Capture of nucleic acids using a nucleic acid-guided nuclease-based system

Abstract

Provided herein are methods and compositions for the capture of nucleic acids, for example by using a nucleic acid-guided nuclease-based system.

What is claimed is: 
     
         1 . A method of capturing target nucleic acid sequences comprising:
 (a) providing a sample comprising a plurality of adapter-ligated nucleic acids, wherein the nucleic acids are ligated to a first adapter at one end and ligated to a second adapter at the other end;   (b) contacting the sample with a plurality of nucleic acid-guided nuclease-gNA complexes, wherein the gNAs are complementary to targeted sites of interest contained in a subset of the nucleic acids, thereby generating a plurality of nucleic acid fragments ligated to a first or second adapter at one end and no adapter at the other end; and   (c) contacting the plurality of nucleic acid fragments with third adapters, thereby generating a plurality of nucleic acid fragments ligated to either the first or second adapter at one end and the third adapter at the other end.   
     
     
         2 . The method of  claim 1 , wherein the nucleic acid-guided nuclease is a CRISPR/Cas system protein. 
     
     
         3 . The method of  claim 1 , wherein the nucleic acid-guided nuclease is a non-CRISPR/Cas system protein. 
     
     
         4 . The method of  claim 1 , wherein the nucleic acid-guided nuclease is selected from the group consisting of CAS Class I Type I, CAS Class I Type III, CAS Class I Type IV, CAS Class II Type II, and CAS Class II Type V. 
     
     
         5 . The method of  claim 1 , wherein the nucleic acid-guided nuclease is selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cmr5, Csf1, C2c2, and NgAgo. 
     
     
         6 . The method of any one of  claims 1  to  5 , wherein the gNAs are gRNAs. 
     
     
         7 . The method of any one of  claims 1  to  5 , wherein the gNAs are gDNAs. 
     
     
         8 . The method of any one of  claims 1  to  7 , wherein the contacting with the plurality of nucleic acid-guided nuclease-gNA complexes cleaves the targeted sites of interest contained in a subset of the nucleic acids, thereby generating a plurality of nucleic acid fragments comprising a first or second adapter at one end and no adapter at the other end. 
     
     
         9 . The method of any one of  claims 1  to  8 , wherein the method further comprises amplifying the product of step (c) using first or second and third adapter-specific PCR. 
     
     
         10 . The method of any one of  claims 1  to  9 , wherein the nucleic acids are selected from the group consisting of single stranded DNA, double stranded DNA, single stranded RNA, double stranded RNA, and a DNA/RNA hybrid. 
     
     
         11 . The method of  claim 10 , wherein the nucleic acids are double stranded DNA. 
     
     
         12 . The method of any one of  claims 1  to  11 , wherein nucleic acids are from genomic DNA. 
     
     
         13 . The method of  claim 12 , wherein the genomic DNA is human. 
     
     
         14 . The method of any one of  claims 1  to  13 , wherein the nucleic acids which are adapter-ligated are from 20 bp to 5000 bp in length. 
     
     
         15 . The method of any one of  claims 1  to  14 , wherein the targeted sites of interest are single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), cancer genes, inserts, deletions, structural variations, exons, genetic mutations, or regulatory regions. 
     
     
         16 . The method of  claim 9 , wherein amplified products are used for cloning, sequencing, or genotyping. 
     
     
         17 . The method of any one of  claims 1  to  16 , wherein the adapters are from 20 bp to 100 bp in length. 
     
     
         18 . The method of any one of  claims 1  to  17 , wherein the adapters comprise primer binding sites. 
     
     
         19 . The method of any one of  claims 1  to  18 , wherein the adapters comprise sequencing adapters or restriction sites. 
     
     
         20 . The method of any one of  claims 1  to  19 , wherein the targeted sites of interest represent less than 50% of the total nucleic acid in the sample. 
     
     
         21 . The method of any one of  claims 1  to  20 , wherein the sample is obtained from a biological sample a clinical sample, a forensic sample, or an environmental sample. 
     
     
         22 . The method of any one of  claims 1  to  21 , wherein the first and second adapters are identical. 
     
     
         23 . The method of any one of  claims 1  to  21 , wherein the first and second adapters are different. 
     
