Brian is one of those crazy people who never leave school (University Professor) and was fascinated by everything involved in yoyoing. He wrote this to me as a sharing of thoughts, and I thought it was so cool I asked if I could post it. Enjoy
I just did some back-of-the-envelope calculations to compare yo-yo string to DNA, and I thought you might find them amusing.
If we consider the average yo-yo string as being a double helical structure similar to DNA, but with a diameter of about 2 mm, that makes it about 1 million times thicker than the DNA in our cells (the helix of double stranded DNA has a diameter of about 20 Angstroms (0.0000000002 meters)). The human genome has about 3 billion base pairs, and each base pair is about 3.32 Angstroms long, so the human genome comprises almost exactly 1 meter of DNA.
So if it were yo-yo string, it would be a million meters (1,000 km) long. And, as you probably know, most of our cells have two copies of our genomes (one from our mother and one from our father), so each cell has about 2 m of DNA packed away in its nucleus, which would be equivalent to almost enough yo-yo string to reach from Vancouver to Winnipeg. For comparison, the nucleus of a cell is about 10 µm in diameter, so that Vancouver-to-Winnipeg yo-yo string is packed into a ball 1 m in diameter (about the size of one of those yoga balls).
But, our genomes don't exist as single molecules of DNA, they're broken up into chromosomes. A big chromosome like chromosome 1 has 249 million base pairs, so the DNA molecule in it is about 8.3 cm long, which would be a yo-yo string 83 km long. Even the smallest chromosome, the Y-chromosome that makes males different than females, has 50 million base pairs, making it equivalent to a yo-yo string 17 km long. That would be a lot of string for playing with.
Yo-yos themselves remind me of "histones". The DNA in our cells isn't floating around loose; it's wrapped around proteins that actually look a lot like yo-yos. Histones assemble into disk-like structures with grooves in them for DNA to wrap around, and they have to spin along the DNA molecule like an off-string yo-yo to get out of the way of the other proteins that express the genes in the DNA or duplicate it when the cell divides.
The other way in which yo-yo string is a lot like DNA is in it's propensity to get over- or under-wound, and then twist around itself making a terrible mess. In DNA this is called 'supercoiling'. When a twisted duplex like DNA or yo-yo string is overwound (by twisting the duplex in the same direction as the individual strands are wound around each other) it becomes 'positively supercoiled'. Twisting the duplex in the opposite direction (such that it becomes under wound) is 'negative supercoiling'. In either case, if there is no force acting on the duplex to keep it straight (such as gravity), the duplex will 'writhe', coiling around itself to release the energy of the torque the over- or under-winding has stored in the structure. Cells generally keep their DNA in a negatively supercoiled state, because, as you know from putting strings on yo-yos, under-wound duplexes are easier to separate into their individual strands.
So negatively supercoiled DNA can be separated into it's individual strands to allow for gene expression or DNA replication more easily. In contrast, some cells (like bacteria that live in hot springs) store their DNA in a positively supercoiled state, for exactly the same reasons; the heat of their environment would cause their DNA to separate into its component strands (DNA is held together by hydrogen bonds just like ice, and just like ice, heat will cause it to melt), and the positive supercoiling prevents this from happening.
Something cells have that yo-yo players don't (and would really benefit from) are enzymes called 'topoisomerases'. Topoisomerases are enzymes that facilitate the interconversion of topological states of DNA. Topoisomerase I releases the energy in supercoiled DNA (rather like taking the string off your finger, and letting it spin freely until it's relaxed), but it does this without any ends having to be released (it's actually cutting one of the strands of the duplex, letting the cut end spin around the uncut strand, and then re-attaching it when it comes around). Topoisomerase II is even more useful; it allows one duplex to pass through another (they don't even have to be part of the same molecule), so it's like the ultimate knot-undoer; this is why our cells can have meters of DNA coiled up in their nuclei and it never gets tangled - Topoisomerase II is there passing molecules through each other like magic.
That's probably more than you ever wanted to know about DNA topology. But watching you and your colleagues (and now Ian) dextrously whirling yo-yos through weaves of colourful string certainly brings to mind many new ways in which to present the molecular macramé occurring in our cells to undergraduate students. I've really enjoyed it.
Department of Biology
University of New Brunswick
Fredericton, NB, Canada