Organic Chemists Contributing to Whole Genome Sequencing

Background - Why is this important?

DNA Bases
Our ability to rapidly, cheaply and accurately read the complete DNA coding region of individuals is arguably one of the grandest current challenges for the life sciences. Such technology would herald a new and exciting era of truly personalised medicine where individual disease susceptibility and response to treatment could be monitored in real time. 

How such knowledge will be managed and used is an ongoing and important ethical debate; however, for the individual patient, the opportunity to better understand disease, apply the most appropriate existing therapies or to discover new ones provides real hope.

What did the organic chemists do?

Progress in genome sequencing is underpinned by extensive and concerted application of powerful technologies from many scientific disciplines including genetics, molecular biology, engineering, and chemistry. 

Using synthetic fluorophores

Synthetic organic chemists working at Pacific Biosciences developed an innovative DNA sequencing technology which relies upon the availability of DNA bases uniquely labelled with synthetic fluorophores. The sequencing technology used DNA polymerase; the same enzyme that builds the DNA double helix. 

The enzyme is tethered to the bottom of micro-plate wells. DNA fragments are loaded into the wells, which are then washed with the uniquely labelled DNA bases. A digital camera records the sequence that these labelled bases are incorporated into the growing DNA strand by the DNA polymerase. The phosphodiester bond formation catalyzed by DNA polymerase results in release of the fluorophore from the incorporated nucleotide generating natural, unmodified DNA and a unique fluorescence identifier. The sequence of light emissions can be decoded to identify the structure of the growing strand.1

Synthesis of fluorophore-labelled DNA base (Ref 2)

Synthesis of a fluorophore-labelled DNA base

Each nucleotide base component has a unique fluorophore linked through an aminoalkyl chain to the terminal phosphate of a pentaphosphate linker moiety. This long linker has been shown to increase the efficiency of incorporation into the growing DNA strand. Successful implementation of the technology required the development of an efficient synthetic chemistry method for fluorophore incorporation which would be applicable to all 4 nucleotide bases.2 The synthetic route applies the well known carbonyldiimidazole (CDI) coupling reagent, which was discovered in the 1960's, to form the phosphoester linkers;3 the second coupling applies a novel variation using MgCl24 to increase the coupling efficiency.

Nanopore-based sequencer

UK scientists working at Oxford Nanopore Technologies synthesised stable nanopores based upon the heptameric protein alpha-hemolysin (AHL) by protein engineering techniques.5,6 In this example, each uniquely engineered nanopore incorporates a different nucleotide recognition sequence. 

Nucleotide interaction with these sequences triggers a detectable current modulation across the nanopore. As the stand passes over the nanopore, individual bases on a single DNA strand can, in principle, be identified. This is a powerful exemplification of molecular recognition linked to analytical detection. This impressive recognition technology is equally applicable to the detection of small molecules or proteins.7,8

What is the impact?

The scientific community has thrown its weight behind the human genome sequencing challenge and progress has been dramatic. The first “human genome” sequence cost over $1 billion and was an assembly of DNA sequences taken from several volunteers. In recent years there has been significant progress in reducing the cost, according to the National Genome Research Institute the cost per genome is currently $7,666. 

The impact of many scientific disciplines including genetics, molecular biology, engineering, and chemistry has already impacted upon our ability to sequence individual genomes and the implementation of the methods described here, as well as others, will herald a new era of truly personalised medicine where individual disease susceptibility and response to treatment can be monitored in real time.


1 J Eid et al., Science2009, 323, 133 
2 J Korlach et al., Nucleosides, Nucleotides and Nucleic Acids2008, 27, 1072
3 A Sood et al., J.Am.Chem. Soc., 2005,  127, 2394
4 M Kadokura et al., Tetrahedron Lett., 1997, 38, 8359
5 K R Liberman et al.,  J. Am. Chem. Soc., 2010, 132, 17961
6 D Branton et al., Nat. Biotechnol., 2008, 26, 1146
7 X-F Kang, S Cheley, X Guan and H Bayley, J. Am. Chem. Soc., 2006, 128, 10684
8 S Cheley, H Xie and H Bayley, Chem. BioChem., 2006, 7, 1923

Also of interest

Nanopore sequencing

Nanopore sequencing bags its first genome

21 February 2012

Oxford Nanopore sequences a viral genome and aims to launch its sequencing platforms within the year

DNA sequencer chip

Sequencing chip decodes DNA proton by proton

21 July 2011

pH-sensing silicon chips could make the $1000 genome a reality in just two years


Reading DNA base by base

22 February 2009

A technique to electrically detect DNA bases from a single DNA strand could lead to cheap and simple sequencing

Contact and Further Information

Dr Anne Horan
Programme Manager, Life Sciences
Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, CB4 0WF
Tel: 01223 432699