     
         24 . The method of any one of  claims 1  to  23 , wherein the sample comprises a sequencing library. 
     
     
         25 . A method of introducing labeled nucleotides at targeted sites of interest comprising:
 (a) providing a sample comprising a plurality of nucleic acid fragments;   (b) contacting the sample with a plurality of nucleic acid-guided nuclease nickase-gNA complexes wherein the gNAs are complementary to targeted sites of interest in the nucleic acid fragments, thereby generating a plurality of nicked nucleic acid fragments at the targeted sites of interest; and   (c) contacting the plurality of nicked nucleic acid fragments with an enzyme capable of initiating nucleic acid synthesis at a nicked site, and labeled nucleotides, thereby generating a plurality of nucleic acid fragments comprising labeled nucleotides in the targeted sites of interest.   
     
     
         26 . The method of  claim 25 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of CAS Class I Type I nickase, CAS Class I Type III nickase, CAS Class I Type IV nickase, CAS Class II Type II nickase, and CAS Class II Type V nickase. 
     
     
         27 . The method of  claim 25 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of Cas9 nickase, Cpf1 nickase, Cas3 nickase, Cas8a-c nickase, Cas10 nickase, Cse1 nickase, Csy1 nickase, Csn2 nickase, Cas4 nickase, Csm2 nickase, Cm5 nickase, Csf1 nickase, C2C2 nickase, CPF1 nickase, and NgAgo nickase. 
     
     
         28 . The method of any one of  claims 25  to  27 , wherein the gNAs are gRNAs. 
     
     
         29 . The method of any one of  claims 25  to  27 , wherein the gNAs are gDNAs. 
     
     
         30 . The method of any one of  claims 25  to  29 , wherein the nucleic acid fragments are selected from the group consisting of single stranded DNA fragments, double stranded DNA fragments, single stranded RNA fragments, double stranded RNA fragments, and a DNA/RNA hybrid fragments. 
     
     
         31 . The method of  claim 30 , wherein the nucleic acid fragments are double stranded DNA fragments. 
     
     
         32 . The method of  claim 31 , wherein double stranded DNA fragments are from genomic DNA. 
     
     
         33 . The method of  claim 32 , wherein the genomic DNA is human. 
     
     
         34 . The method of any one of  claims 25  to  33 , wherein the nucleic acid fragments are from 20 bp to 5000 bp in length. 
     
     
         35 . The method of any one of  claims 25  to  34 , wherein the targeted sites of interest are single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), cancer genes, inserts, deletions, structural variations, exons, genetic mutations, or regulatory regions. 
     
     
         36 . The method of any one of  claims 25  to  35 , wherein the targeted sites of interest represent less than 50% of the total nucleic acid in the sample. 
     
     
         37 . The method of any one of  claims 25  to  36 , wherein the sample is obtained from a biological sample a clinical sample, a forensic sample, or an environmental sample. 
     
     
         38 . The method of any one of  claims 25  to  37 , wherein the labeled nucleotides are biotinylated nucleotides. 
     
     
         39 . The method of any one of  claims 25  to  37 , wherein the labeled nucleotides are part of an antibody conjugate pair. 
     
     
         40 . The method of  claim 38 , further comprising contacting the nucleic acid fragments comprising biotinylated nucleotides with avidin or strepavidin, thereby capturing the targeted sites of interest. 
     
     
         41 . The method of any one of  claims 25  to  40 , wherein the enzyme capable of initiating nucleic acid synthesis at a nicked site is DNA Polymerase I, a Klenow fragment, a TAQ polymerase, or a Bst DNA Polymerase. 
     
     
         42 . The method of any one of  claims 25  to  41 , wherein the nucleic acid-guided nuclease nickase nicks the 5′ end of the nucleic acid fragments. 
     
     
         43 . The method of any one of  claims 25  to  42 , wherein the nucleic acid fragments are from 20 bp to 5000 bp in length. 
     
     
         44 . The method of any one of  claims 25  to  43 , wherein the sample is obtained from a biological sample a clinical sample, a forensic sample, or an environmental sample. 
     
