General composition framework for ligand-controlled regulatory systems
First Claim
1. A polynucleotide comprising:
- (1) a modular actuator domain having one or more functional activities, wherein said modular actuator domain is not a ribozyme,(2) a modular sensor domain that detects concentration change of a molecule, or status change of an environmental condition (pH, ion concentration, temperature), and,(3) an information transmission domain between the modular actuator domain and the modular sensor domain, said information transmission domain comprising;
(a) a general transmission region,(b) a switching strand,(c) a competing strand,wherein the switching strand and the competing strand are in a continuous sequence and compete to bind to the general transmission region through hybridization interactions;
wherein detection of the concentration or status change by the modular sensor domain favors a conformation change in the modular actuator domain;
wherein said conformation change is mediated by a strand-displacement mechanism in the information transmission domain to favor the binding of the general transmission region to one of said switching strand and said competing strand; and
,wherein said conformation change modulates said functional activities.
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Abstract
The invention provides an improved design for the construction of extensible nucleic acid-based, ligand-controlled regulatory systems, and the nucleic acid regulatory systems resulting therefrom. The invention contemplates improving the design of the switches (ligand-controlled regulatory systems) through the design of an information transmission domain (ITD). The improved ITD eliminates free-floating ends of the switching and the competing strands, and localizes competitive hybridization events to a contiguous strand of competing and switching strands in a strand-displacement mechanism-based switch, thereby improving the kinetics of strand-displacement. The improved regulatory systems have many uses in various biological systems, including gene expression control or ligand-concentration sensing.
117 Citations
30 Claims
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1. A polynucleotide comprising:
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(1) a modular actuator domain having one or more functional activities, wherein said modular actuator domain is not a ribozyme, (2) a modular sensor domain that detects concentration change of a molecule, or status change of an environmental condition (pH, ion concentration, temperature), and, (3) an information transmission domain between the modular actuator domain and the modular sensor domain, said information transmission domain comprising; (a) a general transmission region, (b) a switching strand, (c) a competing strand, wherein the switching strand and the competing strand are in a continuous sequence and compete to bind to the general transmission region through hybridization interactions; wherein detection of the concentration or status change by the modular sensor domain favors a conformation change in the modular actuator domain; wherein said conformation change is mediated by a strand-displacement mechanism in the information transmission domain to favor the binding of the general transmission region to one of said switching strand and said competing strand; and
,wherein said conformation change modulates said functional activities. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30)
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17. A method for rational design of a modular polynucleotide, the method comprising:
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(1) providing a modular actuator domain having one or more functional activities, wherein said modular actuator domain is not a ribozyme, (2) providing a modular sensor domain that detects concentration change of a molecule, or status change of an environmental condition (pH, ion concentration, temperature), and, (3) providing an information transmission domain between the modular actuator domain and the modular sensor domain, said information transmission domain comprising; (a) a general transmission region, (b) a switching strand, (c) a competing strand, wherein the switching strand and the competing strand are in a continuous sequence and compete to bind to the general transmission region through hybridization interactions, wherein detection of the concentration or status change by the modular sensor domain favors a conformation change in the modular actuator domain; wherein said conformation change is mediated by a strand-displacement mechanism in the information transmission domain to favor the binding of the general transmission region to one of said switching strand and said competing strand; and
,wherein said conformation change modulates said functional activities.
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18. A method for improving the design of a sensor-regulated polynucleotide, said polynucleotide comprising:
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(1) an actuator domain having one or more functional activities, wherein said actuator domain is not a ribozyme, and, (2) a sensor domain that detects concentration change of a molecule, or status change of an environmental condition (pH, ion concentration, temperature), the method comprising;
providing an information transmission domain between the actuator domain and the sensor domain, said information transmission domain comprising;(a) a general transmission region, (b) a switching strand, (c) a competing strand, wherein the switching strand and the competing strand are in a continuous sequence and compete to bind to the general transmission region through hybridization interactions; wherein detection of the concentration or status change by the sensor domain favors a conformation change in the actuator domain; wherein said conformation change is mediated by a strand-displacement mechanism in the information transmission domain to favor the binding of the general transmission region to one of said switching strand and said competing strand; and
,wherein said conformation change modulates said functional activities.
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Specification