Finding a needle in a haystack: How RecA slides in to the rescue

RecA is well-practiced at finding a needle in a haystack – its job is to track down the right sequence of DNA out of 3,000,000,000 letters. But until now, it was not clear how it did this: does it jump from one bit of DNA to the next or does it slide along?

Damage to DNA is one of the biggest threats that we face – it is one the main driving factors in developing cancer. However, evolution has provided us with many tools to prevent and fix any problems. One advantage of DNA being a double helix is that if only one strand of the helix breaks, the DNA is still held in place by the second and so it can be easily fixed. However, if both strands break it becomes far more difficult to piece the DNA back together.

The single strand break (left) can be easily patched up - the DNA helix is still held in one piece. However, the double strand break (right) means that the sequence is split into two and it's not possible to stitch them back together.

The single strand break (left) can be easily patched up – the DNA helix is still held in one piece. However, the double strand break (right) means that the sequence is split into two and it’s not possible to stitch them back together.

In a double-strand break, the broken strands separate from each other because they can’t be put back together. To be repaired, a broken strand needs to line up with an undamaged molecule of DNA and use it as a template. However, finding the right sequence to align with is not easy when there are 3 billion nucleotides to search through.

These broken strands rely on a protein known as RecA to act as matchmaker and find the perfect partner sequence of DNA. Several molecules of RecA attach themselves to the strand, straightening it out and forming what is called the pre-synaptic filament. Taekjip Ha from the University of Illinois wanted to find out if this filament is able to slide along the DNA or if it has to rely on jumping from place to place. To test this they used a technique known as FRET (fluorescence resonance energy transfer), which can tell you the distance between two fluorescent tags that are attached to different molecules. One tag was attached to the filament and the other was attached to a short stretch of DNA that would not match with the filament. The researchers were able to see the distance changing very quickly, showing that the RecA-DNA filament was sliding back and forth along the short length of DNA, unsuccessfully trying to find a match.

Several copies of RecA bind to a stretch of single-stranded DNA

Several copies of RecA bind to a stretch of single-stranded DNA (shown in black) to help it find a match

The ‘bait’ DNA was then changed so that it had two patches that matched the sequence of the filament. By attaching fluorescent tags to each patch, the filament could be seen sticking to one of the two sections, and then sliding along and binding to the other. From the speed of the sliding, the researchers estimated that RecA could help to slide along up to 300 base pairs of DNA before reattaching somewhere else. This could help speed up the search for the matching sequence by over 200-fold, making it a much more efficient technique than randomly hopping from sequence to sequence.

This kind of sliding movement is the first that has been seen in a protein-DNA complex and improves our understanding of this highly important process. Fortunately, one lab has made a (low-budget) video to show how RecA works. Enjoy…

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Red Alert: How red hair can cause skin cancer without sun exposure

I’m not usually that interested in research completely based on mouse studies, but any paper that starts with ‘People with pale skin, red hair, freckles and an inability to tan…‘ is always going to get my attention.

People like me, with the ‘red hair/fair skin’ phenotype, are pretty bad at dealing with the sun. Not only do we get sunburnt much more easily, but we have the highest risk of developing melanoma, the deadliest form of skin cancer. It is (hopefully) very well known that exposure to UV light increases the risk of melanoma. However, unlike other other skin cancers, melanoma also appears to develop independently of UV light, although this has been poorly studied to date.

The sun can be your worst enemy when you’re ginger. (Photo credit: coltera)

In a letter published in Nature this week, researchers wanted to see if hair-colour pigments affect this UV-independent pathway for melanoma. To do this, they engineered mice to mimic human complexions by mutating a gene known as MC1R. This is responsible for producing the pigment eumelanin which is dark coloured and results in dark hair. Most people with red hair have an inactive form of MC1R, which instead leads to the red-coloured pheomelanin being produced.

The researchers compared mice with black hair (active MC1R), red hair (inactivated MC1R) and albinism (produces neither pigment). In addition, all the mice had a specific mutation that causes benign moles, but leaves them predisposed to developing melanoma. The mice were kept away from sources of UV light and their health was charted over time.

The differences are startling. In under a year 50% of the red-haired mice had died compared to only 20% of the black-haired or albino mice. This, and further tests, seem to suggest that producing pheomelanin is actually harmful, increasing the rate of melanoma when there is no UV light.

Pheomelanin is responsible for the colour of red hair, but could also cause cancer

It was also apparent that the DNA of the red-haired mice had suffered twice as much oxidative damage as the albino mice. It is known that UV light causes oxidative DNA damage and that this increases the chances of mutations occurring. In previous studies looking at UV radiation, it was thought that eumelanin protects against this damage. However, the mice in this study show that pheomelanin is actually harmful and eumelanin has little effect under these conditions. It’s still not clear how this damage was created in the absence of UV light or why production of pheomelanin made it worse.

The authors of the paper make it very clear that UV radiation is still an important factor in the development of skin cancer, but suggest that this UV-independent pathway should be considered in the future for strategies to prevent melanoma, especially for gingers.

Redheads have long understood that we lack the natural sun protection that others enjoy, but it is still quite a shock to think that our distinctive colouring is actively causing us damage. However, this study was done under very artificial conditions, and the rates that the researchers saw are far higher than we can plainly observe. After all, we don’t see half of redheads dying every year. But whatever your hair colour, melanoma is still very deadly – one American dies from melanoma every hour. So make sure you don’t forget your sunscreen.