     
         45 . A method of capturing target nucleic acid sequences of interest comprising:
 (a) providing a sample comprising a plurality of adapter-ligated nucleic acids, wherein the nucleic acids are ligated to a first adapter at one end and are ligated to a second adapter at the other end; and   (b) contacting the sample with a plurality of catalytically dead nucleic acid-guided nuclease-gNA complexes, wherein the catalytically dead nucleic acid-guided nuclease is fused to a transposase, wherein the gRNAs are complementary to targeted sites of interest contained in a subset of the nucleic acids, and wherein the complexes are loaded with a plurality of third adapters, to generate a plurality of nucleic acids fragments comprising either a first or second adapter at one end, and a third adapter at the other end.   
     
     
         46 . The method of  claim 45 , wherein the method further comprises amplifying the product of step (b) using first or second adapter and third adapter-specific PCR. 
     
     
         47 . The method of  claim 45 , wherein the catalytically dead nucleic acid-guided nuclease is derived from a CRISPR/Cas system protein. 
     
     
         48 . The method of  claim 45 , wherein the catalytically dead nucleic acid-guided nuclease is derived from a non-CRISPR/Cas system protein. 
     
     
         49 . The method of  claim 45 , wherein the catalytically dead nucleic acid-guided nuclease is selected from the group consisting of dead CAS Class I Type I, dead CAS Class I Type III, dead CAS Class I Type IV, dead CAS Class II Type II, and dead CAS Class II Type V. 
     
     
         50 . The method of  claim 45 , wherein the catalytically dead nucleic acid-guided nuclease is selected from the group consisting of dCas9, dCpf1, dCas3, dCas8a-c, dCas10, dCse1, dCsy1, dCsn2, dCas4, dCsm2, dCmr5, dCsf1, dC2C2, and dNgAgo. 
     
     
         51 . The method of any one of  claims 45  to  50 , wherein the gNAs are gRNAs. 
     
     
         52 . The method of any one of  claims 45  to  50 , wherein the gNAs are gDNAs. 
     
     
         53 . The method of any one of  claims 45  to  52 , wherein nucleic acids sequences are from genomic DNA. 
     
     
         54 . The method of  claim 53 , wherein the genomic DNA is human. 
     
     
         55 . The method of any one of  claims 45  to  54 , wherein the catalytically dead nucleic acid-guided nuclease is fused to the N-terminus of the transposase. 
     
     
         56 . The method of any one of  claims 45  to  54 , wherein the catalytically dead nucleic acid-guided nuclease is fused to the C-terminus of the transposase. 
     
     
         57 . The method of any one of  claims 45  to  56 , wherein the nucleic acids, which are adapter ligated, are from 20 bp to 5000 bp in length. 
     
     
         58 . The method of any one of  claims 45  to  57 , wherein the contacting of step (b) allows for the insertion of the second adapter into the targeted nucleic acid sequences. 
     
     
         59 . The method of any one of  claims 45  to  58 , wherein the targeted sites of interest are single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), cancer genes, inserts, deletions, structural variations, exons, genetic mutations, or regulatory regions. 
     
     
         60 . The method of  claim 46 , wherein amplified products are used for cloning, sequencing, or genotyping. 
     
     
         61 . The method of any one of  claims 45  to  59 , wherein the adapters are from 20 bp to 100 bp in length. 
     
     
         62 . The method of any one of  claims 45  to  61 , wherein the adapters comprise primer binding sites. 
     
     
         63 . The method of any one of  claims 45  to  62 , wherein the adapters comprise sequencing adapters or restriction sites. 
     
     
         64 . The method of any one of  claims 45  to  63 , wherein the targeted sites of interest represent less than 50% of the total nucleic acid in the sample. 
     
     
         65 . The method of any one of  claims 45  to  64 , wherein the sample is obtained from a biological sample a clinical sample, a forensic sample, or an environmental sample. 
     
