Polynucleotide barcodes for long read sequencing

A method of amplifying tagged complements of a plurality of sample polynucleotides, the method comprising:

• a. hybridizing to each of the plurality of sample polynucleotides a plurality of interposing oligonucleotide barcodes, each of the interposing oligonucleotide barcodes comprising from 5′ to 3′:
• i. a first hybridization pad complementary to a first sequence of a sample polynucleotide;
• ii. a first stem region comprising a sequence common to the plurality of interposing oligonucleotide barcodes;
• iii. a loop region comprising a barcode sequence, wherein the barcode sequence, alone or in combination with a sequence of one or both of (a) the sample polynucleotide, or (b) one or more additional barcode sequences, uniquely distinguishes the sample polynucleotide from other sample polynucleotides in the plurality;
• iv. a second stem region comprising a sequence complementary to the first stem region, wherein the second stem region is capable of hybridizing to the first stem region under hybridization conditions;
• and
• v. a second hybridization pad complementary to a second sequence of the sample polynucleotide;
• b. extending the 3′ ends of the second hybridization pads with one or more polymerases to create extension products;
• and
• c. ligating adjacent ends of extension products hybridized to the same sample polynucleotide thereby making integrated strands comprising complements of the plurality of sample polynucleotides tagged with a plurality of interposing oligonucleotide barcodes;
• and
• d. amplifying the integrated strands by an amplification reaction thereby amplifying the tagged complements of the plurality of sample polynucleotides.