Researchers have obtained the first glimpse of the shape adopted by folded DNA structures called G-quadruplexes under molecularly crowded cell-like conditions. The findings, if confirmed, could have implications for drug discovery because G-quadruplexes may be sites of action for cancer drugs.
G-quadruplexes are three-dimensional DNA structures that are believed to form at the chromosome end caps, known as telomeres. Structural studies over nearly the past two decades—one by crystallography and five by solution NMR—have found that G-quadruplexes can adopt six different shapes. But until now, researchers had not known which, if any, of these shapes are likely to be present on human telomeres in living cells.
Biomacromolecular structure specialist Anh Tuân Phan and coworker Brahim Heddi of Nanyang Technological University, in Singapore, have now used circular dichroi and NMR to obtain the first G-quadruplex structure in a solution like that in cells (J. Am. Chem. Soc., DOI: 10.1021/ja200786q). They achieved crowding by using solutes that deplete water from the surface of DNA, which mimics the way biomolecules in live cells block water from reaching the DNA surface.
Phan and Heddi show that human telomeric G-quadruplexes adopt a conformation in crowded solution that is different from the five structures found previously by NMR but the same as the one obtained previously via crystallography. In addition, four of the NMR structures convert reversibly to the crowded-solution form when exposed to molecularly crowded conditions, giving further confidence that this is the form present in live cells. The study also shows that under molecularly crowded conditions, human telomeric DNA can form a previously unknown higher order structure in which two or more G-quadruplex units are stacked.
The findings are consistent with some, but not all, previous studies predicting the form G-quadruplexes would adopt in cell-like conditions. Those studies were carried out by researchers such as biomolecular structure and function expert Daisuke Miyoshi of Konan University, in Kobe, Japan. Miyoshi comments that it will be important to develop models of cell-like conditions that are more sophisticated than water-depleting solutes. He adds, however, that “this groundbreaking paper gives quantitative insights into the properties of nucleic acids in living cells and should open new avenues to finding native and functionally active structures of other biomolecules under cell-mimicking conditions.”
“It’s a significant paper that brings together and rationalizes a large number of previous studies and provides an important starting point for future work,” comments nucleic acid structure and cancer drug expert Stephen Neidle of the University of London School of Pharmacy, whose group obtained the crystallographic G-quadruplex structure in 2002 (Nature, DOI: 10.1038/nature755). “It shows that crystallography and NMR can be in bed together quite happily and gives greater confidence to drug design,” he says.
