METHODS AND COMPOSITIONS FOR TARGET DETECTION

1 . A method of identifying a target in a sample comprising:

a. contacting nucleic acid from a sample with a plurality of guide nucleic acid (gNA)-nucleic acid-guided nuclease system protein complexes, wherein the complexes are targeted to at least one target, and wherein the nucleic acid, the gNA-nucleic acid-guided nuclease system protein complexes, or both the nucleic acid and the gNA-nucleic acid-guided nuclease system protein complexes comprise a label; and

b. identifying the target in the sample, wherein the identifying is achieved by detecting a specific signal from the label, wherein the presence of a specific signal indicates binding of the gNA-nucleic acid-guided nuclease system protein complex to the nucleic acid.

2 . The method of claim 1 , wherein the nucleic acid comprises a label.

3 . The method of claim 2 , wherein the label is an intercalating label.

4 . The method of claim 2 , wherein the nucleic acid is labeled prior to the contacting step.

5 . The method of claim 2 , wherein the nucleic acid is labeled after the contacting step.

6 . The method of claim 2 , wherein the nucleic acid-guided nuclease system protein is a CRISPR/Cas system protein.

7 . The method of any of claims 1 - 6 , wherein the method further comprises generating droplets, wherein a subset of the droplets comprise a gNA-nucleic acid-guided nuclease system protein complex.

8 . The method of claim 7 , wherein a subset of the droplets comprise a gNA-nucleic acid-guided nuclease system protein complex bound to the nucleic acid.

9 . The method of claim 1 , wherein a plurality of the gNA-nucleic acid-guided nuclease system protein complexes comprise a label.

10 . The method of claim 9 , wherein a plurality of the gNA-nucleic acid-guided nuclease system protein complexes are labeled prior to the contacting step.

11 . The method of claim 9 , wherein a plurality of the gNA-nucleic acid-guided nuclease system protein complexes are labeled after the contacting step.

12 . The method of claim 9 , wherein the nucleic acid comprises a label.

13 . The method of claim 12 , wherein the nucleic acid and the plurality of the gNA-nucleic acid-guided nuclease system protein complexes are both labeled prior to the contacting step.

14 . The method of claim 12 , wherein the nucleic acid and the plurality of the gNA-nucleic acid-guided nuclease system protein complexes are both labeled after the contacting step.

15 . The method of claim 12 , wherein the nucleic acid is labeled prior to contacting, and the plurality of the gNA-nucleic acid-guided nuclease system protein complexes are labeled after the contacting step.

16 . The method of claim 12 , wherein the nucleic acid is labeled after contacting, and the plurality of the gNA-nucleic acid-guided nuclease system protein complexes are labeled before the contacting step.

17 . The method of claim 12 , wherein the nucleic acid comprises a first label and the gNA-nucleic acid-guided nuclease system protein complexes comprise a second label, wherein the first and second label comprise a donor/acceptor pair for fluorescent resonance energy transfer.

18 . The method of any one of claims 1 - 17 , wherein the contacting is carried out at room temperature.

19 . The method of any one of claims 1 - 18 , wherein the identifying comprises detecting a single signal

20 . The method of any one of claims 1 - 18 , wherein the identifying comprises detecting multiple signals.

21 . The method of any one of claims 1 - 20 , wherein the nucleic acid-guided nuclease system protein is a CRISPR/Cas system protein selected from the group consisting of Cas9, CasX, CasY, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5.

22 . The method of claim 21 , wherein the nucleic acid-guided nuclease system protein is a dead nucleic acid-guided nuclease system protein.

23 . The method of claim 22 , wherein the nucleic acid-guided nuclease system protein is dCas9.

24 . The method of claim 21 , wherein the nucleic acid-guided nuclease system protein is a nucleic acid-guided nuclease system nickase protein.

25 . The method of claim 21 , wherein the nucleic acid-guided nuclease system protein exhibits reduced off-target binding.

26 . The method of any one of claims 1 - 25 , wherein the label is selected from the group consisting of an enzyme, an enzyme substrate, an antibody, an antigen binding fragment, a peptide, a chromophore, a lumiphore, a fluorophore, a chromogen, a hapten, an antigen, a radioactive isotope, a magnetic particle, a metal nanoparticle, a redox active marker group, an aptamer, one member of a binding pair, and combinations thereof.

27 . The method of any one of claims 1 - 25 , wherein the label is a detectable label.

28 . The method of any one of claims 1 - 27 , wherein the sample is selected from the group consisting of a clinical sample, a forensic sample, an environmental sample, a metagenomic sample, and a food sample.

29 . The method of any one of claims 1 - 28 , wherein the sample is from a human.

30 . The method of any one of claims 1 - 29 , wherein the sample is not processed prior to the contacting.

31 . The method of any one of claims 1 - 30 , wherein the nucleic acid, the gNA-nucleic acid-guided nuclease system protein complexes, or both the nucleic acid and the gNA-nucleic acid-guided nuclease system protein complexes comprise multiple labels.

