is shown in green and the products in red. Important nucleotides are indicated in the various intermediates