System and Method for Modular and Combinatorial Nucleic Acid Sample Preparation for Sequencing

A composition comprising a pool of modular nucleic acid tags, each of the tags comprising:

• a first strand including i) a segment A defining a 5′ end of the first strand, and ii) a segment B defining a 3′ end of the first strand;
• and a hairpin segment C, positioned between segment A and segment B,
• a second strand including i) a segment B′ defining a 5′ end of the second strand and complementary to the segment B of the first strand, and ii) a segment A′ defining a 3′ end of the second strand and complementary to the segment A of the first strand,
• wherein each of the segments A, A′, B, B′, and C are selected from a set of segments having different nucleic acid sequences,
• wherein each segment of the set of segments has a defined sequence of at least 10 nucleotides, and
• wherein the set of segments is characterized by a pairwise edit distance of at least 3.

A method of preparing a library of nucleic acids with identifiable first and second strands, the method comprising:

• a) combining a pool of different modular nucleic acid tags with a nucleic acid sample, the nucleic acid sample including a plurality of double-stranded target nucleic acids, wherein each of the different modular nucleic acid tags has a first strand and a second strand,
• wherein the first strand includes i) a segment A defining a 5′ end of the first strand, and ii) a segment B defining a 3′ end of the first strand and a hairpin segment C between segment A and segment B,
• wherein the second strand includes i) a segment B′ defining a 5′ end of the second strand and complementary to the segment B of the first strand, and ii) a segment A′ defining a 3′ end of the second strand and complementary to the segment A of the first strand,
• wherein each of the segments A, A′, B, B′, and C are selected from a set of segments having different nucleic acid sequences;
• b) joining the ends of each of the double-stranded target nucleic acids to tags selected from the pool of different modular nucleic acid tags to form a plurality of doubly-tagged target nucleic acids, wherein each tagged end includes an unpaired segment C;
• c) amplifying each of the doubly-tagged target nucleic acids, thereby preparing a library of nucleic acids, wherein only one end includes a copy and a complement of the segment C.