     
         66 . A method of capturing target nucleic acid sequences of interest comprising:
 (a) providing a sample comprising a plurality of adapter-ligated nucleic acids, wherein the nucleic acids are ligated to the adapter at the 5′ end and 3′ ends;   (b) contacting the sample with a plurality of catalytically dead nucleic acid-guided nuclease-gNA complexes, wherein the gNAs are complementary to targeted sites of interest contained in a subset of the nucleic acids, thereby generating a plurality of nucleic acids adapter-ligated at the 5′ and 3′ ends, bound to a catalytically dead nucleic acid-guided nuclease-gNA complex; and   (c) contacting the sample with a plurality of catalytically dead nucleic acid-guided nuclease-gNA complexes, wherein the gNAs are complementary to both targeted sites of interest and targeted sites not of interest in the nucleic acids, thereby generating a plurality of nucleic acid fragments comprising nucleic acid sequences not of interest, adapter ligated at only one of the 5′ or 3′ ends.   
     
     
         67 . The method of  claim 66 , wherein the catalytically dead nucleic acid-guided nuclease is a CRISPR/Cas system protein. 
     
     
         68 . The method of  claim 66 , wherein the catalytically dead nucleic acid-guided nuclease is a non-CRISPR/Cas system protein. 
     
     
         69 . The method of  claim 66 , wherein the catalytically-dead nucleic acid-guided nuclease is selected from the group consisting of dead CAS Class I Type I, dead CAS Class I Type III, dead CAS Class I Type IV, dead CAS Class II Type II, and dead CAS Class II Type V. 
     
     
         70 . The method of  claim 66 , wherein the catalytically dead nucleic acid-guided nuclease is selected from the group consisting of dCas9, dCpf1, dCas3, dCas8a-c, dCas10, dCse1, dCsy1, dCsn2, dCas4, dCsm2, dCm5, dCsf1, dC2C2, dCPF1, and dNgAgo. 
     
     
         71 . The method of any one of  claims 66  to  70 , wherein the gNAs are gRNAs. 
     
     
         72 . The method of any one of  claims 66  to  70 , wherein the gNAs are gDNAs. 
     
     
         73 . The method of any one of  claims 66  to  72 , wherein the contacting of step (c) does not displace the plurality of nucleic acids adapter-ligated at the 5′ and 3′ ends, bound to a catalytically dead nucleic acid-guided nuclease-gNA complex of step (b). 
     
     
         74 . The method of any one of  claims 66  to  73 , wherein the contacting in step (d) cleaves the targeted sites not of interest contained in a subset of the nucleic acids, thereby generating a plurality of nucleic acid fragments comprising nucleic acid sequences not of interest, adapter ligated at only one of the 5′ or 3′ ends. 
     
     
         75 . The method of any one of  claims 66  to  74 , wherein the method further comprises removing the bound catalytically dead nucleic acid-guided nuclease-gNA complex and amplifying the product of step (b) using adapter-specific PCR. 
     
     
         76 . The method of any one of  claims 66  to  75 , wherein the nucleic acids are selected from the group consisting of single stranded DNA, double stranded DNA, single stranded RNA, double stranded RNA, and a DNA/RNA hybrid. 
     
     
         77 . The method of  claim 76 , wherein the nucleic acids are double stranded DNA. 
     
     
         78 . The method of any one of  claims 66  to  77 , wherein nucleic acids are from genomic DNA. 
     
     
         79 . The method of  claim 78 , wherein the genomic DNA is human. 
     
     
         80 . The method of any one of  claims 66  to  79 , wherein the nucleic acids adapter-ligated at the 5′ends and the 3′ends are from 20 bp to 5000 bp. 
     
     
         81 . The method of any one of  claims 66  to  80 , wherein the targeted sites of interest are single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), cancer genes, inserts, deletions, structural variations, exons, genetic mutations, or regulatory regions. 
     
     
         82 . The method of  claim 75 , wherein amplified products are used for cloning, sequencing, or genotyping. 
     
     
         83 . The method of any one of  claims 66  to  82 , wherein the adapters are from 20 bp to 100 bp in length. 
     
     
         84 . The method of any one of  claims 66  to  82 , wherein the adapters comprise primer binding sites. 
     
     
         85 . The method of any one of  claims 66  to  82 , wherein the adapters comprise sequencing adapters or restriction sites. 
     
     
         86 . The method of any one of  claims 66  to  82 , wherein the targeted sites of interest represent less than 50% of the total nucleic acid in the sample. 
     
     
         87 . The method of any one of  claims 66  to  82 , wherein the sample is obtained from a biological sample a clinical sample, a forensic sample, or an environmental sample. 
     