32 . The method of any one of claims 1 - 31 , wherein the complexes are targeted to a plurality of targets.

33 . The method of any one of claims 1 - 32 , wherein the target is an individual.

34 . The method of any one of claims 1 - 32 , wherein the target is a pathogen.

35 . The method of claim 33 , wherein the pathogen is selected from the pathogens in Table 1.

36 . The method of claim 32 , wherein the complexes targeted to different targets comprise different labels.

37 . The method of claim 32 , wherein the complexes targeted to different targets comprise the same label.

38 . The method of any one of claims 1 - 37 , wherein the gNA-nucleic acid-guided nuclease system protein complexes are attached to a substrate.

39 . The method of claim 38 , wherein the substrate is silica, plastic, glass, or metal.

40 . The method of claim 39 , wherein the substrate is a 2-dimensional substrate.

41 . The method of claim 39 , wherein the substrate comprises a 3-dimensional substrate.

42 . The method of claim 39 , wherein the substrate comprises a chamber or is a cylindrical array.

43 . The method of claim 38 , wherein the gNA-nucleic acid-guided nuclease system protein complexes are attached to a substrate in a known order.

44 . The method of any one of claims 38 - 43 , wherein the substrate is reusable.

45 . The method of any one of claims 1 - 37 , wherein the gNA-nucleic acid-guided nuclease system protein complexes are in solution.

46 . The method of any one of claims 1 - 45 , wherein the gNA-nucleic acid-guided nuclease system protein complexes comprise at least 1 unique gNA.

47 . The method of any one of claims 1 - 37 , wherein the contacting takes place in solution.

48 . The method of any one of claims 1 - 37 , wherein the nucleic acid is attached to a substrate.

49 . The method of claim 48 , wherein the substrate is silica, plastic, glass, or metal.

50 . The method of any one of claims 1 - 49 , wherein the nucleic acid is further analyzed by sequencing.

51 . The method of any one of claims 1 - 50 , wherein the nucleic acid is sheared.

52 . The method of any one of claims 1 - 51 , wherein the nucleic acid is amplified.

53 . The method of any one of claims 1 - 52 , wherein the nucleic acid is blocked at one or more termini with non-extendible nucleotides.

54 . The method of any one of claims 1 - 53 , wherein a plurality of targets are simultaneously identified.

55 . The method of any one of claims 1 - 54 , wherein the method is carried out in less than 24 hours.

56 . The method of any one of claims 1 - 55 , wherein the sample is subject to a prior screening step.

57 . The method of any one of claims 1 - 55 , wherein the sample is subject to multi-detection steps.

58 . The method of any of claims 1 - 57 , wherein the binding of a gNA-nucleic acid-guided nuclease system protein complex to the nucleic acid indicates the presence of a target.

59 . The method of any of claims 1 - 57 , wherein the lack of binding of a gNA-nucleic acid-guided nuclease system protein complex to a nucleic acid indicates the absence of a target.

60 . The method of any of claims 1 - 59 , wherein the nucleic acid comprises DNA.

61 . The method of any of claims 1 - 59 , wherein the nucleic acid is DNA.

62 . A collection of guide nucleic acids (gNAs) targeted to at least one target, wherein a plurality of the gNAs comprise a label.

63 . The collection of claim 62 , wherein the collection is targeted to a plurality of targets.

64 . The collection of any one of claims 62 - 63 , wherein the target is an individual.

65 . The collection of any one of claims 62 - 63 , wherein the target is a pathogen.

66 . The collection of claim 65 , wherein the pathogen is selected from the pathogens in Table 1.

67 . The collection of any one of claims 63 - 66 , wherein the gNAs targeted to different targets comprise different labels.

68 . The collection of any one of claims 63 - 66 , wherein the gNAs targeted to different targets comprise the same labels.

69 . The collection of any one of claims 62 - 68 , wherein the label is a detectable label.

70 . The collection of any one of claims 62 - 69 , wherein the label is selected from the group consisting of an enzyme, an enzyme substrate, an antibody, an antigen binding fragment, a peptide, a chromophore, a lumiphore, a fluorophore, a chromogen, a hapten, an antigen, a radioactive isotope, a magnetic particle, a metal nanoparticle, a redox active marker group, an aptamer, one member of a binding pair, and combinations thereof.

71 . The collection of any one of claims 62 - 70 , wherein the gNAs comprise more than one label.

72 . The collection of any one of claims 62 - 71 , wherein the gNAs are attached to a substrate.

73 . The collection of claim 72 , wherein the substrate is silica, plastic, glass, or metal.

74 . The collection of claim 73 , wherein the substrate is a 2-dimensional substrate.

75 . The collection of claim 73 , wherein the substrate comprises a 3-dimensional substrate.

76 . The collection of claim 73 , wherein the substrate comprises a chamber or is a cylindrical array.

77 . The collection of any one of claims 62 - 76 , wherein the gNAs are attached to a substrate in a known order.

78 . The collection of any one of claims 72 - 77 , wherein the substrate is reusable.

