Patent ID: 8114596

Claim:
A method of forming a population of nucleic acid sequence tags, comprising: covalently coupling a first linear target nucleic acid having two free ends to a first end of a first nucleic acid bridge and covalently coupling a second linear target nucleic acid having two free ends to a second end of the first nucleic acid bridge to form a linear chimeric nucleic acid intermediate, wherein the first nucleic acid bridge is disposed between the first linear target nucleic acid and the second linear target nucleic acid, cleaving the linear chimeric nucleic acid intermediate to form a shortened linear chimeric nucleic acid intermediate; and producing from the shortened linear chimeric nucleic acid intermediate a first sequence tag and a second sequence tag, wherein the first nucleic acid bridge comprises a binding site for a first primer and a binding site for a second primer, and wherein producing comprises amplifying the shortened linear chimeric nucleic acid intermediate in the presence of the first primer, the second primer, or both, to form the first sequence tag, the second sequence tag, or both, wherein the first sequence tag comprises at least a portion of the first target nucleic acid and at least a portion of the first nucleic acid bridge, and wherein the second sequence tag comprises at least a portion of the second target nucleic acid and at least a portion of the first nucleic acid bridge, wherein the at least a first portion of the first target nucleic acid comprises a first addressable portion and wherein the at least a first portion of the second target nucleic acid comprises a second addressable portion; wherein the first linear target nucleic acid and the second linear target nucleic acid are not covalently linked until coupling to the nucleic acid bridge, and wherein the first target nucleic acid and the second target nucleic acid are produced from the same nucleic acid sample, wherein the first nucleic acid bridge comprises 2 restriction endonuclease recognition sequences for endonucleases that cleave at a sequence outside of the nucleic acid bridge, wherein the cleavage sequences are outside of opposite ends of the bridge, wherein the 2 restriction endonuclease recognition sequences are separated by a plurality of nucleotides, wherein the first sequence tag and the second sequence tag comprise at least a first bridge portion, wherein the first sequence tag and the second sequence tag are suitable for simultaneous detection without requiring pooling, sorting, or adapter mediated indexing, and wherein the first and second addressable portions have a fixed length of 2 to 30 nucleotides.