     
         88 . A method of capturing target nucleic acid sequences of interest comprising:
 (a) providing a sample comprising a plurality of nucleic acid sequences, wherein the nucleic acid sequences comprise methylated nucleotides, and wherein the nucleic acid sequences are adapter ligated on the 5′ and 3′ ends;   (b) contacting the sample with a plurality of nucleic acid-guided nuclease nickase-gNA complexes, wherein the gNAs are complementary to targeted sites of interest in a subset of the nucleic acid sequences, thereby generating a plurality of nicked sites of interest in the subset of the nucleic acid sequences, and wherein the target nucleic acid sequences are adapter ligated on the 5′ and 3′ ends;   (c) contacting the sample with an enzyme capable of initiating DNA synthesis at a nicked site, and unmethylated nucleotides, thereby generating a plurality of nucleic acid sequences comprising unmethylated nucleotides in the targeted sites of interest and wherein the nucleic acid sequences are adapter ligated on the 5′ and 3′ ends; and   (d) contacting the sample with an enzyme capable of cutting methylated nucleic acids, thereby generating a plurality of nucleic acid fragments comprising methylated nucleic acids, wherein the plurality of nucleic acid fragments comprising methylated nucleic acids that are adapter ligated on at most one of the 5′ and 3′ ends.   
     
     
         89 . The method of  claim 88 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of CAS Class I Type I nickase, CAS Class I Type III nickase, CAS Class I Type IV nickase, CAS Class II Type II nickase, and CAS Class II Type V nickase. 
     
     
         90 . The method of  claim 88 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of Cas9 nickase, Cpf1 nickase, Cas3 nickase, Cas8a-c nickase, Cas10 nickase, Cse1 nickase, Csy1 nickase, Csn2 nickase, Cas4 nickase, Csm2 nickase, Cmr5 nickase, Csf1 nickase, C2C2 nickase, and NgAgo nickase. 
     
     
         91 . The method of  claim 88 , wherein the gNAs are gRNAs. 
     
     
         92 . The method of  claim 88 , wherein the gNAs are gDNAs. 
     
     
         93 . The method of any one of  claims 88  to  92 , wherein the DNA is double stranded DNA. 
     
     
         94 . The method of  claim 93 , wherein the double stranded DNA is from genomic DNA. 
     
     
         95 . The method of  claim 94 , wherein the genomic DNA is human. 
     
     
         96 . The method of any one of  claims 88  to  95 , wherein the DNA sequences are from 20 bp to 5000 bp in length. 
     
     
         97 . The method of any one of  claims 88  to  96 , wherein the targeted sites of interest are single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), cancer genes, inserts, deletions, structural variations, exons, genetic mutations, or regulatory regions. 
     
     
         98 . The method of any one of  claims 88  to  97 , wherein the targeted sites of interest represent less than 50% of the total DNA in the sample. 
     
     
         99 . The method of any one of  claims 88  to  98 , wherein the sample is obtained from a biological sample a clinical sample, a forensic sample, or an environmental sample. 
     
     
         100 . The method of any one of  claims 88  to  99 , wherein the enzyme capable of initiating nucleic acid synthesis at a nicked site is a DNA Polymerase I, Klenow fragment a TAQ polymerase, or a Bst DNA Polymerase. 
     
     
         101 . The method of any one of  claims 88  to  100 , wherein the nucleic acid-guided nuclease nickase nicks the 5′ end of the DNA sequences. 
     
     
         102 . The method of any one of  claims 88  to  101 , wherein the enzyme capable of cutting methylated DNA is DpnI. 
     
     
         103 . A method of capturing target DNA sequences of interest comprising:
 (a) contacting the sample with a plurality of nucleic acid-guided nuclease nickase-gNA complexes, wherein the gNAs are complementary to targeted sites of interest flanking a region of interest in a subset of the DNA sequences, thereby generating a plurality of nicked DNA at sites adjacent to the regions of interest;   (b) heating the sample to 65° C. thereby causing cause nicks in close proximity to generate a double stranded breaks;   (c) contacting the double stranded breaks with a thermostable ligase thereby allowing ligation of adapter sequences at these sites only; and   (d) repeating steps a-c to place a second adapter on the other side of the region of interest, thus allowing enrichment of the region of interest.   
     
