In normal PCR, you have your two PCR primers that flank the target region, and the target region is amplified from the genomic DNA after 30 cycles of PCR. That is standard for most cases.
I am trying to understand how index PCR works where one of the two PCR primers contains a index-tag (say a 6bp tag), and you go ahead and PCR amplify your target region from genomic DNA with 30 cycle PCR like normal, but the index tag remains in the final PCR product along with your target region. How does the index still remain in the final PCR product, while in the first case above for normal PCR, your primer sequences just anneal but don't remain as part of your final target region? How is it that in this index-PCR, the primer sequence with the index tag remains..how is this PCR done?
I post it in this forum because I know Illumina sequencing does a lot of this where it reads through an index sequence. I understand how the index is read and sequenced, but what I don't understand how the PCR purified product contains an index tag in the final PCR. Does anyone know?
I am trying to understand how index PCR works where one of the two PCR primers contains a index-tag (say a 6bp tag), and you go ahead and PCR amplify your target region from genomic DNA with 30 cycle PCR like normal, but the index tag remains in the final PCR product along with your target region. How does the index still remain in the final PCR product, while in the first case above for normal PCR, your primer sequences just anneal but don't remain as part of your final target region? How is it that in this index-PCR, the primer sequence with the index tag remains..how is this PCR done?
I post it in this forum because I know Illumina sequencing does a lot of this where it reads through an index sequence. I understand how the index is read and sequenced, but what I don't understand how the PCR purified product contains an index tag in the final PCR. Does anyone know?
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