STEP I - DNA Library Preparation

Preparation of the DNA library consists of fractionation of genomic DNA (gDNA) into smaller fragments (300-500 bp) that are subsequently polished (blunted) and then, short Adaptors (A and B) are ligated onto both ends. These adaptors provide priming sequences for the amplification and the sequencing of the sample-library fragments. Adaptor B contains a 5'-biotin tag that enables immobilization of the library onto streptavidin coated beads. After nick repair, the non-biotinylated strand is released and used as a single-stranded template DNA (sstDNA) library. The sstDNA library is assessed for its quality and the optimal amount (DNA copies per bead) needed for emPCR™ is determined by titration.




STEP II- emPCR

The sstDNA library is immobilized onto beads. The beads containing a library fragment carry a single sstDNA molecule. The bead-bound library is emulsified with the amplification reagents in a water-in-oil mixture. Each bead is captured within its own microreactor where PCR amplification occurs. This results in bead-immobilized, clonally amplified DNA fragments.




STEP III- Sequencing

sstDNA library beads are added to the DNA Bead Incubation Mix (containing DNA polymerase) and are layered with Enzyme Beads (containing sulfurylase and luciferase) onto the PicoTiterPlate™ device. The layer of Enzyme Beads ensures that the DNA beads remain positioned in the wells during the sequencing reaction. The bead-deposition process maximizes the number of wells that contain a single amplified library bead (avoiding more than one sstDNA library bead per well).





The loaded PicoTiterPlate device is placed into the instrument. The fluidics sub-system flows sequencing reagents (buffers and nucleotides) across the wells of the plate. Nucleotides are flowed sequentially in a fixed order across the PicoTiterPlate device during a sequencing run. During the nucleotide flow, each of the hundreds of thousands of beads with millions of copies of DNA is sequenced in parallel. If a nucleotide complementary to the template strand is flowed into a well, the polymerase extends the existing DNA strand by adding nucleotide(s). Addition of one (or more) nucleotide(s) results in a reaction that generates a light signal that is recorded by the CCD camera in the Instrument. The signal strength is proportional to the number of nucleotides, for example, homopolymer stretches, incorporated in a single nucleotide flow.



* The Genome Sequencer 20 / FLX System (GS 20 / GS FLX) is a product by Roche Applied Science developed by 454 Life Sciences