79 . The collection of any one of claims 62 - 71 , wherein the gNAs are in solution.

80 . The collection of any one of claims 62 - 79 , wherein the collection comprises at least 1 unique gNA.

81 . The collection of any one of claims 62 - 80 , wherein the gNAs are complexed to nucleic acid-guided nuclease system proteins.

82 . The collection of claim 81 , wherein the nucleic acid-guided nuclease system proteins are CRISPR/Cas system proteins.

83 . The collection of claim 82 , wherein the CRISPR/Cas system proteins are selected from the group consisting of Cas9, CasX, CasY, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5.

84 . The collection of claim 81 , wherein the nucleic acid-guided nuclease system protein is a dead nucleic acid-guided nuclease system protein.

85 . The collection of claim 84 , wherein the nucleic acid-guided nuclease system protein is dCas9.

86 . The collection of claim 81 , wherein the nucleic acid-guided nuclease system protein is nucleic acid-guided nuclease system nickase protein.

87 . The collection of claim 81 , wherein the nucleic acid-guided nuclease system protein exhibits reduced off-target binding.

88 . The collection of any one of claims 62 - 87 , wherein the nucleic acid-guided nuclease system proteins further comprise a label.

89 . A collection of guide nucleic acid (gNA)-nucleic acid-guided nuclease system protein complexes, wherein the gNAs are targeted to at least one target, and wherein a plurality of the complexes comprise a label.

90 . The collection of claim 89 , wherein the nucleic acid-guided nuclease system protein is a CRISPR/Cas system protein.

91 . The collection of claim 89 , wherein a plurality of the gNAs comprise a label.

92 . The collection of claim 89 , wherein a plurality of nucleic acid-guided nuclease system proteins comprise a label.

93 . The collection of claim 89 , wherein both a plurality of gNAs and a plurality of nucleic acid-guided nuclease system proteins comprise a label.

94 . The collection of any one of claims 89 - 93 , wherein the gNAs are targeted a plurality of targets.

95 . The collection of any one of claims 89 - 94 , wherein the target is an individual.

96 . The collection of any one of claims 89 - 94 , wherein the target is a pathogen.

97 . The collection of claim 96 , wherein the pathogen is selected from the pathogens in Table 1.

98 . The collection of any one of claims 89 - 97 , wherein the gNAs targeted to different targets comprise different labels.

99 . The collection of any one of claims 89 - 97 , wherein the gNAs targeted to different targets comprise the same label.

100 . The collection of any one of claims 89 - 97 , wherein the nucleic acid-guided nuclease system proteins comprise different labels.

101 . The collection of any one of claims 89 - 97 , wherein the nucleic acid-guided nuclease system proteins comprise the same label.

102 . The collection of any one of claims 89 - 101 , wherein the label is a detectable label.

103 . The collection of any one of claims 89 - 101 , wherein the label is selected from the group consisting of an enzyme, an enzyme substrate, an antibody, an antigen binding fragment, a peptide, a chromophore, a lumiphore, a fluorophore, a chromogen, a hapten, an antigen, a radioactive isotope, a magnetic particle, a metal nanoparticle, a redox active marker group, an aptamer, one member of a binding pair, and combinations thereof.

104 . The collection of any one of claims 89 - 103 , wherein the complexes comprise more than one label.

105 . The collection of any one of claims 89 - 104 , wherein the complexes are attached to a substrate.

106 . The collection of claim 105 , wherein the gNAs are attached to the substrate.

107 . The collection of claim 105 , wherein the nucleic acid-guided nuclease system proteins are attached to the substrate.

108 . The collection of claim 105 , wherein the substrate is silica, plastic, glass, or metal.

109 . The collection of claim 108 , wherein the substrate is a 2-dimensional substrate.

110 . The collection of claim 108 , wherein the substrate is a 3-dimensional substrate.

111 . The collection of claim 108 , wherein the substrate comprises a chamber or is a cylindrical array.

112 . The collection of any one of claims 89 - 105 , wherein the complexes are attached to a substrate in a known order.

113 . The collection of any one of claims 89 - 112 , wherein the substrate is reusable.

114 . The collection of any one of claims 89 - 104 , wherein the complexes are in solution.

115 . The collection of any one of claims 89 - 114 , wherein the collection comprises at least 1 unique gNA.

116 . The collection of any one of claims 89 - 115 , wherein the nucleic acid-guided nuclease system protein is a CRISPR/Cas system protein selected from the group consisting of Cas9, CasX, CasY, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5.

117 . The collection of claim 116 , wherein the nucleic acid-guided nuclease system protein is a dead nucleic acid-guided nuclease system protein.

118 . The collection of claim 117 , wherein the nucleic acid-guided nuclease system protein is dCas9.

119 . The collection of claim 116 , wherein the nucleic acid-guided nuclease system protein is a nucleic acid-guided nuclease system nickase protein.

120 . The collection of claim 116 , wherein the nucleic acid-guided nuclease system protein exhibits reduced off-target binding.

121 . A kit comprising anyone of the collections of claims 62 to 120 .