US 9,809,814 B1
Compositions and methods of nucleic acid-targeting nucleic acids
Andrew Paul May, San Francisco, CA (US); Rachel E. Haurwitz, Kensington, CA (US); Jennifer A. Doudna, Berkeley, CA (US); James M. Berger, Baltimore, MD (US); Matthew Merrill Carter, Berkeley, CA (US); and Paul Daniel Donohoue, Berkeley, CA (US)
Assigned to Caribou Biosciences, Inc., Berkeley, CA (US)
Filed by Caribou Biosciences, Inc., Berkeley, CA (US)
Filed on Jul. 26, 2017, as Appl. No. 15/660,906.
Application 15/660,906 is a continuation of application No. 15/159,619, filed on May 19, 2016, granted, now 9,725,714.
Application 15/159,619 is a continuation of application No. 14/977,514, filed on Dec. 21, 2015.
Application 14/977,514 is a continuation of application No. 14/416,338, granted, now 9,260,752, issued on Feb. 16, 2016, previously published as PCT/US2014/023828, filed on Mar. 12, 2014.
Claims priority of provisional application 61/906,211, filed on Nov. 19, 2013.
Claims priority of provisional application 61/903,232, filed on Nov. 12, 2013.
Claims priority of provisional application 61/902,723, filed on Nov. 11, 2013.
Claims priority of provisional application 61/900,311, filed on Nov. 5, 2013.
Claims priority of provisional application 61/899,712, filed on Nov. 4, 2013.
Claims priority of provisional application 61/883,804, filed on Sep. 27, 2013.
Claims priority of provisional application 61/865,743, filed on Aug. 14, 2013.
Claims priority of provisional application 61/859,661, filed on Jul. 29, 2013.
Claims priority of provisional application 61/858,767, filed on Jul. 26, 2013.
Claims priority of provisional application 61/845,714, filed on Jul. 12, 2013.
Claims priority of provisional application 61/832,690, filed on Jun. 7, 2013.
Claims priority of provisional application 61/822,002, filed on May 10, 2013.
Claims priority of provisional application 61/818,382, filed on May 1, 2013.
Claims priority of provisional application 61/818,386, filed on May 1, 2013.
Claims priority of provisional application 61/781,598, filed on Mar. 14, 2013.
Claims priority of provisional application 61/907,777, filed on Nov. 22, 2013.
Claims priority of provisional application 61/907,216, filed on Nov. 21, 2013.
Claims priority of provisional application 61/906,335, filed on Nov. 19, 2013.
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/68 (2006.01); C12N 15/11 (2006.01); C12N 15/85 (2006.01); C12N 15/90 (2006.01); C12N 15/52 (2006.01); C12N 15/10 (2006.01); C12N 9/22 (2006.01); A61K 47/64 (2017.01); A61K 38/46 (2006.01); C12N 15/113 (2010.01)
CPC C12N 15/11 (2013.01) [A61K 38/465 (2013.01); A61K 47/6455 (2017.08); C12N 9/22 (2013.01); C12N 15/102 (2013.01); C12N 15/52 (2013.01); C12N 15/85 (2013.01); C12N 15/90 (2013.01); C12N 15/902 (2013.01); C12N 15/907 (2013.01); C12Q 1/68 (2013.01); C12Q 1/686 (2013.01); C12Q 1/6806 (2013.01); C12Q 1/6818 (2013.01); C12Q 1/6869 (2013.01); C12Q 1/6874 (2013.01); C12N 15/113 (2013.01); C12N 2310/20 (2017.05); C12N 2310/531 (2013.01); C12N 2310/533 (2013.01); C12N 2800/80 (2013.01)] 20 Claims
 
1. A method for detecting if two complexes are in proximity to one another comprising:
providing a first complex, wherein the first complex comprises a first site-directed polypeptide comprising a first non-native sequence that comprises a first portion of an endonuclease split system and a first nucleic acid-targeting nucleic acid comprising a first nucleic acid sequence complementary to a first target nucleic acid, wherein the first complex contacts the first target nucleic acid;
providing a second complex, wherein the second complex comprises a second site-directed polypeptide comprising a second non-native sequence that comprises a second portion of an endonuclease split system and a second nucleic acid-targeting nucleic acid comprising a second nucleic acid sequence complementary to a second target nucleic acid, wherein the second complex contacts the second target nucleic acid; and
detecting an interaction between the first portion and the second portion, wherein (i) the endonuclease split system forms an active endonuclease when the first portion of the endonuclease split system and the second portion of the endonuclease split system are in proximity, (ii) the interaction results in cleavage of the first target sequence and the second target sequence by the active endonuclease, and (iii) the detecting indicates the first complex and the second complex are in proximity to one another.