Dna-based molecular switches and uses thereof
OwnerYamuna Krishnan, Saikat Chakrabortyinventors
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Abstract
Disclosed are nucleic acid-based molecular switches that respond to changes in pH. The switches may be used in DNA nanodevices. The switches may also act as sensors for measuring the pH of a sample, including cells, regions thereof, and whole organisms. The switch includes an A-motif that forms at acidic pH. Also disclosed are compositions and methods for measuring the pH of cells or regions thereof, such as vesicles, the nucleus, mitochondrial matrix, or the Golgi lumen.
Claims21
-20. (canceled)
A method for determining a capacity of an agent to effect pH, the method comprising:
- contacting a test sample with a) one or more indicators having at least two poly dA nucleic acid strands comprising a signaling system, wherein the one or more indicators transition between first and second stable conformations in response to a change in pH, and b) the agent, and
- detecting the presence, absence, or magnitude of a signal from the signaling system to determine the pH of the sample contacted by the agent
- whereby a change in the presence, absence, or magnitude of the signal compared to the signal detected in a sample not contacted by the agent indicates the capacity of the agent to effect pH.
A kit for determining the pH of a sample, the kit comprising:
- one or more indicators having at least two poly dA nucleic acid strands comprising a signaling system, wherein the one or more indicators transition between first and second stable conformations in response to a change in pH, and optionally instructions for use.
A nucleic acid assembly comprising one or more modules comprising an A-motif forming nucleic acid, wherein the A-motif forming nucleic acid-transitions between first and second stable conformations in response to a change in pH in order to join the modules in a nucleic acid assembly, wherein at least one A-motif-forming nucleic acid is selected from the group consisting of 5′-AAAAAAAAAA AAAAAACATG CCGGTATTT AAAGCCTTTC GAAGATATCG TGGTTCGAGA AAAAAAAAAA AAAAA-3′ (SEQ ID NO:
- 5), 5′-CGAGCTGCAG CAGCTGTTAT TTAGGCTTTA AATACCGGCA TG-3′ (SEQ ID NO:
- 6), 5′-CTCGAACCAC GATATCTTCG TTATAACAGC TGCTGCAGC TCG-3′ (SEQ ID NO:
- 7), 5′-ATGCCGGTAT TTAAAGCCT TTCGAAGATA TCGTGGTTCG AG-3′ (SEQ ID NO:
- 8), and 5′-TTTTTTTTTT TTTTTTCATG CCGGTATTTA AAGCCTTTCG AAGATATCG TGGTTCGAG TTTTTTTTT TTTTTTT-3′ (SEQ ID NO:
- 9).
Dependencies are inferred from the claim text.