Bacterial DNA lightly unzipped - DNA

Bacterial DNA lightly unzipped
12-11-2006
by Laura Durnford
Radio Netherlands

By unzipping the DNA of bacteria, using 'laser tweezers', Dutch researchers have made a technological breakthrough, and could have opened a new avenue for research towards anti-bacterial medications.
'Laser tweezers', also known as 'optical tweezers', may sound like something a Star Trek character might use for plucking her eyebrows in some futuristic fashion, but in fact they've been around for about 20 years. And the objects they can manipulate are actually about one hundredth of the diameter of a human hair.
Various researchers around the world have used the technology to study the interactions of proteins with single pieces of genetic material, DNA, but a team from Amsterdam's Free University (VU) have recently succeeded in simultaneously manipulating two pieces of DNA. Their report was published recently in the prestigious scientific journal Nature.
The team leader, Dr Gijs Wuite, who's an Assistant Professor in the 'Physics of Complex Systems' section, describes this advance as a "breakthrough", because "many biological processes involve multiple pieces of DNA and proteins, which are enzymes that interact with DNA", and because his team has demonstrated how these processes can be studied: "it is possible and you can make important discoveries".
Understanding the HNS protein
What Dr Wuite and his colleagues have discovered relates to the way that genetic material is arranged and accessed within bacteria. Unlike a human cell, where genetic material is neatly housed within a compartment called the nucleus, bacterial DNA is to be found in a more diffuse region called the 'nucleoid'.
Optical Tweezers use light to manipulate microscopic objects as small as a single atom. The radiation pressure from a focused laser beam is able to trap small particles. The forces felt by the trapped particle consist of the light scattering and gradient forces due to the interaction of the particle with the bending light. (From: Standford University, Optical Tweezers, An Introduction)

"It's really free-floating through the whole bacterium, but of course it still has to be organised", Dr Wuite explains. And one of the known key players in this is a protein called 'HNS'.
"It was known that it can compact and organise the DNA, but how it actually does that was, up to now, very difficult to understand."
Another key question unanswered until now was, "how is it possible for proteins which are responsible for reading the genes - like RNA-polymerase - how they are able to move through the nucleoid while it's compacted?"
Multiple tweezers
To tease these questions apart, the biophysicist and his team used multiple optical tweezers to grasp the ends of two pieces of DNA, while studying the 'bridges' that formed when they added HNS in a highly controlled way.
"When we add HNS we can see if there's a link, and if we pulled on these two pieces of DNA we could see how these proteins break one by one when we try to unzip it."
In this way they measured the force needed to unravel the DNA as "in the order of eight pico-Newtons, which is three or four times smaller than the forces which can be generated by an RNA-polymerase."
This result indicates that RNA-polymerase "doesn't need any helper proteins or anything else to do its job, it can just plough through this HNS protein without any problem," says Dr Wuite. And although this is basic research, he believes that it could ultimately be important, because it provides a part of the puzzle of understanding how bacteria can respond to environmental changes," for example when they enter the human gut.

Possible medical applications
To function in its new surroundings, a bacterium "needs to respond by generating different kinds of proteins," which are encoded in its genetic material, "so it needs to have access to different pieces of DNA". By discovering "how it's possible that HNS can be organising the DNA while still being dynamic in its nature," Dr Wuite says this is a "significant piece of the puzzle". And he hopes that one day it could prove useful in the fight against disease:
"If this puzzle slowly gets completed, people can of course think about how to maybe generate better medication against bacterial infections."
In the meantime, the Amsterdam team is already at work on three follow-up projects using optical tweezers to manipulate proteins plus multiple pieces of DNA.
"This is really the start. There are just so many biologically relevant problems where you would need this unique tool, and now that we have it, yes, we're certainly going to continue using it!"