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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