Saturday, December 10, 2011

Single Molecule DNA Sequencing

The Maxam-Gilbert technique relies on the cleaving of nucleotides by chemical and is most efficient with small nucleotide polymers. This technique was developed by Maxam-Gilbert in 1976-1977 and was published two years after the enlightening papers on Plus-Minus sequencing by Sanger and Coulson. Unlike in Sanger’s initial method, which required that each read start be cloned for the synthesis of single-stranded DNA, this method used the purified DNA directly, which made it very popular.

Although due to the advancements in chain termination methodology, the Maxam-Gilbert method has become redundant. It was made obsolete due to it being less ergonomically feasible. It is also considered unsafe because of the extensive use of toxic chemicals. As recently reported by Genome.gov, DNA Sequencing costs have dramatically dropped over the past 10 years for most large-scale programs. The cost base chart below is taken directly from the site and represents the cost per megabase, or per genome, of a given sequential analysis.

In order to present a proper model of DNA, this three-dimensional representation will allow you to zoom in and out as well as rotate and segregate various sections of the DNA model. This novel sequencing-by-synthesis approach measures the increased charge as nucleotides are added to DNA templates attached to a tethered bead. Opposing electrical, hydrodynamic and entropic forces will be used to measure the bead displacement, which is a function of the length of DNA attached to the bead. The much lower per-bead copy number required compared to the 454 system should enable amplification options other than emulsion PCR, such as bridge PCR, making initial sample preparation easier and cheaper.

The simplest way to do chain sequencing is to manipulate the chemistry of the molecule. Instead of catering to DNA with normal nucleotides, it’s possible to synthesize one in absence of the hydroxyl group, which is essential for the polymerase that adds to the next base. This technique is also known as Sanger method and is named after the discoverer Fredrick Sanger.