BRANCHED AND MULTI-CHAIN NUCLEIC ACID SWITCHES FOR SENSING AND SCREENING
First Claim
1. A branched or multichain nucleic acid switch adapted to switch from a first conformation to a second conformation upon ligand binding, said switch comprising:
- a probe strand P comprising a ligand binding domain;
a switching framework comprising a cover strand (C);
a tether that holds P and C together while the switch changes between the first and second conformations; and
a signaling apparatus comprising a combination of signaling entities.
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Abstract
Embodiments of the invention relate to a branched or multichain nucleic acid switch adapted to switch from a first conformation to a second conformation upon ligand binding. The switch includes a probe strand, P, which includes the ligand binding domain; a switching framework which includes a cover strand (C), and a tether that holds P and C together and a signaling apparatus. Some embodiments include a toggle strand (T) where now the tether holds P, C, T, and the signaling apparatus together. As the switch changes between the first and second conformations; the signaling apparatus reports the state of the switch. The signaling entity is typically a lumiphore and a quencher located along the switching framework. Nucleic acid switches have applications in real time assays for diverse agents including infectious agents, environmental toxins, and terrorist agents, as well as screening methods for such agents. Further applications are found for nanoelectronics, nanofabrication and nanomachines.
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Citations
29 Claims
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1. A branched or multichain nucleic acid switch adapted to switch from a first conformation to a second conformation upon ligand binding, said switch comprising:
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a probe strand P comprising a ligand binding domain; a switching framework comprising a cover strand (C); a tether that holds P and C together while the switch changes between the first and second conformations; and a signaling apparatus comprising a combination of signaling entities. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28)
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21. A method of chemical screening comprising:
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providing a bistable branched or multichain switch, comprising an analog of an RNA or DNA, wherein the analog comprises the ligand binding domain, a molecular framework and a signaling apparatus; contacting the branched or multichain switch with the ligand in the absence of a screened chemical entity; monitoring a signal produced from the signaling apparatus in the absence of the chemical entity; contacting the branched or multichain switch with the ligand in the presence of the chemical entity; monitoring a signal produced from the signaling apparatus in the presence of the chemical entity; and comparing the signal produced in the absence of the chemical entity with the signal produced in the presence of the chemical entity to determine the effect of the chemical entity on the ligand binding. - View Dependent Claims (22, 23, 24, 25, 26)
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27. A molecular switch adapted to switch from a first energy state to a second energy state upon application of triggering photons, said switch comprising:
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a photosensitive ligand binding domain comprising a combinatorially-derived sequence; a molecular framework comprising the photosensitive ligand binding domain adapted to switch from a first stable conformation to a second stable conformation upon binding of the photosensitive ligand by the ligand binding domain; and a signaling apparatus along the molecular framework comprising a combination of signaling entities that vary upon application of the triggering photons when the molecular framework switches between first and second stable conformations.
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29. A branched or multichain switch adapted to switch from a first conformation to a second conformation upon ligand binding, said switch comprising:
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a first strand comprising a ligand binding domain; a second strand; and a fastener to couple the two strands together; wherein the first strand and second strand hybridize to each other in the first conformation and the ligand binding domain is free in the second conformation.
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Specification