Brand New Method of DNA Sequencing

choi

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Nicholas Wade, Decoding DNA With Semiconductors; New machine offers faster, cheaper way to sequence genome. New York Times, July 21, 2011.
http://www.nytimes.com/2011/07/21/science/21genome.html

Excerpt in the window of print: It will take years to make sense of much of teh data a novel technology reveals.

My comment:
(a) Techmnology. Ion Torrent, undated.
http://www.iontorrent.com/technology-scalability-simplicity-speed/

Go to "How does it work?" in the left column. Clcik "Read more" and you reach the text. By comparing the video clip, it is clear that the sequence of the DNA for the last several nucleosides are 5'-T-G-A-C-T-T-3'.

(b) To be frank, I was not taught that a hydrogen ion would be released. The following is what we are taught in biochemistry.

See the figure at page 866, in

Reginald Garrett and Charles M. Grisham. Biochemistry, fourth edition. publisher: Mary Finch, 2010.
http://books.google.com/books?id=iGPsen3fSOIC&pg=PA866&lpg=PA866&dq=%22dna+polymerase%22+elongation+5'+biochemistry+%223'+oh%22&source=bl&ots=P9_lkwuZ03&sig=Jl74E6oEjomoKueuR6F7XWyAO-Q&hl=en&ei=UHkoTuHyH8idgQeGlLRc&sa=X&oi=book_result&ct=result&resnum=2&ved=0CBwQ6AEwAQ#v=onepage&q&f=false
("FIGURE 28.4  The chain elongation reaction catalyzed by DNA polymerase.The 3-OH carries out a nucleophilic attack on the -phosphoryl group of the incoming dNTP to form a phosphoester bond, and PP is released. The subsequent hydrolysis of PP, by inorganic pyrophosphatase renders teh reaction effectively irreversible")

* dNTP is a short hand for deoxyNucleotide TriPhosphate. See the left panel of the first, color graphic in
http://en.wikipedia.org/wiki/Nucleotide
* For layperson, DNA elongation proceeds from 5' to 3'. The the phosphate of the incoming dNTP would combine with the hydroxyl (OH) of 3' end.


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