There are actually about 3 billion base pairs that make up the complete set of DNA instructions in humans. This is about a metre of DNA. This enormous string of molecular information has to be precisely organised by coiling it up tightly so that it can be squeezed into the nucleus of cells.
To study the structure of DNA when it is crammed into cells, the researchers needed to replicate this coiling of DNA.
To investigate how the winding changed what the circles looked like, the researchers wound and then unwound the tiny DNA circles – 10 million times shorter in length than the DNA contained within our cells – a single turn at a time.
The researchers devised a test to make sure that the tiny twisted up DNA circles that they made in the laboratory acted in the same way as the full-length DNA strands within our cells, when it is referred to as ‘biologically active’.
They used an enzyme called ‘human topoisomerase II alpha’ that manipulates the twist of DNA. The test showed that the enzyme relieved the winding stress from all of the supercoiled circles, even the most coiled ones, which is its normal job in the human body. This result means that the DNA in the circles must look and act like the much longer DNA that the enzyme encounters in human cells.
Coiling the tiny DNA circles caused them to form a zoo of beautiful and unexpected shapes. “Some of the circles had sharp bends, some were figure-8s, and others looked like handcuffs or racquets or even sewing needles. Some looked like rods because they were so coiled,” said the author.
The cryo-electron tomography of the tiny DNA circles also revealed another surprise finding. Base pairs in DNA are like a genetic alphabet, in which the letters on one side of the DNA double helix only pair with a particular letter on the other side. While the researchers expected to see the opening of base pairs – that is, the separation of the paired letters in the genetic alphabet – when the DNA was under-wound, they were surprised to see this opening for the over-wound DNA. This is because over-winding is supposed to make the DNA double helix stronger.
The researchers hypothesise that this disruption of base pairs may cause flexible hinges, allowing the DNA to bend sharply, perhaps helping to explain how a meter of DNA can be jammed into a single human cell.