     
         104 . The method of  claim 103 , wherein the gNAs are gRNAs. 
     
     
         105 . The method of  claim 103 , wherein the gNAs are gDNAs. 
     
     
         106 . The method of any one of  claims 103  to  105 , wherein the the nucleic acid-guided nuclease nickase is selected from the group consisting of CAS Class I Type I nickase, CAS Class I Type III nickase, CAS Class I Type IV nickase, CAS Class II Type II nickase, and CAS Class II Type V nickase. 
     
     
         107 . The method of any one of  claims 103  to  105 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of Cas9 nickase, Cpf1 nickase, Cas3 nickase, Cas8a-c nickase, Cas10 nickase, Cse1 nickase, Csy1 nickase, Csn2 nickase, Cas4 nickase, Csm2 nickase, Cmr5 nickase, Csf1 nickase, C2C2 nickase, and NgAgo nickase. 
     
     
         108 . The method of  claim 103 , wherein the DNA is double stranded DNA. 
     
     
         109 . The method of  claim 108 , wherein the double stranded DNA is from genomic DNA. 
     
     
         110 . The method of  claim 109 , wherein the genomic DNA is human. 
     
     
         111 . The method of any one of  claims 103  to  110 , wherein the DNA sequences are from 20 bp to 5000 bp in length. 
     
     
         112 . The method of any one of  claims 103  to  111 , wherein the targeted sites of interest are single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), cancer genes, inserts, deletions, structural variations, exons, genetic mutations, or regulatory regions. 
     
     
         113 . The method of any one of  claims 103  to  112 , wherein the targeted sites of interest represent less than 50% of the total DNA in the sample. 
     
     
         114 . The method of any one of  claims 103  to  113 , wherein the sample is obtained from a biological sample, a clinical sample, a forensic sample, or an environmental sample. 
     
     
         115 . The method of any one of  claims 103  to  113 , wherein the thermostable ligase capable of contacting the double stranded break is thermostable 5′App DNA/RNA ligase or T4 RNA ligase. 
     
     
         116 . The method of any one of  claims 103  to  115 , wherein the nucleic acid-guided nuclease nickase nicks the 5′ end of the DNA sequences. 
     
     
         117 . A method of enriching a sample for sequences of interest, comprising:
 (a) providing a sample comprising sequences of interest and targeted sequences for depletion, wherein the sequences of interest comprise less than 50% of the sample; and   (b) contacting the sample with a plurality of either nucleic acid-guided RNA endonuclease-gRNA complexes or a plurality of nucleic acid-guided DNA endonuclease-gDNA complexes, wherein the gRNAs and gDNAs are complementary to the targeted sequences, and whereby the targeted sequences are cleaved.   
     
     
         118 . The method of  claim 117 , further comprising extracting the sequences of interest and the targeted sequences for depletion from the sample. 
     
     
         119 . The method of  claim 118 , further comprising fragmenting the extracted sequences. 
     
     
         120 . The method of any one of  claims 117  to  119 , wherein the cleaved targeted sequences are removed by size-exclusion. 
     
     
         121 . The method of any one of  claims 117  to  120 , wherein the sample is any one of a biological sample, a clinical sample, a forensic sample or an environmental sample. 
     
     
         122 . The method of any one of  claims 117  to  121 , wherein the sample comprises host nucleic acid sequences targeted for depletion and non-host nucleic acid sequences of interest. 
     
     
         123 . The method of  claim 122 , wherein the non-host nucleic acid sequences comprise microbial nucleic acid sequences. 
     
     
         124 . The method of  claim 123 , wherein the microbial nucleic acid sequences are bacterial, viral or eukaryotic parasitic nucleic acid sequences. 
     
     
         125 . The method of any one of  claims 117  to  124 , wherein the gRNAs and gDNAs are complementary to ribosomal RNA sequences, spliced transcripts, unspliced transcripts, introns, exons, or noncoding RNAs. 
     
     
         126 . The method of  claim 118 , wherein the extracted nucleic acids include single-stranded or double-stranded RNA. 
     
