New DNA Sequencing Technologies
Topic: Biology
All I have to say is - brilliant!

Two new awesome DNA sequencing technologies were reported this week in Nature and Science (as mentioned in a previous post).

So how do these work?

Well both techniques start by linking the genomic DNA fragments to a short DNA sequence (aka a primer or oligonucleotide) that has a biotin on the end. Biotin sticks very strongly to avidin and beads coated with avidin are used to trap the genomic DNA fragments - the ratio of DNA fragments to beads are fixed so that there is one fragment per bead. Now excess DNA primers (linked to biotin) are then added in excess to the bead. These primers are used to amplify the genomic fragment by PCR.

So now we have a population of beads each with many copies of a single stretch of DNA sequence. The beads can be immobilized to a sticky surface or inside microwells. These two techniques allow the monitoring of many beads in a conventional microscope.

OK for non-biologists - the following will be very technical ...

In method number one, "anchor primers" that are complementary to the linkage primer are annealed to the DNA-bead preparations. Then degenerate 9mers are mixed in - if the 9mer can bind to the genomic fragment that lies adjacent to the anchor primer the ligase will link the two ligated to the anchor primers. Depending on the identity of the query base (lets say base #4 of the degenerate sequence), the primer is conjugated to one of four fluorophores, each correlating with the identity of the query base (so blue for primers with base #4 being an A, Green for T, Red for C, Infrared for G). Conditions are tweaked until only perfect matches can base pair. After ligating the sequences with DNA ligase, the color of each bead is monitored by microscope. Thus identity of base #4 is revealed. Depending on how many beads you can visualize (potentially up to 500 000 per image) you will know the identity of base #4 for all those DNA fragments. Now you can wash off the anchor primer-query primer ligation product and use new anchor primer to ligate a different 9mer probe (but to querry a different base). Using some tricks the researchers inserted multiple primers into each sequence so that with this "ligation based sequencing" you can figure out the identity of potentially 20 to 100 nucleotides on every visualized bead. (500 000 beads X 100 nucleotides = half a billion nucleotides sequenced!) The authors claim that this sequencing method utilizes reagents off the shelf.

In the second paper, the authors annealed their anchor, then added DNA polymerase, pyrophosphatase and one type of nucleotide to their beads. If the primer can be extended with the given nuclerotide, DNA polymerase will utilize the nucleotide and release pyrophosphate that can be further processed into free phosphate by pyrophosphatase. This last reaction can be monitored on a microscope. So if the researchers add "T", every bead (this time in a microwell) whose first base has an A (thus needing a T to form the base pair) will catalyze the reaction ... and light up. Everything is then washed off the beads and the next nucleotide (say "C") is added. By monitoring which bead lights up during each round the authors can figure out each individual sequence simultaneously. Incredible!

Shendure et al., Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science. (2005) Published online 4 August

Margulies et al., Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) Published online 31st July