A mathematical model created by Aalto University (Finland) researcher Timo Ikonen explains for the first time how the DNA chains in our genome are translocated through nanopores that are only a couple of nanometres thick.

A research paper soon to be published in Physical Review E explains the basic physics related to the phenomenon referred to as polymer translocation. Exploring this phenomenon could help to create third generation genome sequencing technologies.

With the help of these technologies, sequencing a patient's genome could become a routine health care procedure.

Full genome sequencing is one of the major accomplishments of humankind. The method for sequencing the millions of base pairs that make up the human DNA molecule chain was revealed in the 1970s, but the entire human genome was not sequenced until 2001.

Sequencing the first human genome cost almost 3 billion dollars. The analysis is still extremely laborious: sequencing the genome of one person costs over 10,000 dollars.

The translocation phenomenon examined by Ikonen enables researchers to use a much simpler method for determining the base sequence of genes. As early as in the 1990s, researchers discovered that when a DNA chain is forced through a small nanopore with the help of an electric current, different types of bases can be identified by monitoring the changes occurring in the current.

Experimental physicists hurried to find out whether the phenomenon could be applied to determining the base sequence of a genome. A small number of theorists began exploring what happened during the actual translocation process. The first translocation theory was presented by Professor Sung's group in 1996. Sung is now Ikonen's research partner.

The first DNA sequencer based on translocation will soon be on the market, but the theory itself has been controversial. Tests have revealed that when an electric current is used to drive a DNA chain through a pore that is only a couple of nanometres thick, the first monomers of the chain go through the pore very rapidly. Then the process slows down, but later on it speeds up again.

"The million dollar question has been why this happens," researcher Timo Ikonen says.

In his article, Ikonen presents a mathematical model that explains the events of the translocation process. The researcher compares the DNA chain to a garden hose curled up on the ground.

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DNA tug of war