A needle in a haystack: How does a broken DNA molecule get repaired?

May 03, 2012

Scientists from the Kavli Institute of Nanoscience at Delft University of Technology have discovered a key element in the mechanism of DNA repair. When the DNA double helix breaks, the broken end goes searching for the similar sequence and uses that as a template for repair.

Using a smart new dual-molecule technique, the Delft group has now found out how the DNA molecule is able to perform this search and recognition process in such an efficient way. This week, the researchers report their findings in Molecular Cell.

A staggering problem

Sometimes, the gets broken: both strands are accidentally cut. This presents a vital problem because cells cannot cope with such damaged DNA. Genomic DNA instabilities such as these, are a known cause of cancer. The good news is that an intricate system exists which is impressively error-proof and efficient. How does this work?

First, proteins form a filamentous structure on the broken DNA end. Second, this filament examines recently copied DNA or the second DNA chromosome (remember that we have two copies of each chromosome) in search of a DNA sequence that matches that of the broken end. Note that this is a daunting task: given that, for example, our contains three billion base pairs, finding your few hundred base pairs of interest, is really like finding a needle in a haystack.

'Still this search process occurs within minutes and with great efficiency. How that is achieved, has been a mystery for decades. The new experiments from our group now resolve this by revealing the key step in the process, the molecular recognition step', says scientist Iwijn de Vlaminck, who was the postdoc that did the experiments in the group of prof. Cees Dekker at Delft.

Search operation

'In bacteria, the so-called RecA protein is responsible for conducting the search operation. In E. coli bacteria, a filament of RecA protein formed on DNA, searches and pairs a sequence within a second with remarkable speed and fidelity. To do so, individual molecules of RecA first come together to form a filamentous structure on the broken DNA. The filament then grabs DNA molecules in its vicinity and compares their sequence to the sequence of the broken DNA. When a sequence match is found, both molecules bind tightly to one another allowing repair to ensue', says De Vlaminck (since recently at Stanford University).

'We found that the filament's secondary DNA-binding site interacts with a single strand of the incoming double-stranded DNA during homology sampling. Recognition is achieved upon binding of both strands of the incoming DNA to each of two DNA-binding sites in the filament.'

The data indicate that the fidelity of the search process is governed by the distance between the DNA binding sites. The Delft experiments clarify what exactly happens in the sequence comparison of the two molecules, making clear why a 'wrong' sequence leads to quick dissociation of the molecules while a 'correct' sequence makes a strong bond leading up to further repair. These are the two elements that lead to the impressive speed and high efficiency of the DNA repair process.

New instrument

The team from TU Delft developed a unique new instrument that makes it possible to independently manipulate an individual DNA molecule and an individual RecA filament and to measure the strength of intermolecular interactions. This dual-molecule manipulation instrument combines magnetic-tweezer and laser-trapping-based DNA-molecule manipulation with a laminar flow system. The setup also allowed to unwind the DNA helix a bit, thus opening local regions where the normal duplex was destabilized. This effect turned out to be crucial for the molecular recognition process. Thus, the team was able to directly probe the strength of the two-molecule interactions involved in search and recognition and build a new model for it.

Explore further: Researchers successfully clone adult human stem cells

add to favorites email to friend print save as pdf

Related Stories

Study shows how DNA finds its match

Feb 08, 2012

It's been more than 50 years since James Watson and Francis Crick showed that DNA is a double helix of two strands that complement each other. But how does a short piece of DNA find its match, out of the millions ...

Real-time observation of the DNA-repair mechanism

May 22, 2008

For the first time, researchers at Delft University of Technology have witnessed the spontaneous repair of damage to DNA molecules in real time. They observed this at the level of a single DNA molecule. Insight into this ...

Recommended for you

Researchers successfully clone adult human stem cells

Apr 18, 2014

(Phys.org) —An international team of researchers, led by Robert Lanza, of Advanced Cell Technology, has announced that they have performed the first successful cloning of adult human skin cells into stem ...

Researchers develop new model of cellular movement

Apr 18, 2014

(Phys.org) —Cell movement plays an important role in a host of biological functions from embryonic development to repairing wounded tissue. It also enables cancer cells to break free from their sites of ...

For resetting circadian rhythms, neural cooperation is key

Apr 17, 2014

Fruit flies are pretty predictable when it comes to scheduling their days, with peaks of activity at dawn and dusk and rest times in between. Now, researchers reporting in the Cell Press journal Cell Reports on April 17th h ...

User comments : 0

More news stories

Plants with dormant seeds give rise to more species

Seeds that sprout as soon as they're planted may be good news for a garden. But wild plants need to be more careful. In the wild, a plant whose seeds sprouted at the first warm spell or rainy day would risk disaster. More ...

Researchers successfully clone adult human stem cells

(Phys.org) —An international team of researchers, led by Robert Lanza, of Advanced Cell Technology, has announced that they have performed the first successful cloning of adult human skin cells into stem ...

Airbnb rental site raises $450 mn

Online lodging listings website Airbnb inked a $450 million funding deal with investors led by TPG, a source close to the matter said Friday.

Health care site flagged in Heartbleed review

People with accounts on the enrollment website for President Barack Obama's signature health care law are being told to change their passwords following an administration-wide review of the government's vulnerability to the ...