Barcoding Nucleic Acids

Abstract

Methods of barcoding nucleic acids, such as genomic DNA, are provided herein. In some embodiments, a fragment of genomic DNA may comprise a first and a second barcode.

1 - 16 . (canceled) 
     
     
         17 . A population of at least partially double-stranded oligonucleotide adaptors, the adaptors comprising:
 a stem-loop oligonucleotide comprising an intramolecular inverted repeat and a loop, wherein the inverted repeat includes a barcode.   
     
     
         18 . The population of adaptors according to  claim 17 , wherein the loop of the stem-loop oligonucleotide comprises a cleavable base or sequence. 
     
     
         19 . The population of adaptors according to  claim 18 , wherein the cleavable base or sequence comprises deoxyuridine, an abasic site, or hexaethylene glycol. 
     
     
         20 . The population of adaptors according to  claim 17 , wherein the first barcode comprises a known or partially known sequence. 
     
     
         21 . The population of adaptors according to  claim 17 , wherein the 5′ end of the double-stranded oligonucleotide adaptor lacks a phosphate. 
     
     
         22 . The population of adaptors according to  claim 21 , wherein the 5′ end of the double-stranded oligonucleotide adaptor consists of a nucleotides that lacks a phosphate. 
     
     
         23 . The population of adaptors according to  claim 17 , wherein the loop of the stem-loop oligonucleotide adaptor or a region of the stem adjacent to the loop of the stem-loop oligonucleotide adaptor comprises a replication stop. 
     
     
         24 . The population of adaptors according to  claim 23 , wherein the replication stop is a cleavable replication stop. 
     
     
         25 . The population of adaptors according to  claim 17 , wherein the intramolecular inverted repeats of the stem-loop oligonucleotides of the population comprise identical sequences. 
     
     
         26 . The population of adaptors according to  claim 17 , wherein the intramolecular inverted repeats of the stem-loop oligonucleotides of the population do not comprise identical sequences. 
     
     
         27 . A kit comprising:
 (a) an at least partially double-stranded oligonucleotide adaptor comprising a stem-loop oligonucleotide comprising an intramolecular inverted repeat and a loop, wherein the inverted repeat includes a barcode; and   (b) a primer comprising a first portion complementary to the stem-loop oligonucleotide and a second portion comprising a second barcode.   
     
     
         28 . The kit according to  claim 27 , wherein the first portion of the primer anneals to a portion of the first barcode. 
     
     
         29 . The kit according to  claim 27 , wherein the first portion of the primer does not anneal within the first barcode. 
     
     
         30 . The kit according to  claim 27 , wherein the loop of the stem-loop oligonucleotide comprises a cleavable base or sequence. 
     
     
         31 . The kit according to  claim 30 , wherein the cleavable base or sequence comprises deoxyuridine, an abasic site, or hexaethylene glycol. 
     
     
         32 . The kit according to  claim 27 , wherein the 5′ end of the double-stranded oligonucleotide adaptor lacks a phosphate. 
     
     
         33 . The kit according to  claim 32 , wherein the 5′ end of the double-stranded oligonucleotide adaptor consists of a nucleotides that lacks a phosphate. 
     
     
         34 . The population of adaptors according to  claim 27 , wherein the loop of the stem-loop oligonucleotide adaptor or a region of the stem adjacent to the loop of the stem-loop oligonucleotide adaptor comprises a replication stop. 
     
     
         35 . The population of adaptors according to  claim 34 , wherein the replication stop is a cleavable replication stop. 
     
     
         36 . The kit according to  claim 27 , wherein the kit comprises a population of at least partially double-stranded oligonucleotide adaptors each comprising a stem-loop oligonucleotide comprising an intramolecular inverted repeat and a loop, wherein the inverted repeat includes a barcode.