     
         127 . The method of  claim 118 , wherein the extracted nucleic acids include single-stranded or double-stranded DNA. 
     
     
         128 . The method of any one of  claims 117  to  127 , wherein the sequences of interest comprise less than 10% of the extracted nucleic acids. 
     
     
         129 . The method of any one of  claims 117  to  128 , wherein the nucleic acid-guided RNA endonuclease comprises C2c2. 
     
     
         130 . The method of  claim 129 , wherein the C2c2 is catalytically dead. 
     
     
         131 . The method of any one of  claims 117  to  128 , wherein the nucleic acid-guided DNA endonuclease comprises NgAgo. 
     
     
         132 . The method of  claim 131 , wherein the NgAgo is catalytically dead. 
     
     
         133 . The method of any one of  claims 117  to  132 , wherein the sample is selected from whole blood, plasma, serum, tears, saliva, mucous, cerebrospinal fluid, teeth, bone, fingernails, feces, urine, tissue, and a biopsy. 
     
     
         134 . A method of enriching a sample comprising:
 (a) providing a sample comprising host nucleic acids and non-host nucleic acids;   (b) contacting the sample with a plurality of nucleic acid-guided RNA endonuclease-gRNA complexes or a plurality of nucleic acid-guided DNA endonuclease-gDNA complexes, wherein the gRNAs and gDNAs are complementary to targeted sites in the host nucleic acids, and   (c) enriching the sample for non-host nucleic acids.   
     
     
         135 . The method of  claim 134 , wherein the nucleic acid-guided RNA endonuclease comprises C2c2. 
     
     
         136 . The method of  claim 134 , wherein the nucleic acid-guided RNA endonuclease comprises catalytically dead C2c2. 
     
     
         137 . The method of  claim 134 , wherein the nucleic acid-guided DNA endonuclease comprises NgAgo. 
     
     
         138 . The method of  claim 134 , wherein the nucleic acid-guided DNA endonuclease comprises catalytically dead NgAgo. 
     
     
         139 . The method of anyone of  claims 134  to  138 , wherein the host is selected from the group consisting of a human, cow, horse, sheep, pig, monkey, dog, cat, gerbil, bird, mouse, and rat. 
     
     
         140 . The method of anyone of  claims 134  to  138 , wherein the non-host is a prokaryotic organism. 
     
     
         141 . The method of anyone of  claims 134  to  138 , wherein the non-host is selected from the group consisting of a eukaryote, a virus, a bacterium, a fungus, and a protozoan. 
     
     
         142 . The method of anyone of  claims 134  to  141 , wherein the adapter-ligated host nucleic acids and non-host nucleic acids range from 50 bp to 1000 bp. 
     
     
         143 . The method of anyone of  claims 134  to  142 , wherein the non-host nucleic acids comprise less than 50% of the total nucleic acids in the sample. 
     
     
         144 . The method of anyone of  claims 134  to  143 , wherein the sample is any one of a biological sample, a clinical sample, a forensic sample or an environmental sample. 
     
     
         145 . The method of anyone of  claims 134  to  144 , wherein step (c) comprises reverse-transcribing the product of step (b) into cDNA. 
     
     
         146 . The method of anyone of  claims 134  to  145 , wherein step (c) comprises removing the host nucleic acids by size-exclusion. 
     
     
         147 . The method of anyone of  claims 134  to  145 , wherein step (c) comprises removing the host nucleic acids with the use of biotin. 
     
     
         148 . The method of anyone of  claims 134  to  147 , wherein the sample is selected from whole blood, plasma, serum, tears, saliva, mucous, cerebrospinal fluid, teeth, bone, fingernails, feces, urine, tissue, and a biopsy. 
     
     
         149 . A composition comprising a nucleic acid fragment, a nucleic acid-guided nuclease nickase-gNA complex, and labeled nucleotides. 
     
     
         150 . The composition of  claim 149 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of CAS Class I Type I nickase, CAS Class I Type III nickase, CAS Class I Type IV nickase, CAS Class II Type II nickase, and CAS Class II Type V nickase. 
     
