Table 2. Recent synthetic riboswitches and aptazymes and their (potential) applications.

Application area (contribution)	RNA Unit Device	Function	Host	Description	Strategy	Reference
Environmental (bioremediation) Medicine (disease sites recognition)	Small-molecule responsive riboswitch	Translational initiation control	E. coli	Engineering cells to seek and destroy atrazine	In vitro evolved sensor (aptamer) In vivo evolved adaptor (expression platform)	58
Environmental (bioremediation) Medicine (disease sites recognition)	Small-molecule responsive riboswitch	Translational initiation control	E. coli	Engineering cells motility to navigate toward theophylline (predecessor of system above)	In vitro evolution of complete RNA device and tested in vivo	59
Synthetic Biology (RNA adaptor)	Slippage-like small-molecule responsive riboswitch	Translational initiation control	B. subtilis S. coelicolor	Engineering theophylline riboswitch with a new response mechanism	In vivo development of a RNA adaptor based on a slippage mechanism It was tested in S. coelicolor to confirm portability	121, 122
Synthetic Biology (RNA device)	Small-molecule responsive aptazyme	Translational initiation control	E. coli	Engineering Hammerhead ribozyme to be theophylline responsive and upon scission of mRNA turn translation ON	In vivo evolved RNA adaptor Natural scissile adaptor2 and sensor	111
Molecular Biology (small-molecule concentration detector)	Small-molecule responsive riboswitch	Translational initiation control	E. coli	Application of an adenosylcobalamin -sensitive natural riboswitch for the detection and study of B12 metabolism and transport	Natural sensor fused to different actuators	123
Metabolic Engineering (gene expression controllers)	Allosteric riboswitches (aptazymes)	Degradation-mediated gene expression control	E. coli	Model-driven engineered glmS-like aptazymes to control gene expression Additional contribution: computer-assisted design method	In vitro, in vivo and in silico engineered sensor and scissile adaptor2 assembled into catalytic regulator	60
Synthetic Biology (new RNA device)	Small-molecule responsive riboswitch	Translational control	E. coli	Reversed natural thiamine pyrophosphate riboswitch by dual genetic selection	In vivo evolution of adaptor	124
Synthetic Biology (a “universal” riboswitch)	Small-molecule responsive riboswitches	Gene expression control	E. coli A. baylyi A. baumannii A. tumefacians M. magneticum M. smegmatis B. subtilis S. pyogenes	Engineering 5 synthetic riboswitches that show gene expression control over 8 different bacterial species	Rational design and in vivo screening of ligand-sensitive regulators	125
Molecular Biology (Study of essential genes through hypomorphic mutants)	Small-molecule responsive riboswitch	Translational initiation control	E. coli	The natural theophylline riboswitch was used to control gene expression in hypomorphic mutants to study CsrA1	Rational design and in vivo screening of ligand-sensitive regulators	126
Medicine and molecular biology (riboswitch-based system to control gene expression)	Small-molecule responsive riboswitch	Translational control	M. Tuberculosis	Transcription promoter coupled to synthetic theophylline riboswitch for expression control	DNA transcriptional regulator coupled to a synthetic ligand-sensitive regulator	127 This is a continuation of ref.58
Molecular Biology (gene regulation and intracellular sensor)	Small-molecule responsive aptazyme	Translational control	E. coli	Changed aptamer from a previously engineered aptazyme to a theophylline-sensitive one	Interchangeable sensor coupled to a scissile adaptor2	128
Molecular Biology (intracellular sensor)	Small-molecule responsive aptazyme	Translational control	E. coli	Co-factor recognition aptamer fused to a Hammerhead ribozyme and anti-Ribosome Binding Site (RBS) sequence System detected enzyme co-factor concentrations	Interchangeable sensor coupled to a scissile adaptor2	129
Molecular Biology (biodetectors)	Small-molecule responsive riboswitch	Translational control	E. coli	Explored the applications of fusing synthetic riboswitches to gene reporters as a genetic screening method	In vitro evolved synthetic ligand-responsive regulator	130

¹ CsrA: Carbon Storage Regulator “A” protein. ²Scissile adaptor: an RNA, DNA or protein sequence that is cleaved for the part that it connects to, to perform its function (e.g., expression platform in aptazymes). ³Amber suppression: a tRNA has been modified to recognize the amber stop codon and instead insert an amino acid thus suppressing translation termination.¹³¹