Modular aptamer-regulated ribozymes
First Claim
1. An aptamer-regulated ribozyme, comprising:
- (a) a cis-acting hammerhead ribozyme comprising a catalytic core and stem I, stem II and stem III duplex regions extending therefrom, said stem I having a loop I single-stranded loop region opposite to said catalytic core, and said stem II having a loop II single-stranded loop region opposite to said catalytic core;
(b) an information transmission domain (ITD) having a first end and a second end, which information transmission domain is directly coupled to said loop I or loop II through said first end; and
(c) an aptamer coupled to said information transmission domain through said second end, said aptamer binds to a ligand,wherein said ITD is between the cis-acting hammerhead ribozyme and the aptamer, and comprises;
(i) a general transmission region,(ii) a switching strand that hybridizes with the general transmission region in the absence of the ligand, and,(iii) a competing strand that hybridizes with the general transmission region in the presence of the ligand,wherein the switching strand and the competing strand compete to bind to the general transmission region through hybridization interactions,wherein binding of said ligand to said aptamer favors a conformation change in the aptamer,wherein said conformation change causes the ITD to favor the binding of the general transmission region to said competing strand via a strand-displacement mechanism; and
,wherein hybridization between the general transmission region and the competing strand causes, via the interaction of said information transmission domain with one or more of said loop, said stem or said catalytic core, said ribozyme to undergo self-cleavage of a backbone phosphodiester bond at a rate dependent upon the presence or absence of said ligand.
1 Assignment
0 Petitions
Accused Products
Abstract
An extensible RNA-based framework for engineering ligand-controlled gene regulatory systems, called ribozyme switches, that exhibit tunable regulation, design modularity, and target specificity is provided. These switch platforms typically contain a sensor domain, comprised of an aptamer sequence, and an actuator domain, comprised of a hammerhead ribozyme sequence. A variety of modes of standardized information transmission between these domains can be employed, and this application demonstrates a mechanism that allows for the reliable and modular assembly of functioning synthetic hammerhead ribozyme switches and regulation of ribozyme activity in response to various effectors. In some embodiments aptamer-regulated cis-acting hammerhead ribozymes are provided.
98 Citations
33 Claims
-
1. An aptamer-regulated ribozyme, comprising:
-
(a) a cis-acting hammerhead ribozyme comprising a catalytic core and stem I, stem II and stem III duplex regions extending therefrom, said stem I having a loop I single-stranded loop region opposite to said catalytic core, and said stem II having a loop II single-stranded loop region opposite to said catalytic core; (b) an information transmission domain (ITD) having a first end and a second end, which information transmission domain is directly coupled to said loop I or loop II through said first end; and (c) an aptamer coupled to said information transmission domain through said second end, said aptamer binds to a ligand, wherein said ITD is between the cis-acting hammerhead ribozyme and the aptamer, and comprises; (i) a general transmission region, (ii) a switching strand that hybridizes with the general transmission region in the absence of the ligand, and, (iii) a competing strand that hybridizes with the general transmission region in the presence of the ligand, wherein the switching strand and the competing strand compete to bind to the general transmission region through hybridization interactions, wherein binding of said ligand to said aptamer favors a conformation change in the aptamer, wherein said conformation change causes the ITD to favor the binding of the general transmission region to said competing strand via a strand-displacement mechanism; and
,wherein hybridization between the general transmission region and the competing strand causes, via the interaction of said information transmission domain with one or more of said loop, said stem or said catalytic core, said ribozyme to undergo self-cleavage of a backbone phosphodiester bond at a rate dependent upon the presence or absence of said ligand. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33)
-
-
19. A method for rendering expression of a target gene in a cell dependent on the presence or absence of a ligand, comprising introducing into the cell an expression construct including a coding sequence that for the target gene, which when transcribed to an mRNA transcript, also includes one or more cis-acting aptamer-regulated ribozymes in said mRNA that regulate expression of the target gene, said cis-acting aptamer-regulated ribozyme comprising:
-
(a) a catalytic core and stem I, stem II and stem III duplex regions extending therefrom, said stem I having a loop I single-stranded loop region opposite to said catalytic core, and said stem II having a loop II single-stranded loop region opposite to said catalytic core; (b) an information transmission domain having a first end and a second end, which information transmission domain is directly coupled to said loop I or loop II through said first end; and (c) an aptamer coupled to said information transmission domain through said second end, said aptamer binds to a ligand, wherein said ITD is between the cis-acting hammerhead ribozyme and the aptamer, and comprises; (i) a general transmission region, (ii) a switching strand that hybridizes with the general transmission region in the absence of the ligand, and, (iii) a competing strand that hybridizes with the general transmission region in the presence of the ligand, wherein the switching strand and the competing strand compete to bind to the general transmission region through hybridization interactions, wherein binding of said ligand to said aptamer favors a conformation change in the aptamer, wherein said conformation change causes the ITD to favor the binding of the general transmission region to said competing strand via a strand-displacement mechanism; and
,wherein hybridization between the general transmission region and the competing strand causes, via the interaction of said information transmission domain with one or more of said loop, said stem or said catalytic core, said ribozyme to undergo self-cleavage of a backbone phosphodiester bond at a rate dependent upon the presence or absence of said ligand so as to render expression of target gene dependent on said ligand. - View Dependent Claims (20, 21, 22)
-
-
23. A method of determining the amount of an analyte in a cell which expresses a reporter gene, comprising
(i) introducing into the cell an expression construct including a coding sequence for the reporter gene, which when transcribed to an mRNA transcript, also includes one or more cis-acting aptamer-regulated ribozymes in said mRNA that regulate expression of the reporter gene, said cis-acting aptamer-regulated ribozyme comprising: -
(a) a catalytic core and stem I, stem II and stem III duplex regions extending therefrom, said stem I having a loop I single-stranded loop region opposite to said catalytic core, and said stem II having a loop II single-stranded loop region opposite to said catalytic core; and (b) an information transmission domain having a first end and a second end, which information transmission domain is directly coupled to said loop I or loop II through said first end; and (c) an aptamer coupled to said information transmission domain through said second end, said aptamer binds to an analyte, wherein said ITD is between the cis-acting hammerhead ribozyme and the aptamer, and comprises; (i) a general transmission region, (ii) a switching strand that hybridizes with the general transmission region in the absence of the analyte, and, (iii) a competing strand that hybridizes with the general transmission region in the presence of the analyte, wherein the switching strand and the competing strand compete to bind to the general transmission region through hybridization interactions, wherein binding of said analyte to said aptamer favors a conformation change in the aptamer, wherein said conformation change causes the ITD to favor the binding of the general transmission region to said competing strand via a strand-displacement mechanism; and
,wherein hybridization between the general transmission region and the competing strand causes, via the interaction of said information transmission domain with one or more of said loop, said stem or said catalytic core, said ribozyme to undergo self-cleavage of a backbone phosphodiester bond at a rate dependent upon the presence or absence of said analyte so as to render expression of reporter gene dependent on said analyte; (ii) measuring the amount of expression of said reporter gene; and (iii) correlating the amount of expression of said reporter gene with the amount of analyte, thereby determining the amount of the ligand in the cell.
-
Specification