     
         151 . The composition of  claim 149 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of Cas9 nickase, Cpf1 nickase, Cas3 nickase, Cas8a-c nickase, Cas10 nickase, Cse1 nickase, Csy1 nickase, Csn2 nickase, Cas4 nickase, Csm2 nickase, Cmr5 nickase, Csf1 nickase, C2C2 nickase, and NgAgo nickase. 
     
     
         152 . The composition of any one of  claims 149  to  151 , wherein the gNAs are gRNAs. 
     
     
         153 . The composition of any one of  claims 149  to  151 , wherein the gNAs are gDNAs. 
     
     
         154 . The composition of any one of  claims 149  to  153 , wherein the nucleic acid fragment comprises DNA. 
     
     
         155 . The composition of any one of  claims 149  to  153 , wherein the nucleic acid fragment comprises RNA. 
     
     
         156 . The composition of any one of  claims 149  to  155 , wherein the nucleotides are labeled with biotin. 
     
     
         157 . The composition of any one of  claims 149  to  156 , wherein the nucleotides are part of an antibody conjugate pair. 
     
     
         158 . A composition comprising a nucleic acid fragment and a catalytically dead nucleic acid-guided nuclease-gNA complex, wherein the catalytically dead nucleic acid-guided nuclease is fused to a transposase. 
     
     
         159 . The composition of  claim 158 , wherein the catalytically-dead nucleic acid-guided nuclease is selected from the group consisting of dead CAS Class I Type I, dead CAS Class I Type III, dead CAS Class I Type IV, dead CAS Class II Type II, and dead CAS Class II Type V. 
     
     
         160 . The composition of  claim 158 , wherein the catalytically dead nucleic acid-guided nuclease is selected from the group consisting of dCas9, dCpf1, dCas3, dCas8a-c, dCas10, dCse1, dCsy1, dCsn2, dCas4, dCsm2, dCmr5, dCsf1, dC2C2, and dNgAgo. 
     
     
         161 . The composition of any one of  claims 158 ,  159 , or  160 , wherein the gNAs are gRNAs. 
     
     
         162 . The composition of any one of  claims 158  to  161 , wherein the gNAs are gDNAs. 
     
     
         163 . The composition of any one of  claims 158  to  162 , wherein the nucleic acid fragment comprises DNA. 
     
     
         164 . The composition of any one of  claims 158  to  163 , wherein the nucleic acid fragment comprises RNA. 
     
     
         165 . The composition of any one of  claims 158  to  164 , wherein the catalytically dead nucleic acid-guided nuclease is fused to the N-terminus of the transposase. 
     
     
         166 . The composition of any one of  claims 158  to  165 , wherein the catalytically dead nucleic acid-guided nuclease is fused to the C-terminus of the transposase. 
     
     
         167 . A composition comprising a nucleic acid fragment comprising methylated nucleotides, a nucleic acid-guided nuclease nickase-gNA complex, and unmethylated nucleotides. 
     
     
         168 . The composition of  claim 167 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of CAS Class I Type I nickase, CAS Class I Type III nickase, CAS Class I Type IV nickase, CAS Class II Type II nickase, and CAS Class II Type V nickase. 
     
     
         169 . The composition of  claim 167 , wherein the nucleic acid-guided nuclease nickase is selected from the group consisting of Cas9 nickase, Cpf1 nickase, Cas3 nickase, Cas8a-c nickase, Cas10 nickase, Cse1 nickase, Csy1 nickase, Csn2 nickase, Cas4 nickase, Csm2 nickase, Cmr5 nickase, Csf1 nickase, C2C2 nickase, and NgAgo nickase. 
     
     
         170 . The composition of any one of  claims 167 ,  168 , or  169 , wherein the gNAs are gRNAs. 
     
     
         171 . The composition of any one of  claims 167  to  170 , wherein the gNAs are gDNAs. 
     
     
         172 . The composition of any one of  claims 167  to  171 , wherein the nucleic acid fragment comprises DNA. 
     
     
         173 . The composition of any one of  claims 167  to  171 , wherein the nucleic acid fragment comprises RNA. 
     
     
         174 . The composition of any one of  claims 167  to  173 , wherein the nucleotides are labeled with biotin. 
     
     
         175 . The composition of any one of  claims 167  to  174 , wherein the nucleotides are part of an antibody conjugate pair.