How to Spot Invisible DNA Shapes with Shape-Based Sorting ✎ bioRxiv

Original: "Native Hydrogen/Deuterium Exchange Ion Mobility Mass Spectrometry of Structured DNA Oligonucleotides"
· M Ranz, R Guisiano, E Largy, V Gabelica
b42w:2609.90049 · the paper's page · 2026-09-08 · CC BY-NC 4.0 · independent analysis · 1 min
Scientists have figured out how to separate DNA molecules that have the same mass but different shapes, and they can now measure how quickly each shape unfolds.

If you weigh a handful of coins of the same denomination but different minting, you will learn only the average weight. But if you sort them by shape, you can see which coin bends more easily. The same goes for DNA: in solution it can adopt several shapes with the same mass, and the usual method saw only the average. The new approach adds sorting by shape, and now each shape can be studied on its own.

Here is how the method works: molecules are passed through a tube filled with gas, and compact shapes arrive faster than extended ones. It is like throwing a stone and a leaf into water: the stone sinks faster, even though they weigh the same.

Using this method, scientists saw that one DNA shape unfolds three times faster than another. This matters because such structures can be targets for cancer drugs, and you need to know which shape is more stable. Now drugs can be tested more precisely, without the risk that the result will be spoiled by an admixture of another shape.

Guanine quadruplexes can form structures reminiscent of a stack of pancakes: flat guanine tetrads pile on top of one another, and potassium ions sit between them like filling.

The idea of separating molecules by shape in the gas phase is reminiscent of a fictional "sorter" from a Philip K. Dick story, where objects are classified by nonobvious features. Only here, instead of a fantastic device, there is a drift tube filled with helium.

counts(t_D) = \sum_i A_i \exp\left(-\frac{(t_D - x_{c,i})^2}{2w_i^2}\right)
The signal as a function of drift time is represented as a sum of Gaussian peaks, each corresponding to a separate conformation.
NUS = \frac{(m/z)_{centroid,t} - (m/z)_{centroid,\infty}}{m_D - m_H} \cdot \frac{D_{t=0} - D_{t=\infty}}{D_{t=0} - D_{t=\infty}}
The number of unexchanged sites is calculated from the shift of the mass centroid between the current moment and full exchange, taking into account the mass difference between deuterium and hydrogen and the initial/final deuterium fraction.

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Not published on arXiv. Here are its page, the PDF and the formalization: you can check it yourself, not only read our account.

Scientists
Charles-Augustin de CoulombJohannes RydbergTheodore LymanArnold SommerfeldJohann Jakob BalmerJoseph von Fraunhofer
Concepts
dna damage DNA