Nucleic Acid Probe and Method of Detecting Genomic Fragments

Abstract

Provided herein, among other things, is a method of processing a nucleic acid sample. In some embodiments, the method comprises a) hybridizing a sample comprising a target fragment to a nucleic acid probe comprising: i. a head sequence and a tail sequence, wherein the head and tail sequences are at the ends of a first oligonucleotide molecule; and ii. a splint sequence comprising, in order: an upstream flanking sequence that is complementary to the head sequence; a target complementary sequence that is complementary to the target fragment; and a downstream flanking sequence that is complementary to the tail sequence; thereby producing a hybridization product in which the ends of the target fragment are ligatably adjacent to the ends of the head and tail sequences in the first oligonucleotide molecule; and b) ligating the ends of the target fragment to the ends of the head and tail sequences of the first oligonucleotide molecule, thereby producing a cyclic product that comprises the target fragment and the head and tail sequences. Probes and kits for performing the method are also provided.

1 - 73 . (canceled) 
     
     
         74 . A kit comprising:
 a first set of at least 1,000 targeting oligonucleotides, each comprising:
 (i) an internal target-complementary sequence that is in the range of 10 to 100 nucleotides in length and complementary to a sequence in human chromosome 21, wherein the different members of the first set have different internal target-complementary sequences, 
 (ii) an upstream flanking sequence of at least 10 nucleotides that is not complementary to human genomic DNA, and 
 (iii) a downstream flanking sequence of at least 10 nucleotides that is not complementary to human genomic DNA. 
   
     
     
         75 . The kit of  claim 74 , further comprising:
 a second oligonucleotide, wherein the second oligonucleotide comprises a head sequence at that is complementary to the upstream flanking sequence of (i) and a tail sequence that is complementary to the downstream flanking sequence of (ii).   
     
     
         76 . The kit of  claim 75 , wherein the second oligonucleotide comprises a custom sequence between the head and tail sequences, wherein the custom sequence is not complementary to human genomic DNA. 
     
     
         77 . The kit of  claim 74 , wherein the internal target-complementary sequence is in the range of 10 to 50 nucleotides in length. 
     
     
         78 . The kit of  claim 74 , wherein the upstream and downstream flanking sequences of (ii) and (iii) are independently in the range of 10 to 40 nucleotides in length. 
     
     
         79 . The kit of  claim 74 , wherein the first set of targeting oligonucleotides comprises at least 5,000 targeting oligonucleotides. 
     
     
         80 . The kit of  claim 74 , further comprising a second set of at least 1,000 targeting oligonucleotides, each comprising:
 (i) an internal target-complementary sequence that is in the range of 10 to 100 nucleotides in length and complementary to a sequence in the human genome that is not in human chromosome 21, wherein the different members of the second set have different internal target-complementary sequences   (ii) the upstream flanking sequence, and   (iii) the downstream flanking sequence.   
     
     
         81 . The kit of  claim 80 , wherein the internal target-complementary sequences of the second set are complementary to a sequences in human chromosome 13 or 18.