Diagnostic sequencing with small nucleic acid circles
Methods, substrates, and systems for diagnostic sequencing are provided. Small circles of nucleic acids from about 10 bases to about 200 bases can be sequenced, for example using template dependent sequencing by synthesis. The use of small circles of nucleic acids allows for repeated sequencing of the same portions of the nucleic acid, providing for higher accuracy sequence determinations.
1. A method for sequencing a circular template nucleic acid comprising:
carrying out template dependent nucleic acid synthesis in a reaction mixture comprising a polymerase, a primer, nucleotides or nucleotide analogs, and a circular template nucleic acid under conditions which allow for identification of added nucleotides or nucleotide analogs during the synthesis, and repeatedly sequencing the circular template nucleic acid, wherein the circular template nucleic acid comprises both a double-stranded segment and one or more linking oligonucleotides that comprise at least one primer recognition sequence, wherein the one or more linking oligonucleotides form a connecting loop between a 3′ end of one strand of the double stranded segment and a 5′ end of another strand of the double stranded segment, and the primer is complementary to the at least one primer recognition sequence.
2. The method of claim 1 wherein the double-stranded segment has about 10 bases to about 200 bases.
3. The method of claim 1 wherein the one or more, linking oligonucleotides have a length smaller than about 20 bases.
4. The method of claim 1 wherein the one or more linking oligonucleotides have a length smaller than about 12 bases.
5. The method of claim 1 wherein the one or more linking oligonucleotides have about 4 to about 20 nucleotides.
6. The method of claim 1 wherein said sequencing the circular template nucleic acid is carried out using single molecule sequencing.
7. The method of claim 1 wherein the circular template nucleic acid comprises DNA.
8. The method of claim 1 wherein said sequencing the circular template nucleic acid comprises single molecule sequencing for real-time detection of said added nucleotides or nucleotide analogs.
9. The method of claim 1 wherein at least one of the one or more linking oligonucleotides has a length greater than about 20 bases.
10. The method of claim 1 wherein the one or more linking oligonucleotides comprise two asymmetric linking oligonucleotides.
11. The method of claim 1 wherein at least one of the one or more linking oligonucleotides comprises non-natural or non-native nucleotides or nucleotide analogs.
12. The method of claim 1 further comprising providing the circular template nucleic acid by ligating the one or more linking oligonucleotides to the double-stranded segment.
13. The method of claim 1 wherein the circular template nucleic acid comprises both single-stranded and double-stranded portions.