Barcoding nucleic acids
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. An at least partially double-stranded oligonucleotide adaptor, the adaptor comprising:
a stem-loop oligonucleotide comprising an intramolecular inverted repeat, a loop, and a cleavable base or sequence comprising deoxyuridine, an abasic site, or hexaethylene glycol, wherein the inverted repeat includes a barcode, wherein the 5′ end of the double-stranded oligonucleotide adaptor consists of a nucleotide that lacks a phosphate.
2. The adaptor according to claim 1 , wherein the loop of the stem-loop oligonucleotide comprises the cleavable base or sequence.
3. The adaptor according to claim 2 , wherein the cleavable base is deoxyuridine.
4. The adaptor according to claim 1 , wherein the barcode comprises a known or partially known sequence.
5. The adaptor according to claim 1 , 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.
6. The adaptor according to claim 5 , wherein the replication stop is a cleavable replication stop.